#!/usr/bin/python ######################## # COPYRIGHT 2005 # # Alexander Kozik # # http://www.atgc.org/ # # akozik@atgc.org # ######################## def HelpTranslation(): print "" print " SEQS PROCESSOR HELP: " print " ------------------- " help_text = """ Input file must be in FASTA format. Description of output: if no translation frame is chosen "0" then four output files will be generated: 1. *.fasta - contains processed sequences in FASTA format 2. *.stat - contains information about GC% content per sequence 3. *.tab - tab delimited file with sequences 4. *.01BIN - binary DNA representation (A-00 T-11 G-01 C-10) if first translation frame is chosen "1" then eleven output files will be generated: 1. *.fasta - contains processed sequences in FASTA format 2. *.forwrd - forward orientation, all non ATGCN letters replaced by "N" 3. *.revcom - reverse-compliment orientation based on "forward" sequences 4. *.stat - contains information about GC% content per sequence 5. *.tab - tab delimited file with sequences 6. *.tr_frame1 - translated sequences - frame 1 7. *.tr_longest_frame - extracted longest frame 8. *.tr_single_frame - extracted sequences with single ORF 9. *.x0_log - log file with general info and error messages 10. *.x1_log - log file with statistical info about translation - frame 1 11. *.01BIN - binary DNA representation (A-00 T-11 G-01 C-10) if three translation frames are chosen "3" then sixteen output files will be generated: 1. *.fasta - contains processed sequences in FASTA format 2. *.forwrd - forward orientation, all non ATGCN letters replaced by "N" 3. *.revcom - reverse-compliment orientation based on "forward" sequences 4. *.stat - contains information about GC% content per sequence 5. *.tab - tab delimited file with sequences 6. *.tr_frame1 - translated sequences - frame 1 7. *.tr_frame2 - translated sequences - frame 2 8. *.tr_frame3 - translated sequences - frame 3 9. *.tr_longest_frame - extracted longest frame 10. *.tr_single_frame - extracted sequences with single ORF 11. *.x0_log - log file with general info and error messages 12. *.x1_log - log file with statistical info about translation - frame 1 13. *.x2_log - log file with statistical info about translation - frame 2 14. *.x3_log - log file with statistical info about translation - frame 3 15. *.xx_log - log file with statistical info about all three translation ORFs 16. *.01BIN - binary DNA representation (A-00 T-11 G-01 C-10) if six translation frames are chosen "6" then twenty two output files will be generated: 1. *.fasta - contains processed sequences in FASTA format 2. *.forwrd - forward orientation, all non ATGCN letters replaced by "N" 3. *.revcom - reverse-compliment orientation based on "forward" sequences 4. *.stat - contains information about GC% content per sequence 5. *.tab - tab delimited file with sequences 6. *.tr_frame1 - translated sequences - frame 1 7. *.tr_frame2 - translated sequences - frame 2 8. *.tr_frame3 - translated sequences - frame 3 9. *.tr_frame4 - translated sequences - frame 4 10. *.tr_frame5 - translated sequences - frame 5 11. *.tr_frame6 - translated sequences - frame 6 12. *.tr_longest_frame - extracted longest frame 13. *.tr_single_frame - extracted sequences with single ORF 14. *.x0_log - log file with general info and error messages 15. *.x1_log - log file with statistical info about translation - frame 1 16. *.x2_log - log file with statistical info about translation - frame 2 17. *.x3_log - log file with statistical info about translation - frame 3 18. *.x4_log - log file with statistical info about translation - frame 4 19. *.x5_log - log file with statistical info about translation - frame 5 20. *.x6_log - log file with statistical info about translation - frame 6 21. *.xx_log - log file with statistical info about all six translation ORFs 22. *.01BIN - binary DNA representation (A-00 T-11 G-01 C-10) Note, log files must be viewed using Excel like spreadsheet editor """ print help_text def CodonTranslation1(): ### STANDARD TRANSLATION ### print "" print "TRANSLATION TABLE 1" print "" time.sleep(2) global gl_Ter global gl_Phe, gl_Leu, gl_Ser, gl_Tyr, gl_Cys, \ gl_Trp, gl_Pro, gl_His, gl_Gln, gl_Arg, \ gl_Ile, gl_Met, gl_Thr, gl_Asn, gl_Lys, \ gl_Val, gl_Ala, gl_Asp, gl_Glu, gl_Gly global gl_Any global gl_AmAcLib gl_Ter = [ "TAA", "TAG", "TGA" ] gl_Phe = [ "TTT", "TTC" ] gl_Leu = [ "TTA", "TTG", "CTT", "CTC", "CTA", "CTG", "CTN" ] gl_Ser = [ "TCT", "TCC", "TCA", "TCG", "TCN", "AGT", "AGC" ] gl_Tyr = [ "TAT", "TAC" ] gl_Cys = [ "TGT", "TGC" ] gl_Trp = [ "TGG" ] gl_Pro = [ "CCT", "CCC", "CCA", "CCG", "CCN" ] gl_His = [ "CAT", "CAC" ] gl_Gln = [ "CAA", "CAG" ] gl_Arg = [ "CGT", "CGC", "CGA", "CGG", "CGN", "AGA", "AGG" ] gl_Ile = [ "ATT", "ATC", "ATA" ] gl_Met = [ "ATG" ] gl_Thr = [ "ACT", "ACC", "ACA", "ACG", "ACN" ] gl_Asn = [ "AAT", "AAC" ] gl_Lys = [ "AAA", "AAG" ] gl_Val = [ "GTT", "GTC", "GTA", "GTG", "GTN" ] gl_Ala = [ "GCT", "GCC", "GCA", "GCG", "GCN" ] gl_Asp = [ "GAT", "GAC" ] gl_Glu = [ "GAA", "GAG" ] gl_Gly = [ "GGT", "GGC", "GGA", "GGG", "GGN" ] gl_Any = [ "AAN", "ATN", "AGN", \ "TAN", "TTN", "TGN", \ "GAN", \ "CAN", \ "ANA", "ANT", "ANG", "ANC", \ "TNA", "TNT", "TNG", "TNC", \ "GNA", "GNT", "GNG", "GNC", \ "CNA", "CNT", "CNG", "CNC", \ "NAA", "NAT", "NAG", "NAC", \ "NTA", "NTT", "NTG", "NTC", \ "NGA", "NGT", "NGG", "NGC", \ "NCA", "NCT", "NCG", "NCC", \ "NNA", "NNT", "NNG", "NNC", \ "ANN", "TNN", "GNN", "CNN", \ "NAN", "NTN", "NGN", "NCN", \ "NNN" ] ###################################### gl_AmAcLib = [ gl_Ter, \ gl_Phe, gl_Leu, gl_Ser, gl_Tyr, gl_Cys, \ gl_Trp, gl_Pro, gl_His, gl_Gln, gl_Arg, \ gl_Ile, gl_Met, gl_Thr, gl_Asn, gl_Lys, \ gl_Val, gl_Ala, gl_Asp, gl_Glu, gl_Gly, \ gl_Any ] ###################################### def CodonTranslation2(): ### Vertebrate Mitochondrial ### ##################################### # # Differences from the Standard Code: # # Code 2 Standard # # AGA Ter * Arg R # AGG Ter * Arg R # AUA Met M Ile I # UGA Trp W Ter * # ##################################### print "" print "TRANSLATION TABLE 2" print "" time.sleep(2) global gl_Ter global gl_Phe, gl_Leu, gl_Ser, gl_Tyr, gl_Cys, \ gl_Trp, gl_Pro, gl_His, gl_Gln, gl_Arg, \ gl_Ile, gl_Met, gl_Thr, gl_Asn, gl_Lys, \ gl_Val, gl_Ala, gl_Asp, gl_Glu, gl_Gly global gl_Any global gl_AmAcLib gl_Ter = [ "TAA", "TAG", "AGA", "AGG" ] gl_Phe = [ "TTT", "TTC" ] gl_Leu = [ "TTA", "TTG", "CTT", "CTC", "CTA", "CTG", "CTN" ] gl_Ser = [ "TCT", "TCC", "TCA", "TCG", "TCN", "AGT", "AGC" ] gl_Tyr = [ "TAT", "TAC" ] gl_Cys = [ "TGT", "TGC" ] gl_Trp = [ "TGG", "TGA" ] gl_Pro = [ "CCT", "CCC", "CCA", "CCG", "CCN" ] gl_His = [ "CAT", "CAC" ] gl_Gln = [ "CAA", "CAG" ] gl_Arg = [ "CGT", "CGC", "CGA", "CGG", "CGN" ] gl_Ile = [ "ATT", "ATC" ] gl_Met = [ "ATG", "ATA" ] gl_Thr = [ "ACT", "ACC", "ACA", "ACG", "ACN" ] gl_Asn = [ "AAT", "AAC" ] gl_Lys = [ "AAA", "AAG" ] gl_Val = [ "GTT", "GTC", "GTA", "GTG", "GTN" ] gl_Ala = [ "GCT", "GCC", "GCA", "GCG", "GCN" ] gl_Asp = [ "GAT", "GAC" ] gl_Glu = [ "GAA", "GAG" ] gl_Gly = [ "GGT", "GGC", "GGA", "GGG", "GGN" ] gl_Any = [ "AAN", "ATN", "AGN", \ "TAN", "TTN", "TGN", \ "GAN", \ "CAN", \ "ANA", "ANT", "ANG", "ANC", \ "TNA", "TNT", "TNG", "TNC", \ "GNA", "GNT", "GNG", "GNC", \ "CNA", "CNT", "CNG", "CNC", \ "NAA", "NAT", "NAG", "NAC", \ "NTA", "NTT", "NTG", "NTC", \ "NGA", "NGT", "NGG", "NGC", \ "NCA", "NCT", "NCG", "NCC", \ "NNA", "NNT", "NNG", "NNC", \ "ANN", "TNN", "GNN", "CNN", \ "NAN", "NTN", "NGN", "NCN", \ "NNN" ] ###################################### gl_AmAcLib = [ gl_Ter, \ gl_Phe, gl_Leu, gl_Ser, gl_Tyr, gl_Cys, \ gl_Trp, gl_Pro, gl_His, gl_Gln, gl_Arg, \ gl_Ile, gl_Met, gl_Thr, gl_Asn, gl_Lys, \ gl_Val, gl_Ala, gl_Asp, gl_Glu, gl_Gly, \ gl_Any ] ###################################### def CodonTranslation3(): ### Yeast Mitochondrial ### ##################################### # # Differences from the Standard Code: # # Code 3 Standard # # AUA Met M Ile I # CUU Thr T Leu L # CUC Thr T Leu L # CUA Thr T Leu L # CUG Thr T Leu L # UGA Trp W Ter * # # CGA absent Arg R # CGC absent Arg R # ##################################### print "" print "TRANSLATION TABLE 3" print "" time.sleep(2) global gl_Ter global gl_Phe, gl_Leu, gl_Ser, gl_Tyr, gl_Cys, \ gl_Trp, gl_Pro, gl_His, gl_Gln, gl_Arg, \ gl_Ile, gl_Met, gl_Thr, gl_Asn, gl_Lys, \ gl_Val, gl_Ala, gl_Asp, gl_Glu, gl_Gly global gl_Any global gl_AmAcLib gl_Ter = [ "TAA", "TAG" ] gl_Phe = [ "TTT", "TTC" ] gl_Leu = [ "TTA", "TTG" ] gl_Ser = [ "TCT", "TCC", "TCA", "TCG", "TCN", "AGT", "AGC" ] gl_Tyr = [ "TAT", "TAC" ] gl_Cys = [ "TGT", "TGC" ] gl_Trp = [ "TGG", "TGA" ] gl_Pro = [ "CCT", "CCC", "CCA", "CCG", "CCN" ] gl_His = [ "CAT", "CAC" ] gl_Gln = [ "CAA", "CAG" ] # gl_Arg = [ "CGT", "CGC", "CGA", "CGG", "CGN", "AGA", "AGG" ] gl_Arg = [ "CGT", "CGG", "CGN", "AGA", "AGG" ] gl_Ile = [ "ATT", "ATC" ] gl_Met = [ "ATG", "ATA" ] gl_Thr = [ "ACT", "ACC", "ACA", "ACG", "ACN", "CTT", "CTC", "CTA", "CTG", "CTN" ] gl_Asn = [ "AAT", "AAC" ] gl_Lys = [ "AAA", "AAG" ] gl_Val = [ "GTT", "GTC", "GTA", "GTG", "GTN" ] gl_Ala = [ "GCT", "GCC", "GCA", "GCG", "GCN" ] gl_Asp = [ "GAT", "GAC" ] gl_Glu = [ "GAA", "GAG" ] gl_Gly = [ "GGT", "GGC", "GGA", "GGG", "GGN" ] gl_Any = [ "AAN", "ATN", "AGN", \ "TAN", "TTN", "TGN", \ "GAN", \ "CAN", \ "ANA", "ANT", "ANG", "ANC", \ "TNA", "TNT", "TNG", "TNC", \ "GNA", "GNT", "GNG", "GNC", \ "CNA", "CNT", "CNG", "CNC", \ "NAA", "NAT", "NAG", "NAC", \ "NTA", "NTT", "NTG", "NTC", \ "NGA", "NGT", "NGG", "NGC", \ "NCA", "NCT", "NCG", "NCC", \ "NNA", "NNT", "NNG", "NNC", \ "ANN", "TNN", "GNN", "CNN", \ "NAN", "NTN", "NGN", "NCN", \ "NNN" ] ###################################### gl_AmAcLib = [ gl_Ter, \ gl_Phe, gl_Leu, gl_Ser, gl_Tyr, gl_Cys, \ gl_Trp, gl_Pro, gl_His, gl_Gln, gl_Arg, \ gl_Ile, gl_Met, gl_Thr, gl_Asn, gl_Lys, \ gl_Val, gl_Ala, gl_Asp, gl_Glu, gl_Gly, \ gl_Any ] ###################################### def Seqs_Translator(proper_id, have_seqs, trans_fr, gen_code): abc_list = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', \ 'J','K','L','M','N','O','P','Q','R','S','T', \ 'U','V','W','X','Y','Z'] bad_list = [ 'B', 'D', 'E', 'F', 'H', 'I', \ 'J','K','L','M', 'O','P','Q','R','S', \ 'U','V','W','X','Y','Z'] # REMOVED A T G C N global gl_Ter global gl_Phe, gl_Leu, gl_Ser, gl_Tyr, gl_Cys, \ gl_Trp, gl_Pro, gl_His, gl_Gln, gl_Arg, \ gl_Ile, gl_Met, gl_Thr, gl_Asn, gl_Lys, \ gl_Val, gl_Ala, gl_Asp, gl_Glu, gl_Gly global gl_Any global gl_AmAcLib global gl_tr_file1, gl_tr_file2, gl_tr_file3, \ gl_tr_file4, gl_tr_file5, gl_tr_file6, \ gl_fw_file7, gl_rc_file8, gl_l0_file9, \ gl_l1_file9, gl_l2_file9, gl_l3_file9, \ gl_l4_file9, gl_l5_file9, gl_l6_file9, \ gl_ls_file9, gl_s_file10, gl_l_file10, \ tab_out1, tab_out2, out_n2a_frw, out_n2a_rev ### DEBUGGING ### # print proper_id + " " + "FRAME: " + `trans_fr` + " -=- GENE_CODE: " + `gen_code` t = have_seqs # DNA sequence t = string.upper(t) # all uppercase t = re.sub("-", "", t) # remove all dashes t = list(t) # string -> list of chars ######################################################### ### ONLY A T G C N ARE ALLOWED ### ### EVERYTHING ELSE IS REPLACED BY "N" ### mooba = 0 # COUNTER OF ALL LETTERS booba = 0 # COUNTER OF BAD LETTERS for item in t: if item in bad_list: t[mooba] = "N" booba = booba + 1 mooba = mooba + 1 ######################################################### ### AFFY N2A SUB ### foofa = 0 poofa = 0 t_n2a_frw = t[:] for item in t_n2a_frw: if item == "N": t_n2a_frw[foofa] = "A" poofa = poofa + 1 foofa = foofa + 1 # t_n2a_rev = t_n2a_frw[:] t_n2a_rev.reverse() t_n2a_frw = string.join(t_n2a_frw, '') t_n2a_rev = string.join(t_n2a_rev, '') t_n2a_rev = re.sub("A", "t", t_n2a_rev) t_n2a_rev = re.sub("T", "a", t_n2a_rev) t_n2a_rev = re.sub("G", "c", t_n2a_rev) t_n2a_rev = re.sub("C", "g", t_n2a_rev) t_n2a_rev = string.upper(t_n2a_rev) out_n2a_frw.write(">" + proper_id + " forward " + `len(t_n2a_frw)` + " nt" + '\n' + t_n2a_frw + '\n') out_n2a_rev.write(">" + proper_id + " rev-comp " + `len(t_n2a_rev)` + " nt" + '\n' + t_n2a_rev + '\n') ######################################################### t_r = t[:] # will be reverse string t_r.reverse() # inplace reverse the list t = string.join(t, '') # list of strings -> forward string t_r = string.join(t_r, '') # list of strings -> reverse string ######################################### t_r = re.sub("A", "t", t_r) # A -> t t_r = re.sub("T", "a", t_r) # T -> a t_r = re.sub("G", "c", t_r) # G -> c t_r = re.sub("C", "g", t_r) # C -> g ### NOTE THAT "N" REMAINS AS "N" ### ######################################### t_r = string.upper(t_r) # back to uppercase ######################################### l = len(t) # print l l_r = len(t_r) gl_fw_file7.write(">" + proper_id + " forward " + `l` + " nt" + '\n' + t + '\n') gl_rc_file8.write(">" + proper_id + " rev-comp " + `l_r` + " nt" + '\n' + t_r + '\n') tab_out1.write(proper_id + '\t' + `l` + '\t' + t + '\n') tab_out2.write(proper_id + '\t' + `l_r` + '\t' + t_r + '\n') if booba != 0: gl_l0_file9.write(proper_id + '\t' + `booba` + '\t' + "non ATGCN letters" + '\n') if poofa != 0: gl_l0_file9.write(proper_id + '\t' + `poofa` + '\t' + "N-s were replaced by A-s" + '\n') ### TRANSLATION ONE FRAME ### if trans_fr == 1: k1 = 0 stop_count = 0 any_count = 0 longest_fr = 0 longest_orf = "" total_size = 0 frm_number = 0 my_list = [] while k1 < l: m1 = k1 + 3 p1 = t[k1:m1] # triplet frame 1 if p1 in gl_Any: my_list.append("X") any_count = any_count + 1 if p1 in gl_Ter: my_list.append("*") stop_count = stop_count + 1 if p1 in gl_Phe: my_list.append("F") if p1 in gl_Leu: my_list.append("L") if p1 in gl_Ser: my_list.append("S") if p1 in gl_Tyr: my_list.append("Y") if p1 in gl_Cys: my_list.append("C") if p1 in gl_Trp: my_list.append("W") if p1 in gl_Pro: my_list.append("P") if p1 in gl_His: my_list.append("H") if p1 in gl_Gln: my_list.append("Q") if p1 in gl_Arg: my_list.append("R") if p1 in gl_Ile: my_list.append("I") if p1 in gl_Met: my_list.append("M") if p1 in gl_Thr: my_list.append("T") if p1 in gl_Asn: my_list.append("N") if p1 in gl_Lys: my_list.append("K") if p1 in gl_Val: my_list.append("V") if p1 in gl_Ala: my_list.append("A") if p1 in gl_Asp: my_list.append("D") if p1 in gl_Glu: my_list.append("E") if p1 in gl_Gly: my_list.append("G") k1 = k1 + 3 ########### my_string = "".join(my_list) total_size = len(my_string) my_subset = my_string.split('*') for fragment in my_subset: fragment_len = len(fragment) # if fragment_len >= longest_fr: if fragment_len > longest_fr: longest_fr = fragment_len longest_orf = fragment if fragment_len != 0: frm_number = frm_number + 1 full_frame = "UNDEFINED" if longest_fr >= total_size - 1: full_frame = "SINGLE_ORF" if longest_fr < total_size - 1: full_frame = "MULTIPLE_ORFs" gl_tr_file1.write(">" + proper_id + "_fr1" + " translation_frame:1" + \ " STOP:" + `stop_count` + " ANY(X):" + `any_count` + \ " LONGEST:" + `longest_fr` + " TOTAL_LENGTH:" + `total_size` + \ " " + full_frame + ":" + `frm_number` + '\n') gl_tr_file1.write(my_string + '\n') gl_l1_file9.write(proper_id + '\t' + "fr_1" + '\t' + `stop_count` + '\t' + `any_count` + \ '\t' + `longest_fr` + '\t' + `total_size` + '\t' + `frm_number` + '\n') gl_l_file10.write(">" + proper_id + "_fr1" + \ " STOP:" + `stop_count` + " ANY(X):" + `any_count` + \ " LONGEST:" + `longest_fr` + " TOTAL_LENGTH:" + `total_size` + \ " " + full_frame + ":" + `frm_number` + '\n') gl_l_file10.write(longest_orf + '\n') if full_frame == "SINGLE_ORF": ### CHECK FOR POLY_A AND POLY_T ( ..FFFFF.. OR ..KKKKK.. ) ### count_fff = my_string.count("F") count_kkk = my_string.count("K") fract_fff = count_fff*1.0/total_size fract_kkk = count_kkk*1.0/total_size if fract_fff <= 0.70 and fract_kkk <= 0.70: gl_s_file10.write(">" + proper_id + "_fr1 " + `total_size` + " STOP:" + `stop_count` \ + " ANY(X):" + `any_count` + '\n' + my_string + '\n') if fract_fff > 0.70: fract_fff = str(round(fract_fff,2)) gl_l0_file9.write(proper_id + '\t' + fract_fff + '\t' + "poly_FFF translation" + '\n') if fract_kkk > 0.70: fract_kkk = str(round(fract_kkk,2)) gl_l0_file9.write(proper_id + '\t' + fract_kkk + '\t' + "poly_KKK translation" + '\n') ### TRANSLATION THREE FRAMES ### if trans_fr == 3: k1 = 0 k2 = 1 k3 = 2 ############### stop_count1 = 0 any_count1 = 0 longest_fr1 = 0 longest_orf1 = "" total_size1 = 0 frm_number1 = 0 my_list1 = [] ############### stop_count2 = 0 any_count2 = 0 longest_fr2 = 0 longest_orf2 = "" total_size2 = 0 frm_number2 = 0 my_list2 = [] ############### stop_count3 = 0 any_count3 = 0 longest_fr3 = 0 longest_orf3 = "" total_size3 = 0 frm_number3 = 0 my_list3 = [] ############### while k1 < l: m1 = k1 + 3 m2 = k2 + 3 m3 = k3 + 3 p1 = t[k1:m1] # triplet frame 1 p2 = t[k2:m2] # triplet frame 2 p3 = t[k3:m3] # triplet frame 3 ################################# if p1 in gl_Any: my_list1.append("X") any_count1 = any_count1 + 1 if p1 in gl_Ter: my_list1.append("*") stop_count1 = stop_count1 + 1 if p1 in gl_Phe: my_list1.append("F") if p1 in gl_Leu: my_list1.append("L") if p1 in gl_Ser: my_list1.append("S") if p1 in gl_Tyr: my_list1.append("Y") if p1 in gl_Cys: my_list1.append("C") if p1 in gl_Trp: my_list1.append("W") if p1 in gl_Pro: my_list1.append("P") if p1 in gl_His: my_list1.append("H") if p1 in gl_Gln: my_list1.append("Q") if p1 in gl_Arg: my_list1.append("R") if p1 in gl_Ile: my_list1.append("I") if p1 in gl_Met: my_list1.append("M") if p1 in gl_Thr: my_list1.append("T") if p1 in gl_Asn: my_list1.append("N") if p1 in gl_Lys: my_list1.append("K") if p1 in gl_Val: my_list1.append("V") if p1 in gl_Ala: my_list1.append("A") if p1 in gl_Asp: my_list1.append("D") if p1 in gl_Glu: my_list1.append("E") if p1 in gl_Gly: my_list1.append("G") ################################## if p2 in gl_Any: my_list2.append("X") any_count2 = any_count2 + 1 if p2 in gl_Ter: my_list2.append("*") stop_count2 = stop_count2 + 1 if p2 in gl_Phe: my_list2.append("F") if p2 in gl_Leu: my_list2.append("L") if p2 in gl_Ser: my_list2.append("S") if p2 in gl_Tyr: my_list2.append("Y") if p2 in gl_Cys: my_list2.append("C") if p2 in gl_Trp: my_list2.append("W") if p2 in gl_Pro: my_list2.append("P") if p2 in gl_His: my_list2.append("H") if p2 in gl_Gln: my_list2.append("Q") if p2 in gl_Arg: my_list2.append("R") if p2 in gl_Ile: my_list2.append("I") if p2 in gl_Met: my_list2.append("M") if p2 in gl_Thr: my_list2.append("T") if p2 in gl_Asn: my_list2.append("N") if p2 in gl_Lys: my_list2.append("K") if p2 in gl_Val: my_list2.append("V") if p2 in gl_Ala: my_list2.append("A") if p2 in gl_Asp: my_list2.append("D") if p2 in gl_Glu: my_list2.append("E") if p2 in gl_Gly: my_list2.append("G") ################################## if p3 in gl_Any: my_list3.append("X") any_count3 = any_count3 + 1 if p3 in gl_Ter: my_list3.append("*") stop_count3 = stop_count3 + 1 if p3 in gl_Phe: my_list3.append("F") if p3 in gl_Leu: my_list3.append("L") if p3 in gl_Ser: my_list3.append("S") if p3 in gl_Tyr: my_list3.append("Y") if p3 in gl_Cys: my_list3.append("C") if p3 in gl_Trp: my_list3.append("W") if p3 in gl_Pro: my_list3.append("P") if p3 in gl_His: my_list3.append("H") if p3 in gl_Gln: my_list3.append("Q") if p3 in gl_Arg: my_list3.append("R") if p3 in gl_Ile: my_list3.append("I") if p3 in gl_Met: my_list3.append("M") if p3 in gl_Thr: my_list3.append("T") if p3 in gl_Asn: my_list3.append("N") if p3 in gl_Lys: my_list3.append("K") if p3 in gl_Val: my_list3.append("V") if p3 in gl_Ala: my_list3.append("A") if p3 in gl_Asp: my_list3.append("D") if p3 in gl_Glu: my_list3.append("E") if p3 in gl_Gly: my_list3.append("G") ################################## k1 = k1 + 3 k2 = k2 + 3 # next triplet frame2 k3 = k3 + 3 # next triplet frame3 ########### my_string1 = "".join(my_list1) my_string2 = "".join(my_list2) my_string3 = "".join(my_list3) ############################# total_size1 = len(my_string1) total_size2 = len(my_string2) total_size3 = len(my_string3) ############################# my_subset1 = my_string1.split('*') my_subset2 = my_string2.split('*') my_subset3 = my_string3.split('*') ############################# ## 1 for fragment1 in my_subset1: fragment_len1 = len(fragment1) # if fragment_len1 >= longest_fr1: if fragment_len1 > longest_fr1: longest_fr1 = fragment_len1 longest_orf1 = fragment1 if fragment_len1 != 0: frm_number1 = frm_number1 + 1 ## 2 for fragment2 in my_subset2: fragment_len2 = len(fragment2) # if fragment_len2 >= longest_fr2: if fragment_len2 > longest_fr2: longest_fr2 = fragment_len2 longest_orf2 = fragment2 if fragment_len2 != 0: frm_number2 = frm_number2 + 1 ## 3 for fragment3 in my_subset3: fragment_len3 = len(fragment3) # if fragment_len3 >= longest_fr3: if fragment_len3 > longest_fr3: longest_fr3 = fragment_len3 longest_orf3 = fragment3 if fragment_len3 != 0: frm_number3 = frm_number3 + 1 ############################# full_frame1 = "UNDEFINED" full_frame2 = "UNDEFINED" full_frame3 = "UNDEFINED" ############################# ## 1 if longest_fr1 >= total_size1 - 1: full_frame1 = "SINGLE_ORF" if longest_fr1 < total_size1 - 1: full_frame1 = "MULTIPLE_ORFs" ## 2 if longest_fr2 >= total_size2 - 1: full_frame2 = "SINGLE_ORF" if longest_fr2 < total_size2 - 1: full_frame2 = "MULTIPLE_ORFs" ## 3 if longest_fr3 >= total_size3 - 1: full_frame3 = "SINGLE_ORF" if longest_fr3 < total_size3 - 1: full_frame3 = "MULTIPLE_ORFs" ############################# ## 1 gl_tr_file1.write(">" + proper_id + "_fr1" + " translation_frame:1" + \ " STOP:" + `stop_count1` + " ANY(X):" + `any_count1` + \ " LONGEST:" + `longest_fr1` + " TOTAL_LENGTH:" + `total_size1` + \ " " + full_frame1 + ":" + `frm_number1` + '\n') gl_tr_file1.write(my_string1 + '\n') ## 2 gl_tr_file2.write(">" + proper_id + "_fr2" + " translation_frame:2" + \ " STOP:" + `stop_count2` + " ANY(X):" + `any_count2` + \ " LONGEST:" + `longest_fr2` + " TOTAL_LENGTH:" + `total_size2` + \ " " + full_frame2 + ":" + `frm_number2` + '\n') gl_tr_file2.write(my_string2 + '\n') ## 3 gl_tr_file3.write(">" + proper_id + "_fr3" + " translation_frame:3" + \ " STOP:" + `stop_count3` + " ANY(X):" + `any_count3` + \ " LONGEST:" + `longest_fr3` + " TOTAL_LENGTH:" + `total_size3` + \ " " + full_frame3 + ":" + `frm_number3` + '\n') gl_tr_file3.write(my_string3 + '\n') ############################# ## LONGEST ## llen1 = len(longest_orf1) llen2 = len(longest_orf2) llen3 = len(longest_orf3) lfrm = " " lfrm1 = "" lfrm2 = "" lfrm3 = "" dupl_status = " UNIQ_LONG" ## 1 if llen1 >= llen2 and llen1 >= llen3: if llen1 == llen2 or llen1 == llen3: dupl_status = " DUPL_LONG" lfr = "_fr1" lfrm1 = "fr_1" longest_orf = longest_orf1 stop_count = stop_count1 any_count = any_count1 longest_fr = longest_fr1 total_size = total_size1 full_frame = full_frame1 frm_number = frm_number1 longest_len = llen1 gl_l_file10.write(">" + proper_id + lfr + dupl_status + \ " STOP:" + `stop_count` + " ANY(X):" + `any_count` + \ " LONGEST:" + `longest_fr` + " TOTAL_LENGTH:" + `total_size` + \ " " + full_frame + ":" + `frm_number` + '\n') gl_l_file10.write(longest_orf + '\n') ## 2 if llen2 >= llen1 and llen2 >= llen3: if llen2 == llen1 or llen2 == llen3: dupl_status = " DUPL_LONG" lfr = "_fr2" lfrm2 = "fr_2" longest_orf = longest_orf2 stop_count = stop_count2 any_count = any_count2 longest_fr = longest_fr2 total_size = total_size2 full_frame = full_frame2 frm_number = frm_number2 longest_len = llen2 gl_l_file10.write(">" + proper_id + lfr + dupl_status + \ " STOP:" + `stop_count` + " ANY(X):" + `any_count` + \ " LONGEST:" + `longest_fr` + " TOTAL_LENGTH:" + `total_size` + \ " " + full_frame + ":" + `frm_number` + '\n') gl_l_file10.write(longest_orf + '\n') ## 3 if llen3 >= llen1 and llen3 >= llen2: if llen3 == llen1 or llen3 == llen2: dupl_status = " DUPL_LONG" lfr = "_fr3" lfrm3 = "fr_3" longest_orf = longest_orf3 stop_count = stop_count3 any_count = any_count3 longest_fr = longest_fr3 total_size = total_size3 full_frame = full_frame3 frm_number = frm_number3 longest_len = llen3 gl_l_file10.write(">" + proper_id + lfr + dupl_status + \ " STOP:" + `stop_count` + " ANY(X):" + `any_count` + \ " LONGEST:" + `longest_fr` + " TOTAL_LENGTH:" + `total_size` + \ " " + full_frame + ":" + `frm_number` + '\n') gl_l_file10.write(longest_orf + '\n') ############################# gl_l1_file9.write(proper_id + '\t' + "fr_1" + '\t' + `stop_count1` + '\t' + `any_count1` + \ '\t' + `longest_fr1` + '\t' + `total_size1` + '\t' + `frm_number1` + '\n') gl_l2_file9.write(proper_id + '\t' + "fr_2" + '\t' + `stop_count2` + '\t' + `any_count2` + \ '\t' + `longest_fr2` + '\t' + `total_size2` + '\t' + `frm_number2` + '\n') gl_l3_file9.write(proper_id + '\t' + "fr_3" + '\t' + `stop_count3` + '\t' + `any_count3` + \ '\t' + `longest_fr3` + '\t' + `total_size3` + '\t' + `frm_number3` + '\n') ############################# if dupl_status == " UNIQ_LONG": dupl_wr = "UNIQ" if dupl_status == " DUPL_LONG": dupl_wr = "DUPL" lfrm_list = [lfrm1, lfrm2, lfrm3] for l_item in lfrm_list: if l_item != "": # lfrm = lfrm + " " + l_item + " " lfrm = lfrm + l_item + " " # lfrm = lfrm[1:] # lfrm = lfrm[:-1] gl_ls_file9.write(proper_id + '\t' + \ "fr_1" + '\t' + `stop_count1` + '\t' + `any_count1` + \ '\t' + `longest_fr1` + '\t' + `total_size1` + '\t' + `frm_number1` + '\t' + \ "fr_2" + '\t' + `stop_count2` + '\t' + `any_count2` + \ '\t' + `longest_fr2` + '\t' + `total_size2` + '\t' + `frm_number2` + '\t' + \ "fr_3" + '\t' + `stop_count3` + '\t' + `any_count3` + \ '\t' + `longest_fr3` + '\t' + `total_size3` + '\t' + `frm_number3` + '\t' + \ `longest_len` + '\t' + lfrm + '\t' + dupl_wr + '\n') ############################# dupl_frame1 = " ONE_ORF" dupl_frame2 = " ONE_ORF" dupl_frame3 = " ONE_ORF" ############# ## 1 if full_frame1 == "SINGLE_ORF": if full_frame1 == full_frame2: dupl_frame1 = " NOT_UNIQ" if full_frame1 == full_frame3: dupl_frame1 = " NOT_UNIQ" ### CHECK FOR POLY_A AND POLY_T ( ..FFFFF.. OR ..KKKKK.. ) ### count_fff1 = my_string1.count("F") count_kkk1 = my_string1.count("K") fract_fff1 = count_fff1*1.0/total_size1 fract_kkk1 = count_kkk1*1.0/total_size1 if fract_fff1 <= 0.70 and fract_kkk1 <= 0.70: gl_s_file10.write(">" + proper_id + "_fr1 " + `total_size1` + " STOP:" + `stop_count1` \ + " ANY(X):" + `any_count1` + dupl_frame1 + '\n' + my_string1 + '\n') if fract_fff1 > 0.70: fract_fff1 = str(round(fract_fff1,2)) gl_l0_file9.write(proper_id + '\t' + fract_fff1 + '\t' + "poly_FFF translation" + '\n') if fract_kkk1 > 0.70: fract_kkk1 = str(round(fract_kkk1,2)) gl_l0_file9.write(proper_id + '\t' + fract_kkk1 + '\t' + "poly_KKK translation" + '\n') ############# ## 2 if full_frame2 == "SINGLE_ORF": if full_frame2 == full_frame1: dupl_frame2 = " NOT_UNIQ" if full_frame2 == full_frame3: dupl_frame2 = " NOT_UNIQ" ### CHECK FOR POLY_A AND POLY_T ( ..FFFFF.. OR ..KKKKK.. ) ### count_fff2 = my_string2.count("F") count_kkk2 = my_string2.count("K") fract_fff2 = count_fff2*1.0/total_size2 fract_kkk2 = count_kkk2*1.0/total_size2 if fract_fff2 <= 0.70 and fract_kkk2 <= 0.70: gl_s_file10.write(">" + proper_id + "_fr2 " + `total_size2` + " STOP:" + `stop_count2` \ + " ANY(X):" + `any_count2` + dupl_frame2 + '\n' + my_string2 + '\n') if fract_fff2 > 0.70: fract_fff2 = str(round(fract_fff2,2)) gl_l0_file9.write(proper_id + '\t' + fract_fff2 + '\t' + "poly_FFF translation" + '\n') if fract_kkk2 > 0.70: fract_kkk2 = str(round(fract_kkk2,2)) gl_l0_file9.write(proper_id + '\t' + fract_kkk2 + '\t' + "poly_KKK translation" + '\n') ############# ## 3 if full_frame3 == "SINGLE_ORF": if full_frame3 == full_frame1: dupl_frame3 = " NOT_UNIQ" if full_frame3 == full_frame2: dupl_frame3 = " NOT_UNIQ" ### CHECK FOR POLY_A AND POLY_T ( ..FFFFF.. OR ..KKKKK.. ) ### count_fff3 = my_string3.count("F") count_kkk3 = my_string3.count("K") fract_fff3 = count_fff3*1.0/total_size3 fract_kkk3 = count_kkk3*1.0/total_size3 if fract_fff3 <= 0.70 and fract_kkk3 <= 0.70: gl_s_file10.write(">" + proper_id + "_fr3 " + `total_size3` + " STOP:" + `stop_count3` \ + " ANY(X):" + `any_count3` + dupl_frame3 + '\n' + my_string3 + '\n') if fract_fff3 > 0.70: fract_fff3 = str(round(fract_fff3,2)) gl_l0_file9.write(proper_id + '\t' + fract_fff3 + '\t' + "poly_FFF translation" + '\n') if fract_kkk3 > 0.70: fract_kkk3 = str(round(fract_kkk3,2)) gl_l0_file9.write(proper_id + '\t' + fract_kkk3 + '\t' + "poly_KKK translation" + '\n') ############################# ### TRANSLATION SIX FRAMES ### if trans_fr == 6: k1 = 0 k2 = 1 k3 = 2 ############### stop_count1 = 0 any_count1 = 0 longest_fr1 = 0 longest_orf1 = "" total_size1 = 0 frm_number1 = 0 my_list1 = [] ############### stop_count2 = 0 any_count2 = 0 longest_fr2 = 0 longest_orf2 = "" total_size2 = 0 frm_number2 = 0 my_list2 = [] ############### stop_count3 = 0 any_count3 = 0 longest_fr3 = 0 longest_orf3 = "" total_size3 = 0 frm_number3 = 0 my_list3 = [] ############### stop_count4 = 0 any_count4 = 0 longest_fr4 = 0 longest_orf4 = "" total_size4 = 0 frm_number4 = 0 my_list4 = [] ############### stop_count5 = 0 any_count5 = 0 longest_fr5 = 0 longest_orf5 = "" total_size5 = 0 frm_number5 = 0 my_list5 = [] ############### stop_count6 = 0 any_count6 = 0 longest_fr6 = 0 longest_orf6 = "" total_size6 = 0 frm_number6 = 0 my_list6 = [] ############### while k1 < l: m1 = k1 + 3 m2 = k2 + 3 m3 = k3 + 3 p1 = t[k1:m1] # triplet frame 1 p2 = t[k2:m2] # triplet frame 2 p3 = t[k3:m3] # triplet frame 3 p4 = t_r[k1:m1] # triplet frame 4 p5 = t_r[k2:m2] # triplet frame 5 p6 = t_r[k3:m3] # triplet frame 6 ################################# if p1 in gl_Any: my_list1.append("X") any_count1 = any_count1 + 1 if p1 in gl_Ter: my_list1.append("*") stop_count1 = stop_count1 + 1 if p1 in gl_Phe: my_list1.append("F") if p1 in gl_Leu: my_list1.append("L") if p1 in gl_Ser: my_list1.append("S") if p1 in gl_Tyr: my_list1.append("Y") if p1 in gl_Cys: my_list1.append("C") if p1 in gl_Trp: my_list1.append("W") if p1 in gl_Pro: my_list1.append("P") if p1 in gl_His: my_list1.append("H") if p1 in gl_Gln: my_list1.append("Q") if p1 in gl_Arg: my_list1.append("R") if p1 in gl_Ile: my_list1.append("I") if p1 in gl_Met: my_list1.append("M") if p1 in gl_Thr: my_list1.append("T") if p1 in gl_Asn: my_list1.append("N") if p1 in gl_Lys: my_list1.append("K") if p1 in gl_Val: my_list1.append("V") if p1 in gl_Ala: my_list1.append("A") if p1 in gl_Asp: my_list1.append("D") if p1 in gl_Glu: my_list1.append("E") if p1 in gl_Gly: my_list1.append("G") ################################## if p2 in gl_Any: my_list2.append("X") any_count2 = any_count2 + 1 if p2 in gl_Ter: my_list2.append("*") stop_count2 = stop_count2 + 1 if p2 in gl_Phe: my_list2.append("F") if p2 in gl_Leu: my_list2.append("L") if p2 in gl_Ser: my_list2.append("S") if p2 in gl_Tyr: my_list2.append("Y") if p2 in gl_Cys: my_list2.append("C") if p2 in gl_Trp: my_list2.append("W") if p2 in gl_Pro: my_list2.append("P") if p2 in gl_His: my_list2.append("H") if p2 in gl_Gln: my_list2.append("Q") if p2 in gl_Arg: my_list2.append("R") if p2 in gl_Ile: my_list2.append("I") if p2 in gl_Met: my_list2.append("M") if p2 in gl_Thr: my_list2.append("T") if p2 in gl_Asn: my_list2.append("N") if p2 in gl_Lys: my_list2.append("K") if p2 in gl_Val: my_list2.append("V") if p2 in gl_Ala: my_list2.append("A") if p2 in gl_Asp: my_list2.append("D") if p2 in gl_Glu: my_list2.append("E") if p2 in gl_Gly: my_list2.append("G") ################################## if p3 in gl_Any: my_list3.append("X") any_count3 = any_count3 + 1 if p3 in gl_Ter: my_list3.append("*") stop_count3 = stop_count3 + 1 if p3 in gl_Phe: my_list3.append("F") if p3 in gl_Leu: my_list3.append("L") if p3 in gl_Ser: my_list3.append("S") if p3 in gl_Tyr: my_list3.append("Y") if p3 in gl_Cys: my_list3.append("C") if p3 in gl_Trp: my_list3.append("W") if p3 in gl_Pro: my_list3.append("P") if p3 in gl_His: my_list3.append("H") if p3 in gl_Gln: my_list3.append("Q") if p3 in gl_Arg: my_list3.append("R") if p3 in gl_Ile: my_list3.append("I") if p3 in gl_Met: my_list3.append("M") if p3 in gl_Thr: my_list3.append("T") if p3 in gl_Asn: my_list3.append("N") if p3 in gl_Lys: my_list3.append("K") if p3 in gl_Val: my_list3.append("V") if p3 in gl_Ala: my_list3.append("A") if p3 in gl_Asp: my_list3.append("D") if p3 in gl_Glu: my_list3.append("E") if p3 in gl_Gly: my_list3.append("G") ################################## if p4 in gl_Any: my_list4.append("X") any_count4 = any_count4 + 1 if p4 in gl_Ter: my_list4.append("*") stop_count4 = stop_count4 + 1 if p4 in gl_Phe: my_list4.append("F") if p4 in gl_Leu: my_list4.append("L") if p4 in gl_Ser: my_list4.append("S") if p4 in gl_Tyr: my_list4.append("Y") if p4 in gl_Cys: my_list4.append("C") if p4 in gl_Trp: my_list4.append("W") if p4 in gl_Pro: my_list4.append("P") if p4 in gl_His: my_list4.append("H") if p4 in gl_Gln: my_list4.append("Q") if p4 in gl_Arg: my_list4.append("R") if p4 in gl_Ile: my_list4.append("I") if p4 in gl_Met: my_list4.append("M") if p4 in gl_Thr: my_list4.append("T") if p4 in gl_Asn: my_list4.append("N") if p4 in gl_Lys: my_list4.append("K") if p4 in gl_Val: my_list4.append("V") if p4 in gl_Ala: my_list4.append("A") if p4 in gl_Asp: my_list4.append("D") if p4 in gl_Glu: my_list4.append("E") if p4 in gl_Gly: my_list4.append("G") ################################## if p5 in gl_Any: my_list5.append("X") any_count5 = any_count5 + 1 if p5 in gl_Ter: my_list5.append("*") stop_count5 = stop_count5 + 1 if p5 in gl_Phe: my_list5.append("F") if p5 in gl_Leu: my_list5.append("L") if p5 in gl_Ser: my_list5.append("S") if p5 in gl_Tyr: my_list5.append("Y") if p5 in gl_Cys: my_list5.append("C") if p5 in gl_Trp: my_list5.append("W") if p5 in gl_Pro: my_list5.append("P") if p5 in gl_His: my_list5.append("H") if p5 in gl_Gln: my_list5.append("Q") if p5 in gl_Arg: my_list5.append("R") if p5 in gl_Ile: my_list5.append("I") if p5 in gl_Met: my_list5.append("M") if p5 in gl_Thr: my_list5.append("T") if p5 in gl_Asn: my_list5.append("N") if p5 in gl_Lys: my_list5.append("K") if p5 in gl_Val: my_list5.append("V") if p5 in gl_Ala: my_list5.append("A") if p5 in gl_Asp: my_list5.append("D") if p5 in gl_Glu: my_list5.append("E") if p5 in gl_Gly: my_list5.append("G") ################################## if p6 in gl_Any: my_list6.append("X") any_count6 = any_count6 + 1 if p6 in gl_Ter: my_list6.append("*") stop_count6 = stop_count6 + 1 if p6 in gl_Phe: my_list6.append("F") if p6 in gl_Leu: my_list6.append("L") if p6 in gl_Ser: my_list6.append("S") if p6 in gl_Tyr: my_list6.append("Y") if p6 in gl_Cys: my_list6.append("C") if p6 in gl_Trp: my_list6.append("W") if p6 in gl_Pro: my_list6.append("P") if p6 in gl_His: my_list6.append("H") if p6 in gl_Gln: my_list6.append("Q") if p6 in gl_Arg: my_list6.append("R") if p6 in gl_Ile: my_list6.append("I") if p6 in gl_Met: my_list6.append("M") if p6 in gl_Thr: my_list6.append("T") if p6 in gl_Asn: my_list6.append("N") if p6 in gl_Lys: my_list6.append("K") if p6 in gl_Val: my_list6.append("V") if p6 in gl_Ala: my_list6.append("A") if p6 in gl_Asp: my_list6.append("D") if p6 in gl_Glu: my_list6.append("E") if p6 in gl_Gly: my_list6.append("G") ################################## k1 = k1 + 3 k2 = k2 + 3 # next triplet frame2 k3 = k3 + 3 # next triplet frame3 ########### my_string1 = "".join(my_list1) my_string2 = "".join(my_list2) my_string3 = "".join(my_list3) my_string4 = "".join(my_list4) my_string5 = "".join(my_list5) my_string6 = "".join(my_list6) ############################# total_size1 = len(my_string1) total_size2 = len(my_string2) total_size3 = len(my_string3) total_size4 = len(my_string4) total_size5 = len(my_string5) total_size6 = len(my_string6) ############################# my_subset1 = my_string1.split('*') my_subset2 = my_string2.split('*') my_subset3 = my_string3.split('*') my_subset4 = my_string4.split('*') my_subset5 = my_string5.split('*') my_subset6 = my_string6.split('*') ############################# ## 1 for fragment1 in my_subset1: fragment_len1 = len(fragment1) # if fragment_len1 >= longest_fr1: if fragment_len1 > longest_fr1: longest_fr1 = fragment_len1 longest_orf1 = fragment1 if fragment_len1 != 0: frm_number1 = frm_number1 + 1 ## 2 for fragment2 in my_subset2: fragment_len2 = len(fragment2) # if fragment_len2 >= longest_fr2: if fragment_len2 > longest_fr2: longest_fr2 = fragment_len2 longest_orf2 = fragment2 if fragment_len2 != 0: frm_number2 = frm_number2 + 1 ## 3 for fragment3 in my_subset3: fragment_len3 = len(fragment3) # if fragment_len3 >= longest_fr3: if fragment_len3 > longest_fr3: longest_fr3 = fragment_len3 longest_orf3 = fragment3 if fragment_len3 != 0: frm_number3 = frm_number3 + 1 ## 4 for fragment4 in my_subset4: fragment_len4 = len(fragment4) # if fragment_len4 >= longest_fr4: if fragment_len4 > longest_fr4: longest_fr4 = fragment_len4 longest_orf4 = fragment4 if fragment_len4 != 0: frm_number4 = frm_number4 + 1 ## 5 for fragment5 in my_subset5: fragment_len5 = len(fragment5) # if fragment_len5 >= longest_fr5: if fragment_len5 > longest_fr5: longest_fr5 = fragment_len5 longest_orf5 = fragment5 if fragment_len5 != 0: frm_number5 = frm_number5 + 1 ## 6 for fragment6 in my_subset6: fragment_len6 = len(fragment6) # if fragment_len6 >= longest_fr6: if fragment_len6 > longest_fr6: longest_fr6 = fragment_len6 longest_orf6 = fragment6 if fragment_len6 != 0: frm_number6 = frm_number6 + 1 ############################# full_frame1 = "UNDEFINED" full_frame2 = "UNDEFINED" full_frame3 = "UNDEFINED" full_frame4 = "UNDEFINED" full_frame5 = "UNDEFINED" full_frame6 = "UNDEFINED" ############################# ## 1 if longest_fr1 >= total_size1 - 1: full_frame1 = "SINGLE_ORF" if longest_fr1 < total_size1 - 1: full_frame1 = "MULTIPLE_ORFs" ## 2 if longest_fr2 >= total_size2 - 1: full_frame2 = "SINGLE_ORF" if longest_fr2 < total_size2 - 1: full_frame2 = "MULTIPLE_ORFs" ## 3 if longest_fr3 >= total_size3 - 1: full_frame3 = "SINGLE_ORF" if longest_fr3 < total_size3 - 1: full_frame3 = "MULTIPLE_ORFs" ## 4 if longest_fr4 >= total_size4 - 1: full_frame4 = "SINGLE_ORF" if longest_fr4 < total_size4 - 1: full_frame4 = "MULTIPLE_ORFs" ## 5 if longest_fr5 >= total_size5 - 1: full_frame5 = "SINGLE_ORF" if longest_fr5 < total_size5 - 1: full_frame5 = "MULTIPLE_ORFs" ## 6 if longest_fr6 >= total_size6 - 1: full_frame6 = "SINGLE_ORF" if longest_fr6 < total_size6 - 1: full_frame6 = "MULTIPLE_ORFs" ############################# ## 1 gl_tr_file1.write(">" + proper_id + "_fr1" + " translation_frame:1" + \ " STOP:" + `stop_count1` + " ANY(X):" + `any_count1` + \ " LONGEST:" + `longest_fr1` + " TOTAL_LENGTH:" + `total_size1` + \ " " + full_frame1 + ":" + `frm_number1` + '\n') gl_tr_file1.write(my_string1 + '\n') ## 2 gl_tr_file2.write(">" + proper_id + "_fr2" + " translation_frame:2" + \ " STOP:" + `stop_count2` + " ANY(X):" + `any_count2` + \ " LONGEST:" + `longest_fr2` + " TOTAL_LENGTH:" + `total_size2` + \ " " + full_frame2 + ":" + `frm_number2` + '\n') gl_tr_file2.write(my_string2 + '\n') ## 3 gl_tr_file3.write(">" + proper_id + "_fr3" + " translation_frame:3" + \ " STOP:" + `stop_count3` + " ANY(X):" + `any_count3` + \ " LONGEST:" + `longest_fr3` + " TOTAL_LENGTH:" + `total_size3` + \ " " + full_frame3 + ":" + `frm_number3` + '\n') gl_tr_file3.write(my_string3 + '\n') ## 4 gl_tr_file4.write(">" + proper_id + "_fr4" + " translation_frame:4" + \ " STOP:" + `stop_count4` + " ANY(X):" + `any_count4` + \ " LONGEST:" + `longest_fr4` + " TOTAL_LENGTH:" + `total_size4` + \ " " + full_frame4 + ":" + `frm_number4` + '\n') gl_tr_file4.write(my_string4 + '\n') ## 5 gl_tr_file5.write(">" + proper_id + "_fr5" + " translation_frame:5" + \ " STOP:" + `stop_count5` + " ANY(X):" + `any_count5` + \ " LONGEST:" + `longest_fr5` + " TOTAL_LENGTH:" + `total_size5` + \ " " + full_frame5 + ":" + `frm_number5` + '\n') gl_tr_file5.write(my_string5 + '\n') ## 6 gl_tr_file6.write(">" + proper_id + "_fr6" + " translation_frame:6" + \ " STOP:" + `stop_count6` + " ANY(X):" + `any_count6` + \ " LONGEST:" + `longest_fr6` + " TOTAL_LENGTH:" + `total_size6` + \ " " + full_frame6 + ":" + `frm_number6` + '\n') gl_tr_file6.write(my_string6 + '\n') ############################# ## LONGEST ## llen1 = len(longest_orf1) llen2 = len(longest_orf2) llen3 = len(longest_orf3) llen4 = len(longest_orf4) llen5 = len(longest_orf5) llen6 = len(longest_orf6) lfrm = " " lfrm1 = "" lfrm2 = "" lfrm3 = "" lfrm4 = "" lfrm5 = "" lfrm6 = "" dupl_status = " UNIQ_LONG" ## 1 if llen1 >= llen2 and llen1 >= llen3 and llen1 >= llen4 and llen1 >= llen5 and llen1 >= llen6: if llen1 == llen2 or llen1 == llen3 or llen1 == llen4 or llen1 == llen5 or llen1 == llen6: dupl_status = " DUPL_LONG" lfr = "_fr1" lfrm1 = "fr_1" longest_orf = longest_orf1 stop_count = stop_count1 any_count = any_count1 longest_fr = longest_fr1 total_size = total_size1 full_frame = full_frame1 frm_number = frm_number1 longest_len = llen1 gl_l_file10.write(">" + proper_id + lfr + dupl_status + \ " STOP:" + `stop_count` + " ANY(X):" + `any_count` + \ " LONGEST:" + `longest_fr` + " TOTAL_LENGTH:" + `total_size` + \ " " + full_frame + ":" + `frm_number` + '\n') gl_l_file10.write(longest_orf + '\n') ## 2 if llen2 >= llen1 and llen2 >= llen3 and llen2 >= llen4 and llen2 >= llen5 and llen2 >= llen6: if llen2 == llen1 or llen2 == llen3 or llen2 == llen4 or llen2 == llen5 or llen2 == llen6: dupl_status = " DUPL_LONG" lfr = "_fr2" lfrm2 = "fr_2" longest_orf = longest_orf2 stop_count = stop_count2 any_count = any_count2 longest_fr = longest_fr2 total_size = total_size2 full_frame = full_frame2 frm_number = frm_number2 longest_len = llen2 gl_l_file10.write(">" + proper_id + lfr + dupl_status + \ " STOP:" + `stop_count` + " ANY(X):" + `any_count` + \ " LONGEST:" + `longest_fr` + " TOTAL_LENGTH:" + `total_size` + \ " " + full_frame + ":" + `frm_number` + '\n') gl_l_file10.write(longest_orf + '\n') ## 3 if llen3 >= llen1 and llen3 >= llen2 and llen3 >= llen4 and llen3 >= llen5 and llen3 >= llen6: if llen3 == llen1 or llen3 == llen2 or llen3 == llen4 or llen3 == llen5 or llen3 == llen6: dupl_status = " DUPL_LONG" lfr = "_fr3" lfrm3 = "fr_3" longest_orf = longest_orf3 stop_count = stop_count3 any_count = any_count3 longest_fr = longest_fr3 total_size = total_size3 full_frame = full_frame3 frm_number = frm_number3 longest_len = llen3 gl_l_file10.write(">" + proper_id + lfr + dupl_status + \ " STOP:" + `stop_count` + " ANY(X):" + `any_count` + \ " LONGEST:" + `longest_fr` + " TOTAL_LENGTH:" + `total_size` + \ " " + full_frame + ":" + `frm_number` + '\n') gl_l_file10.write(longest_orf + '\n') ## 4 if llen4 >= llen1 and llen4 >= llen2 and llen4 >= llen3 and llen4 >= llen5 and llen4 >= llen6: if llen4 == llen1 or llen4 == llen2 or llen4 == llen3 or llen4 == llen5 or llen4 == llen6: dupl_status = " DUPL_LONG" lfr = "_fr4" lfrm4 = "fr_4" longest_orf = longest_orf4 stop_count = stop_count4 any_count = any_count4 longest_fr = longest_fr4 total_size = total_size4 full_frame = full_frame4 frm_number = frm_number4 longest_len = llen4 gl_l_file10.write(">" + proper_id + lfr + dupl_status + \ " STOP:" + `stop_count` + " ANY(X):" + `any_count` + \ " LONGEST:" + `longest_fr` + " TOTAL_LENGTH:" + `total_size` + \ " " + full_frame + ":" + `frm_number` + '\n') gl_l_file10.write(longest_orf + '\n') ## 5 if llen5 >= llen1 and llen5 >= llen2 and llen5 >= llen3 and llen5 >= llen4 and llen5 >= llen6: if llen5 == llen1 or llen5 == llen2 or llen5 == llen3 or llen5 == llen4 or llen5 == llen6: dupl_status = " DUPL_LONG" lfr = "_fr5" lfrm5 = "fr_5" longest_orf = longest_orf5 stop_count = stop_count5 any_count = any_count5 longest_fr = longest_fr5 total_size = total_size5 full_frame = full_frame5 frm_number = frm_number5 longest_len = llen5 gl_l_file10.write(">" + proper_id + lfr + dupl_status + \ " STOP:" + `stop_count` + " ANY(X):" + `any_count` + \ " LONGEST:" + `longest_fr` + " TOTAL_LENGTH:" + `total_size` + \ " " + full_frame + ":" + `frm_number` + '\n') gl_l_file10.write(longest_orf + '\n') ## 6 if llen6 >= llen1 and llen6 >= llen2 and llen6 >= llen3 and llen6 >= llen4 and llen6 >= llen5: if llen6 == llen1 or llen6 == llen2 or llen6 == llen3 or llen6 == llen4 or llen6 == llen5: dupl_status = " DUPL_LONG" lfr = "_fr6" lfrm6 = "fr_6" longest_orf = longest_orf6 stop_count = stop_count6 any_count = any_count6 longest_fr = longest_fr6 total_size = total_size6 full_frame = full_frame6 frm_number = frm_number6 longest_len = llen6 gl_l_file10.write(">" + proper_id + lfr + dupl_status + \ " STOP:" + `stop_count` + " ANY(X):" + `any_count` + \ " LONGEST:" + `longest_fr` + " TOTAL_LENGTH:" + `total_size` + \ " " + full_frame + ":" + `frm_number` + '\n') gl_l_file10.write(longest_orf + '\n') ############################# gl_l1_file9.write(proper_id + '\t' + "fr_1" + '\t' + `stop_count1` + '\t' + `any_count1` + \ '\t' + `longest_fr1` + '\t' + `total_size1` + '\t' + `frm_number1` + '\n') gl_l2_file9.write(proper_id + '\t' + "fr_2" + '\t' + `stop_count2` + '\t' + `any_count2` + \ '\t' + `longest_fr2` + '\t' + `total_size2` + '\t' + `frm_number2` + '\n') gl_l3_file9.write(proper_id + '\t' + "fr_3" + '\t' + `stop_count3` + '\t' + `any_count3` + \ '\t' + `longest_fr3` + '\t' + `total_size3` + '\t' + `frm_number3` + '\n') gl_l4_file9.write(proper_id + '\t' + "fr_4" + '\t' + `stop_count4` + '\t' + `any_count4` + \ '\t' + `longest_fr4` + '\t' + `total_size4` + '\t' + `frm_number4` + '\n') gl_l5_file9.write(proper_id + '\t' + "fr_5" + '\t' + `stop_count5` + '\t' + `any_count5` + \ '\t' + `longest_fr5` + '\t' + `total_size5` + '\t' + `frm_number5` + '\n') gl_l6_file9.write(proper_id + '\t' + "fr_6" + '\t' + `stop_count6` + '\t' + `any_count6` + \ '\t' + `longest_fr6` + '\t' + `total_size6` + '\t' + `frm_number6` + '\n') ############################# if dupl_status == " UNIQ_LONG": dupl_wr = "UNIQ" if dupl_status == " DUPL_LONG": dupl_wr = "DUPL" lfrm_list = [lfrm1, lfrm2, lfrm3, lfrm4, lfrm5, lfrm6] for l_item in lfrm_list: if l_item != "": # lfrm = lfrm + " " + l_item + " " lfrm = lfrm + l_item + " " # lfrm = lfrm[1:] # lfrm = lfrm[:-1] gl_ls_file9.write(proper_id + '\t' + \ "fr_1" + '\t' + `stop_count1` + '\t' + `any_count1` + \ '\t' + `longest_fr1` + '\t' + `total_size1` + '\t' + `frm_number1` + '\t' + \ "fr_2" + '\t' + `stop_count2` + '\t' + `any_count2` + \ '\t' + `longest_fr2` + '\t' + `total_size2` + '\t' + `frm_number2` + '\t' + \ "fr_3" + '\t' + `stop_count3` + '\t' + `any_count3` + \ '\t' + `longest_fr3` + '\t' + `total_size3` + '\t' + `frm_number3` + '\t' + \ "fr_4" + '\t' + `stop_count4` + '\t' + `any_count4` + \ '\t' + `longest_fr4` + '\t' + `total_size4` + '\t' + `frm_number4` + '\t' + \ "fr_5" + '\t' + `stop_count5` + '\t' + `any_count5` + \ '\t' + `longest_fr5` + '\t' + `total_size5` + '\t' + `frm_number5` + '\t' + \ "fr_6" + '\t' + `stop_count6` + '\t' + `any_count6` + \ '\t' + `longest_fr6` + '\t' + `total_size6` + '\t' + `frm_number6` + '\t' + \ `longest_len` + '\t' + lfrm + '\t' + dupl_wr + '\n') ############################# dupl_frame1 = " ONE_ORF" dupl_frame2 = " ONE_ORF" dupl_frame3 = " ONE_ORF" dupl_frame4 = " ONE_ORF" dupl_frame5 = " ONE_ORF" dupl_frame6 = " ONE_ORF" ############# ## 1 if full_frame1 == "SINGLE_ORF": if full_frame1 == full_frame2: dupl_frame1 = " NOT_UNIQ" if full_frame1 == full_frame3: dupl_frame1 = " NOT_UNIQ" if full_frame1 == full_frame4: dupl_frame1 = " NOT_UNIQ" if full_frame1 == full_frame5: dupl_frame1 = " NOT_UNIQ" if full_frame1 == full_frame6: dupl_frame1 = " NOT_UNIQ" ### CHECK FOR POLY_A AND POLY_T ( ..FFFFF.. OR ..KKKKK.. ) ### count_fff1 = my_string1.count("F") count_kkk1 = my_string1.count("K") fract_fff1 = count_fff1*1.0/total_size1 fract_kkk1 = count_kkk1*1.0/total_size1 if fract_fff1 <= 0.70 and fract_kkk1 <= 0.70: gl_s_file10.write(">" + proper_id + "_fr1 " + `total_size1` + " STOP:" + `stop_count1` \ + " ANY(X):" + `any_count1` + dupl_frame1 + '\n' + my_string1 + '\n') if fract_fff1 > 0.70: fract_fff1 = str(round(fract_fff1,2)) gl_l0_file9.write(proper_id + '\t' + fract_fff1 + '\t' + "poly_FFF translation" + '\n') if fract_kkk1 > 0.70: fract_kkk1 = str(round(fract_kkk1,2)) gl_l0_file9.write(proper_id + '\t' + fract_kkk1 + '\t' + "poly_KKK translation" + '\n') ############# ## 2 if full_frame2 == "SINGLE_ORF": if full_frame2 == full_frame1: dupl_frame2 = " NOT_UNIQ" if full_frame2 == full_frame3: dupl_frame2 = " NOT_UNIQ" if full_frame2 == full_frame4: dupl_frame2 = " NOT_UNIQ" if full_frame2 == full_frame5: dupl_frame2 = " NOT_UNIQ" if full_frame2 == full_frame6: dupl_frame2 = " NOT_UNIQ" ### CHECK FOR POLY_A AND POLY_T ( ..FFFFF.. OR ..KKKKK.. ) ### count_fff2 = my_string2.count("F") count_kkk2 = my_string2.count("K") fract_fff2 = count_fff2*1.0/total_size2 fract_kkk2 = count_kkk2*1.0/total_size2 if fract_fff2 <= 0.70 and fract_kkk2 <= 0.70: gl_s_file10.write(">" + proper_id + "_fr2 " + `total_size2` + " STOP:" + `stop_count2` \ + " ANY(X):" + `any_count2` + dupl_frame2 + '\n' + my_string2 + '\n') if fract_fff2 > 0.70: fract_fff2 = str(round(fract_fff2,2)) gl_l0_file9.write(proper_id + '\t' + fract_fff2 + '\t' + "poly_FFF translation" + '\n') if fract_kkk2 > 0.70: fract_kkk2 = str(round(fract_kkk2,2)) gl_l0_file9.write(proper_id + '\t' + fract_kkk2 + '\t' + "poly_KKK translation" + '\n') ############# ## 3 if full_frame3 == "SINGLE_ORF": if full_frame3 == full_frame1: dupl_frame3 = " NOT_UNIQ" if full_frame3 == full_frame2: dupl_frame3 = " NOT_UNIQ" if full_frame3 == full_frame4: dupl_frame3 = " NOT_UNIQ" if full_frame3 == full_frame5: dupl_frame3 = " NOT_UNIQ" if full_frame3 == full_frame6: dupl_frame3 = " NOT_UNIQ" ### CHECK FOR POLY_A AND POLY_T ( ..FFFFF.. OR ..KKKKK.. ) ### count_fff3 = my_string3.count("F") count_kkk3 = my_string3.count("K") fract_fff3 = count_fff3*1.0/total_size3 fract_kkk3 = count_kkk3*1.0/total_size3 if fract_fff3 <= 0.70 and fract_kkk3 <= 0.70: gl_s_file10.write(">" + proper_id + "_fr3 " + `total_size3` + " STOP:" + `stop_count3` \ + " ANY(X):" + `any_count3` + dupl_frame3 + '\n' + my_string3 + '\n') if fract_fff3 > 0.70: fract_fff3 = str(round(fract_fff3,2)) gl_l0_file9.write(proper_id + '\t' + fract_fff3 + '\t' + "poly_FFF translation" + '\n') if fract_kkk3 > 0.70: fract_kkk3 = str(round(fract_kkk3,2)) gl_l0_file9.write(proper_id + '\t' + fract_kkk3 + '\t' + "poly_KKK translation" + '\n') ## 4 if full_frame4 == "SINGLE_ORF": if full_frame4 == full_frame1: dupl_frame4 = " NOT_UNIQ" if full_frame4 == full_frame2: dupl_frame4 = " NOT_UNIQ" if full_frame4 == full_frame3: dupl_frame4 = " NOT_UNIQ" if full_frame4 == full_frame5: dupl_frame4 = " NOT_UNIQ" if full_frame4 == full_frame6: dupl_frame4 = " NOT_UNIQ" ### CHECK FOR POLY_A AND POLY_T ( ..FFFFF.. OR ..KKKKK.. ) ### count_fff4 = my_string4.count("F") count_kkk4 = my_string4.count("K") fract_fff4 = count_fff4*1.0/total_size4 fract_kkk4 = count_kkk4*1.0/total_size4 if fract_fff4 <= 0.70 and fract_kkk4 <= 0.70: gl_s_file10.write(">" + proper_id + "_fr4 " + `total_size4` + " STOP:" + `stop_count4` \ + " ANY(X):" + `any_count4` + dupl_frame4 + '\n' + my_string4 + '\n') if fract_fff4 > 0.70: fract_fff4 = str(round(fract_fff4,2)) gl_l0_file9.write(proper_id + '\t' + fract_fff4 + '\t' + "poly_FFF translation" + '\n') if fract_kkk4 > 0.70: fract_kkk4 = str(round(fract_kkk4,2)) gl_l0_file9.write(proper_id + '\t' + fract_kkk4 + '\t' + "poly_KKK translation" + '\n') ## 5 if full_frame5 == "SINGLE_ORF": if full_frame5 == full_frame1: dupl_frame5 = " NOT_UNIQ" if full_frame5 == full_frame2: dupl_frame5 = " NOT_UNIQ" if full_frame5 == full_frame3: dupl_frame5 = " NOT_UNIQ" if full_frame5 == full_frame4: dupl_frame5 = " NOT_UNIQ" if full_frame5 == full_frame6: dupl_frame5 = " NOT_UNIQ" ### CHECK FOR POLY_A AND POLY_T ( ..FFFFF.. OR ..KKKKK.. ) ### count_fff5 = my_string5.count("F") count_kkk5 = my_string5.count("K") fract_fff5 = count_fff5*1.0/total_size5 fract_kkk5 = count_kkk5*1.0/total_size5 if fract_fff5 <= 0.70 and fract_kkk5 <= 0.70: gl_s_file10.write(">" + proper_id + "_fr5 " + `total_size5` + " STOP:" + `stop_count5` \ + " ANY(X):" + `any_count5` + dupl_frame5 + '\n' + my_string5 + '\n') if fract_fff5 > 0.70: fract_fff5 = str(round(fract_fff5,2)) gl_l0_file9.write(proper_id + '\t' + fract_fff5 + '\t' + "poly_FFF translation" + '\n') if fract_kkk5 > 0.70: fract_kkk5 = str(round(fract_kkk5,2)) gl_l0_file9.write(proper_id + '\t' + fract_kkk5 + '\t' + "poly_KKK translation" + '\n') ## 6 if full_frame6 == "SINGLE_ORF": if full_frame6 == full_frame1: dupl_frame6 = " NOT_UNIQ" if full_frame6 == full_frame2: dupl_frame6 = " NOT_UNIQ" if full_frame6 == full_frame3: dupl_frame6 = " NOT_UNIQ" if full_frame6 == full_frame4: dupl_frame6 = " NOT_UNIQ" if full_frame6 == full_frame5: dupl_frame6 = " NOT_UNIQ" ### CHECK FOR POLY_A AND POLY_T ( ..FFFFF.. OR ..KKKKK.. ) ### count_fff6 = my_string6.count("F") count_kkk6 = my_string6.count("K") fract_fff6 = count_fff6*1.0/total_size6 fract_kkk6 = count_kkk6*1.0/total_size6 if fract_fff6 <= 0.70 and fract_kkk6 <= 0.70: gl_s_file10.write(">" + proper_id + "_fr6 " + `total_size6` + " STOP:" + `stop_count6` \ + " ANY(X):" + `any_count6` + dupl_frame6 + '\n' + my_string6 + '\n') if fract_fff6 > 0.70: fract_fff6 = str(round(fract_fff6,2)) gl_l0_file9.write(proper_id + '\t' + fract_fff6 + '\t' + "poly_FFF translation" + '\n') if fract_kkk6 > 0.70: fract_kkk6 = str(round(fract_kkk6,2)) gl_l0_file9.write(proper_id + '\t' + fract_kkk6 + '\t' + "poly_KKK translation" + '\n') ############################# ### END OF TRANSLATION ### ########################################## def Seqs_Cleaner(in_name, out_name, seq_type, trans_fr, gen_code): global gl_tr_file1, gl_tr_file2, gl_tr_file3, \ gl_tr_file4, gl_tr_file5, gl_tr_file6, \ gl_fw_file7, gl_rc_file8, gl_l0_file9, \ gl_l1_file9, gl_l2_file9, gl_l3_file9, \ gl_l4_file9, gl_l5_file9, gl_l6_file9, \ gl_ls_file9, gl_s_file10, gl_l_file10, \ tab_out1, tab_out2, out_n2a_frw, out_n2a_rev print "" print in_name + ' ' + out_name print "" in_file = open(in_name, "rb") out_file = open(out_name + '.fasta', "wb") out_stat = open(out_name + '.stat', "wb") out_tab = open(out_name + '.tab', "wb") out_bin1 = open(out_name + '.01BIN', "wb") out_bin2 = open(out_name + '.02BIN', "wb") out_dna1 = open(out_name + '.01DNA', "wb") out_dna2 = open(out_name + '.02DNA', "wb") out_tab3 = open(out_name + '.01TAB', "wb") agct_list = ["A", "G", "C", "T"] binary_list = ["00", "01", "10", "11"] if seq_type == "DNA": ### ACTIVATION OF CODON USAGE TABLE ### if trans_fr != 0: if gen_code == 1: CodonTranslation1() if gen_code == 2: CodonTranslation2() if gen_code == 3: CodonTranslation3() ########################### ### N2A FILE out_n2a_frw = open(out_name + '.affy.n2a.forwrd.fasta', "wb") out_n2a_rev = open(out_name + '.affy.n2a.revcom.fasta', "wb") ########################### if trans_fr == 1: gl_tr_file1 = open(out_name + '.tr_frame1', "wb") gl_fw_file7 = open(out_name + '.forwrd', "wb") gl_rc_file8 = open(out_name + '.revcom', "wb") gl_l0_file9 = open(out_name + '.x0_log', "wb") gl_l1_file9 = open(out_name + '.x1_log', "wb") gl_s_file10 = open(out_name + '.tr_single_frame', "wb") gl_l_file10 = open(out_name + '.tr_longest_frame', "wb") tab_out1 = open(out_name + '.tab_frw', "wb") tab_out2 = open(out_name + '.tab_rev', "wb") # tab_out3 = open(out_name + '.01TAB', "wb") gl_l1_file9.write("SEQ_ID" + '\t' + "FRAME" + '\t' + "STOP" + '\t' + "ANY" + \ '\t' + "LONGEST" + '\t' + "TOTAL" + '\t' + "ORFs" + '\n') if trans_fr == 3: gl_tr_file1 = open(out_name + '.tr_frame1', "wb") gl_tr_file2 = open(out_name + '.tr_frame2', "wb") gl_tr_file3 = open(out_name + '.tr_frame3', "wb") gl_fw_file7 = open(out_name + '.forwrd', "wb") gl_rc_file8 = open(out_name + '.revcom', "wb") gl_l0_file9 = open(out_name + '.x0_log', "wb") gl_l1_file9 = open(out_name + '.x1_log', "wb") gl_l2_file9 = open(out_name + '.x2_log', "wb") gl_l3_file9 = open(out_name + '.x3_log', "wb") gl_ls_file9 = open(out_name + '.xx_log', "wb") gl_s_file10 = open(out_name + '.tr_single_frame', "wb") gl_l_file10 = open(out_name + '.tr_longest_frame', "wb") tab_out1 = open(out_name + '.tab_frw', "wb") tab_out2 = open(out_name + '.tab_rev', "wb") # tab_out3 = open(out_name + '.01TAB', "wb") gl_l1_file9.write("SEQ_ID" + '\t' + "FRAME" + '\t' + "STOP" + '\t' + "ANY" + \ '\t' + "LONGEST" + '\t' + "TOTAL" + '\t' + "ORFs" + '\n') gl_l2_file9.write("SEQ_ID" + '\t' + "FRAME" + '\t' + "STOP" + '\t' + "ANY" + \ '\t' + "LONGEST" + '\t' + "TOTAL" + '\t' + "ORFs" + '\n') gl_l3_file9.write("SEQ_ID" + '\t' + "FRAME" + '\t' + "STOP" + '\t' + "ANY" + \ '\t' + "LONGEST" + '\t' + "TOTAL" + '\t' + "ORFs" + '\n') gl_ls_file9.write("SEQ_ID" + '\t' + \ "FRAME1" + '\t' + "STOP1" + '\t' + "ANY1" + \ '\t' + "LONGEST1" + '\t' + "TOTAL1" + '\t' + "ORFs1" + '\t' + \ "FRAME2" + '\t' + "STOP2" + '\t' + "ANY2" + \ '\t' + "LONGEST2" + '\t' + "TOTAL2" + '\t' + "ORFs2" + '\t' + \ "FRAME3" + '\t' + "STOP3" + '\t' + "ANY3" + \ '\t' + "LONGEST3" + '\t' + "TOTAL3" + '\t' + "ORFs3" + '\t' + \ "LONGEST" + '\t' + "FRAME" + '\t' + "DUPL" + '\n') if trans_fr == 6: gl_tr_file1 = open(out_name + '.tr_frame1', "wb") gl_tr_file2 = open(out_name + '.tr_frame2', "wb") gl_tr_file3 = open(out_name + '.tr_frame3', "wb") gl_tr_file4 = open(out_name + '.tr_frame4', "wb") gl_tr_file5 = open(out_name + '.tr_frame5', "wb") gl_tr_file6 = open(out_name + '.tr_frame6', "wb") gl_fw_file7 = open(out_name + '.forwrd', "wb") gl_rc_file8 = open(out_name + '.revcom', "wb") gl_l0_file9 = open(out_name + '.x0_log', "wb") gl_l1_file9 = open(out_name + '.x1_log', "wb") gl_l2_file9 = open(out_name + '.x2_log', "wb") gl_l3_file9 = open(out_name + '.x3_log', "wb") gl_l4_file9 = open(out_name + '.x4_log', "wb") gl_l5_file9 = open(out_name + '.x5_log', "wb") gl_l6_file9 = open(out_name + '.x6_log', "wb") gl_ls_file9 = open(out_name + '.xx_log', "wb") gl_s_file10 = open(out_name + '.tr_single_frame', "wb") gl_l_file10 = open(out_name + '.tr_longest_frame', "wb") tab_out1 = open(out_name + '.tab_frw', "wb") tab_out2 = open(out_name + '.tab_rev', "wb") # tab_out3 = open(out_name + '.01TAB', "wb") gl_l1_file9.write("SEQ_ID" + '\t' + "FRAME" + '\t' + "STOP" + '\t' + "ANY" + \ '\t' + "LONGEST" + '\t' + "TOTAL" + '\t' + "ORFs" + '\n') gl_l2_file9.write("SEQ_ID" + '\t' + "FRAME" + '\t' + "STOP" + '\t' + "ANY" + \ '\t' + "LONGEST" + '\t' + "TOTAL" + '\t' + "ORFs" + '\n') gl_l3_file9.write("SEQ_ID" + '\t' + "FRAME" + '\t' + "STOP" + '\t' + "ANY" + \ '\t' + "LONGEST" + '\t' + "TOTAL" + '\t' + "ORFs" + '\n') gl_l4_file9.write("SEQ_ID" + '\t' + "FRAME" + '\t' + "STOP" + '\t' + "ANY" + \ '\t' + "LONGEST" + '\t' + "TOTAL" + '\t' + "ORFs" + '\n') gl_l5_file9.write("SEQ_ID" + '\t' + "FRAME" + '\t' + "STOP" + '\t' + "ANY" + \ '\t' + "LONGEST" + '\t' + "TOTAL" + '\t' + "ORFs" + '\n') gl_l6_file9.write("SEQ_ID" + '\t' + "FRAME" + '\t' + "STOP" + '\t' + "ANY" + \ '\t' + "LONGEST" + '\t' + "TOTAL" + '\t' + "ORFs" + '\n') gl_ls_file9.write("SEQ_ID" + '\t' + \ "FRAME1" + '\t' + "STOP1" + '\t' + "ANY1" + \ '\t' + "LONGEST1" + '\t' + "TOTAL1" + '\t' + "ORFs1" + '\t' + \ "FRAME2" + '\t' + "STOP2" + '\t' + "ANY2" + \ '\t' + "LONGEST2" + '\t' + "TOTAL2" + '\t' + "ORFs2" + '\t' + \ "FRAME3" + '\t' + "STOP3" + '\t' + "ANY3" + \ '\t' + "LONGEST3" + '\t' + "TOTAL3" + '\t' + "ORFs3" + '\t' + \ "FRAME4" + '\t' + "STOP4" + '\t' + "ANY4" + \ '\t' + "LONGEST4" + '\t' + "TOTAL4" + '\t' + "ORFs4" + '\t' + \ "FRAME5" + '\t' + "STOP5" + '\t' + "ANY5" + \ '\t' + "LONGEST5" + '\t' + "TOTAL5" + '\t' + "ORFs5" + '\t' + \ "FRAME6" + '\t' + "STOP6" + '\t' + "ANY6" + \ '\t' + "LONGEST6" + '\t' + "TOTAL6" + '\t' + "ORFs6" + '\t' + \ "LONGEST" + '\t' + "FRAME" + '\t' + "DUPL" + '\n') ########################### ### HEADER OF OUTPUT FILE ### out_stat.write("#SEQ_ID" + '\t' + "LENGTH" + '\t' + " A " + '\t' + " T " + '\t' + \ " G " + '\t' + " C " + '\t' + "AT" + '\t' + "GC" + '\t' \ + "ATGC" + '\t' + " N " + '\t' + " X " + '\n') if seq_type == "prot": trans_fr = 0 out_stat.write("#SEQ_ID" + '\t' + "LENGTH" + '\t' + \ " A " + '\t' + " B " + '\t' + \ " C " + '\t' + " D " + '\t' + \ " E " + '\t' + " F " + '\t' + \ " G " + '\t' + " H " + '\t' + \ " I " + '\t' + " J " + '\t' + \ " K " + '\t' + " L " + '\t' + \ " M " + '\t' + " N " + '\t' + \ " O " + '\t' + " P " + '\t' + \ " Q " + '\t' + " R " + '\t' + \ " S " + '\t' + " T " + '\t' + \ " U " + '\t' + " V " + '\t' + \ " W " + '\t' + " X " + '\t' + \ " Y " + '\t' + " Z " + '\t' + \ " * " + '\t' + "***" + '\t' + '\n') fasta_id_array = [] line_counter = 0 have_seqs = "" proper_id = "" my_seqs = [] tot_len = 0 a_tot = 0 b_tot = 0 c_tot = 0 d_tot = 0 e_tot = 0 f_tot = 0 g_tot = 0 h_tot = 0 i_tot = 0 j_tot = 0 k_tot = 0 l_tot = 0 m_tot = 0 n_tot = 0 o_tot = 0 p_tot = 0 q_tot = 0 r_tot = 0 s_tot = 0 t_tot = 0 u_tot = 0 v_tot = 0 w_tot = 0 x_tot = 0 y_tot = 0 z_tot = 0 stop_tot = 0 while 1: t = in_file.readline() if t == '': ### SUB_SEQ FUNCTION ### have_seqs = "".join(my_seqs) seqs_len = len(have_seqs) ### STRING PROCESSING ### if seqs_len != 0: have_seqs = "".join(my_seqs) seqs_len = len(have_seqs) tot_len = tot_len + seqs_len if seqs_len == 0: seqs_len = 1 ### STRING PROCESSING ### abc_up = have_seqs.upper() ### ### BINARY ### out_bin1.write(">" + proper_id + "_R REGULAR BINARY " + `seqs_len` + '\n') out_bin2.write(">" + proper_id + "_S SHIFTED BINARY " + `seqs_len` + '\n') out_tab3.write(proper_id + '\t') bin1_list = list(have_seqs) bin2_list = [] for bin1_item in bin1_list: if bin1_item in agct_list: if bin1_item == "A": out_bin1.write("00") out_tab3.write("00" + '\t') bin2_list.append("00") if bin1_item == "G": out_bin1.write("01") out_tab3.write("01" + '\t') bin2_list.append("01") if bin1_item == "C": out_bin1.write("10") out_tab3.write("10" + '\t') bin2_list.append("10") if bin1_item == "T": out_bin1.write("11") out_tab3.write("11" + '\t') bin2_list.append("11") else: out_bin1.write("--") out_tab3.write("--" + '\t') bin2_list.append("--") out_bin1.write('\n') out_tab3.write('\n') # bin2tr_list = bin2_list[1:-1] bin2_list = "".join(bin2_list) # bin2tr_list = "".join(bin2tr_list) bin2tr_list = bin2_list[1:-1] # print bin2_list # print bin2tr_list out_bin2.write(bin2tr_list + '\n') ### BIN END ### ### BIN AGAIN ### k1 = 0 k2 = 0 l1 = len(bin2_list) l2 = len(bin2tr_list) out_dna1.write(">" + proper_id + "_R REGULAR DNA " + `seqs_len` + '\n') while k1 < l1: m1 = k1 + 2 p1 = bin2_list[k1:m1] # binary duplet if p1 in binary_list: if p1 == "00": out_dna1.write("A") if p1 == "01": out_dna1.write("G") if p1 == "10": out_dna1.write("C") if p1 == "11": out_dna1.write("T") else: out_dna1.write("N") k1 = k1 + 2 out_dna1.write('\n') out_dna2.write(">" + proper_id + "_S SHIFTED DNA " + `seqs_len` + '\n') while k2 < l2: m2 = k2 + 2 p2 = bin2tr_list[k2:m2] # binary duplet if p2 in binary_list: if p2 == "00": out_dna2.write("A") if p2 == "01": out_dna2.write("G") if p2 == "10": out_dna2.write("C") if p2 == "11": out_dna2.write("T") else: out_dna2.write("N") k2 = k2 + 2 out_dna2.write('\n') ### ******* ### ### a_count = abc_up.count("A") a_tot = a_tot + a_count ### b_count = abc_up.count("B") b_tot = b_tot + b_count ### c_count = abc_up.count("C") c_tot = c_tot + c_count ### d_count = abc_up.count("D") d_tot = d_tot + d_count ### e_count = abc_up.count("E") e_tot = e_tot + e_count ### f_count = abc_up.count("F") f_tot = f_tot + f_count ### g_count = abc_up.count("G") g_tot = g_tot + g_count ### h_count = abc_up.count("H") h_tot = h_tot + h_count ### i_count = abc_up.count("I") i_tot = i_tot + i_count ### j_count = abc_up.count("J") j_tot = j_tot + j_count ### k_count = abc_up.count("K") k_tot = k_tot + k_count ### l_count = abc_up.count("L") l_tot = l_tot + l_count ### m_count = abc_up.count("M") m_tot = m_tot + m_count ### n_count = abc_up.count("N") n_tot = n_tot + n_count ### o_count = abc_up.count("O") o_tot = o_tot + o_count ### p_count = abc_up.count("P") p_tot = p_tot + p_count ### q_count = abc_up.count("Q") q_tot = q_tot + q_count ### r_count = abc_up.count("R") r_tot = r_tot + r_count ### s_count = abc_up.count("S") s_tot = s_tot + s_count ### t_count = abc_up.count("T") t_tot = t_tot + t_count ### u_count = abc_up.count("U") u_tot = u_tot + u_count ### v_count = abc_up.count("V") v_tot = v_tot + v_count ### w_count = abc_up.count("W") w_tot = w_tot + w_count ### x_count = abc_up.count("X") x_tot = x_tot + x_count ### y_count = abc_up.count("Y") y_tot = y_tot + y_count ### z_count = abc_up.count("Z") z_tot = z_tot + z_count ### stop_count = abc_up.count("*") stop_tot = stop_tot + stop_count ### a_fract = round((a_count*100.00/seqs_len),2) b_fract = round((b_count*100.00/seqs_len),2) c_fract = round((c_count*100.00/seqs_len),2) d_fract = round((d_count*100.00/seqs_len),2) e_fract = round((e_count*100.00/seqs_len),2) f_fract = round((f_count*100.00/seqs_len),2) g_fract = round((g_count*100.00/seqs_len),2) h_fract = round((h_count*100.00/seqs_len),2) i_fract = round((i_count*100.00/seqs_len),2) j_fract = round((j_count*100.00/seqs_len),2) k_fract = round((k_count*100.00/seqs_len),2) l_fract = round((l_count*100.00/seqs_len),2) m_fract = round((m_count*100.00/seqs_len),2) n_fract = round((n_count*100.00/seqs_len),2) o_fract = round((o_count*100.00/seqs_len),2) p_fract = round((p_count*100.00/seqs_len),2) q_fract = round((q_count*100.00/seqs_len),2) r_fract = round((r_count*100.00/seqs_len),2) s_fract = round((s_count*100.00/seqs_len),2) t_fract = round((t_count*100.00/seqs_len),2) u_fract = round((u_count*100.00/seqs_len),2) v_fract = round((v_count*100.00/seqs_len),2) w_fract = round((w_count*100.00/seqs_len),2) x_fract = round((x_count*100.00/seqs_len),2) y_fract = round((y_count*100.00/seqs_len),2) z_fract = round((z_count*100.00/seqs_len),2) stop_fract = round((stop_count*100.00/seqs_len),2) ### at_fract = a_fract + t_fract gc_fract = g_fract + c_fract atgc_fract = a_fract + t_fract + g_fract + c_fract # atgc_fract = round(atgc_fract) atgc_fract = round(atgc_fract,2) ### STRING ### a_fract = str(a_fract) b_fract = str(b_fract) c_fract = str(c_fract) d_fract = str(d_fract) e_fract = str(e_fract) f_fract = str(f_fract) g_fract = str(g_fract) h_fract = str(h_fract) i_fract = str(i_fract) j_fract = str(j_fract) k_fract = str(k_fract) l_fract = str(l_fract) m_fract = str(m_fract) n_fract = str(n_fract) o_fract = str(o_fract) p_fract = str(p_fract) q_fract = str(q_fract) r_fract = str(r_fract) s_fract = str(s_fract) t_fract = str(t_fract) u_fract = str(u_fract) v_fract = str(v_fract) w_fract = str(w_fract) x_fract = str(x_fract) y_fract = str(y_fract) z_fract = str(z_fract) stop_fract = str(stop_fract) at_fract = str(at_fract) gc_fract = str(gc_fract) atgc_fract = str(atgc_fract) ### TRANSLATION ### if trans_fr == 1 and seqs_len >= 12: # print "TRANSLATION: " + `trans_fr` + " FRAME -=- GENE CODE: " + `gen_code` Seqs_Translator(proper_id, have_seqs, trans_fr, gen_code) if trans_fr == 3 and seqs_len >= 12: # print "TRANSLATION: " + `trans_fr` + " FRAMES -=- GENE CODE: " + `gen_code` Seqs_Translator(proper_id, have_seqs, trans_fr, gen_code) if trans_fr == 6 and seqs_len >= 12: # print "TRANSLATION: " + `trans_fr` + " FRAMES -=- GENE CODE: " + `gen_code` Seqs_Translator(proper_id, have_seqs, trans_fr, gen_code) ### END OF TRANSLATION ### if seq_type == "DNA": out_stat.write(proper_id + '\t' + `seqs_len` + '\t' + a_fract + '\t' + t_fract + '\t' + \ g_fract + '\t' + c_fract + '\t' + at_fract + '\t' + gc_fract + '\t' \ + atgc_fract + '\t' + 'N: ' + n_fract + '\t' + 'X: ' + x_fract + '\n') if seq_type == "prot": out_stat.write(proper_id + '\t' + `seqs_len` + '\t' + \ a_fract + '\t' + b_fract + '\t' + \ c_fract + '\t' + d_fract + '\t' + \ e_fract + '\t' + f_fract + '\t' + \ g_fract + '\t' + h_fract + '\t' + \ i_fract + '\t' + j_fract + '\t' + \ k_fract + '\t' + l_fract + '\t' + \ m_fract + '\t' + n_fract + '\t' + \ o_fract + '\t' + p_fract + '\t' + \ q_fract + '\t' + r_fract + '\t' + \ s_fract + '\t' + t_fract + '\t' + \ u_fract + '\t' + v_fract + '\t' + \ w_fract + '\t' + x_fract + '\t' + \ y_fract + '\t' + z_fract + '\t' + \ stop_fract + '\t' + `stop_count` + '\n') ### STRING PROCESSING END ### # print seqs_len if have_seqs != "": out_file.write('>' + proper_id + ' ' + good_name + '\n') out_file.write(have_seqs + '\n') #### END OF SUB_SEQ #### out_tab.write(proper_id + '\t' + `seqs_len` + '\t' + have_seqs + '\n') ########################## break if '\n' in t: t = t[:-1] if '\r' in t: t = t[:-1] fasta_match = t[0:1] if fasta_match == ">": gi_test = t[0:4] if gi_test == ">gi|": # print gi_test descr_line = t ### REPLACE ALL TABS WITH WHITESPACES ### descr_line = re.sub('\t', " ", descr_line) ############################################# descr_line = re.sub("^>gi\|", "", descr_line) descr_line = re.sub("\|", '\t', descr_line, 1) # print line_counter line_counter += 1 else: descr_line = t ### REPLACE ALL TABS WITH WHITESPACES ### descr_line = re.sub('\t', " ", descr_line) ############################################# descr_line = re.sub("^>", "", descr_line) descr_line = re.sub("\|", " ", descr_line, 1) descr_line = re.sub(" ", '\t', descr_line, 1) # print line_counter line_counter = line_counter + 1 good_head = string.split(descr_line, '\t')[0] try: long_tail = string.split(descr_line, '\t')[1] except: long_tail = "" ############################### dupl_status = "GOOD" ############################### if good_head in fasta_id_array: dupl_status = "BAD" running_text = "\ \n\n Ooops... ID duplication \n\n check input for duplications \n\n\n ID: " + good_head + "\n\n\n" print running_text ### ### INSERT TKINTER TEXT MESSAGE BOX ### break fasta_id_array.append(good_head) print `line_counter` + '\t' + good_head if line_counter != 1: ### SUB_SEQ FUNCTION ### have_seqs = "".join(my_seqs) seqs_len = len(have_seqs) tot_len = tot_len + seqs_len if seqs_len == 0: seqs_len = 1 ### STRING PROCESSING ### abc_up = have_seqs.upper() ### ### BINARY ### # out_bin.write(proper_id + " " + `seqs_len` + '\n') # bin_list = list(have_seqs) # for bin_item in bin_list: # if bin_item in agct_list: # if bin_item == "A": # out_bin.write("00") # if bin_item == "G": # out_bin.write("01") # if bin_item == "C": # out_bin.write("10") # if bin_item == "T": # out_bin.write("11") # else: # out_bin.write("--") # out_bin.write('\n') out_bin1.write(">" + proper_id + "_R REGULAR BINARY " + `seqs_len` + '\n') out_bin2.write(">" + proper_id + "_S SHIFTED BINARY " + `seqs_len` + '\n') out_tab3.write(proper_id + '\t') bin1_list = list(have_seqs) bin2_list = [] for bin1_item in bin1_list: if bin1_item in agct_list: if bin1_item == "A": out_bin1.write("00") out_tab3.write("00" + '\t') bin2_list.append("00") if bin1_item == "G": out_bin1.write("01") out_tab3.write("01" + '\t') bin2_list.append("01") if bin1_item == "C": out_bin1.write("10") out_tab3.write("10" + '\t') bin2_list.append("10") if bin1_item == "T": out_bin1.write("11") out_tab3.write("11" + '\t') bin2_list.append("11") else: out_bin1.write("--") out_tab3.write("--" + '\t') bin2_list.append("--") out_bin1.write('\n') out_tab3.write('\n') # bin2tr_list = bin2_list[1:-1] bin2_list = "".join(bin2_list) # bin2tr_list = "".join(bin2tr_list) bin2tr_list = bin2_list[1:-1] # print bin2_list # print bin2tr_list out_bin2.write(bin2tr_list + '\n') ### BIN END ### ### BIN AGAIN ### k1 = 0 k2 = 0 l1 = len(bin2_list) l2 = len(bin2tr_list) out_dna1.write(">" + proper_id + "_R REGULAR DNA " + `seqs_len` + '\n') while k1 < l1: m1 = k1 + 2 p1 = bin2_list[k1:m1] # binary duplet if p1 in binary_list: if p1 == "00": out_dna1.write("A") if p1 == "01": out_dna1.write("G") if p1 == "10": out_dna1.write("C") if p1 == "11": out_dna1.write("T") else: out_dna1.write("N") k1 = k1 + 2 out_dna1.write('\n') out_dna2.write(">" + proper_id + "_S SHIFTED DNA " + `seqs_len` + '\n') while k2 < l2: m2 = k2 + 2 p2 = bin2tr_list[k2:m2] # binary duplet if p2 in binary_list: if p2 == "00": out_dna2.write("A") if p2 == "01": out_dna2.write("G") if p2 == "10": out_dna2.write("C") if p2 == "11": out_dna2.write("T") else: out_dna2.write("N") k2 = k2 + 2 out_dna2.write('\n') ### ******* ### ### a_count = abc_up.count("A") a_tot = a_tot + a_count ### b_count = abc_up.count("B") b_tot = b_tot + b_count ### c_count = abc_up.count("C") c_tot = c_tot + c_count ### d_count = abc_up.count("D") d_tot = d_tot + d_count ### e_count = abc_up.count("E") e_tot = e_tot + e_count ### f_count = abc_up.count("F") f_tot = f_tot + f_count ### g_count = abc_up.count("G") g_tot = g_tot + g_count ### h_count = abc_up.count("H") h_tot = h_tot + h_count ### i_count = abc_up.count("I") i_tot = i_tot + i_count ### j_count = abc_up.count("J") j_tot = j_tot + j_count ### k_count = abc_up.count("K") k_tot = k_tot + k_count ### l_count = abc_up.count("L") l_tot = l_tot + l_count ### m_count = abc_up.count("M") m_tot = m_tot + m_count ### n_count = abc_up.count("N") n_tot = n_tot + n_count ### o_count = abc_up.count("O") o_tot = o_tot + o_count ### p_count = abc_up.count("P") p_tot = p_tot + p_count ### q_count = abc_up.count("Q") q_tot = q_tot + q_count ### r_count = abc_up.count("R") r_tot = r_tot + r_count ### s_count = abc_up.count("S") s_tot = s_tot + s_count ### t_count = abc_up.count("T") t_tot = t_tot + t_count ### u_count = abc_up.count("U") u_tot = u_tot + u_count ### v_count = abc_up.count("V") v_tot = v_tot + v_count ### w_count = abc_up.count("W") w_tot = w_tot + w_count ### x_count = abc_up.count("X") x_tot = x_tot + x_count ### y_count = abc_up.count("Y") y_tot = y_tot + y_count ### z_count = abc_up.count("Z") z_tot = z_tot + z_count ### stop_count = abc_up.count("*") stop_tot = stop_tot + stop_count ### a_fract = round((a_count*100.00/seqs_len),2) b_fract = round((b_count*100.00/seqs_len),2) c_fract = round((c_count*100.00/seqs_len),2) d_fract = round((d_count*100.00/seqs_len),2) e_fract = round((e_count*100.00/seqs_len),2) f_fract = round((f_count*100.00/seqs_len),2) g_fract = round((g_count*100.00/seqs_len),2) h_fract = round((h_count*100.00/seqs_len),2) i_fract = round((i_count*100.00/seqs_len),2) j_fract = round((j_count*100.00/seqs_len),2) k_fract = round((k_count*100.00/seqs_len),2) l_fract = round((l_count*100.00/seqs_len),2) m_fract = round((m_count*100.00/seqs_len),2) n_fract = round((n_count*100.00/seqs_len),2) o_fract = round((o_count*100.00/seqs_len),2) p_fract = round((p_count*100.00/seqs_len),2) q_fract = round((q_count*100.00/seqs_len),2) r_fract = round((r_count*100.00/seqs_len),2) s_fract = round((s_count*100.00/seqs_len),2) t_fract = round((t_count*100.00/seqs_len),2) u_fract = round((u_count*100.00/seqs_len),2) v_fract = round((v_count*100.00/seqs_len),2) w_fract = round((w_count*100.00/seqs_len),2) x_fract = round((x_count*100.00/seqs_len),2) y_fract = round((y_count*100.00/seqs_len),2) z_fract = round((z_count*100.00/seqs_len),2) stop_fract = round((stop_count*100.00/seqs_len),2) ### at_fract = a_fract + t_fract gc_fract = g_fract + c_fract atgc_fract = a_fract + t_fract + g_fract + c_fract # atgc_fract = round(atgc_fract) atgc_fract = round(atgc_fract,2) ### STRING ### a_fract = str(a_fract) b_fract = str(b_fract) c_fract = str(c_fract) d_fract = str(d_fract) e_fract = str(e_fract) f_fract = str(f_fract) g_fract = str(g_fract) h_fract = str(h_fract) i_fract = str(i_fract) j_fract = str(j_fract) k_fract = str(k_fract) l_fract = str(l_fract) m_fract = str(m_fract) n_fract = str(n_fract) o_fract = str(o_fract) p_fract = str(p_fract) q_fract = str(q_fract) r_fract = str(r_fract) s_fract = str(s_fract) t_fract = str(t_fract) u_fract = str(u_fract) v_fract = str(v_fract) w_fract = str(w_fract) x_fract = str(x_fract) y_fract = str(y_fract) z_fract = str(z_fract) stop_fract = str(stop_fract) at_fract = str(at_fract) gc_fract = str(gc_fract) atgc_fract = str(atgc_fract) ### TRANSLATION ### if trans_fr == 1 and seqs_len >= 12: # print "TRANSLATION: " + `trans_fr` + " FRAME -=- GENE CODE: " + `gen_code` Seqs_Translator(proper_id, have_seqs, trans_fr, gen_code) if trans_fr == 3 and seqs_len >= 12: # print "TRANSLATION: " + `trans_fr` + " FRAMES -=- GENE CODE: " + `gen_code` Seqs_Translator(proper_id, have_seqs, trans_fr, gen_code) if trans_fr == 6 and seqs_len >= 12: # print "TRANSLATION: " + `trans_fr` + " FRAMES -=- GENE CODE: " + `gen_code` Seqs_Translator(proper_id, have_seqs, trans_fr, gen_code) ### END OF TRANSLATION ### if seq_type == "DNA": out_stat.write(proper_id + '\t' + `seqs_len` + '\t' + a_fract + '\t' + t_fract + '\t' + \ g_fract + '\t' + c_fract + '\t' + at_fract + '\t' + gc_fract + '\t' \ + atgc_fract + '\t' + 'N: ' + n_fract + '\t' + 'X: ' + x_fract + '\n') if seq_type == "prot": out_stat.write(proper_id + '\t' + `seqs_len` + '\t' + \ a_fract + '\t' + b_fract + '\t' + \ c_fract + '\t' + d_fract + '\t' + \ e_fract + '\t' + f_fract + '\t' + \ g_fract + '\t' + h_fract + '\t' + \ i_fract + '\t' + j_fract + '\t' + \ k_fract + '\t' + l_fract + '\t' + \ m_fract + '\t' + n_fract + '\t' + \ o_fract + '\t' + p_fract + '\t' + \ q_fract + '\t' + r_fract + '\t' + \ s_fract + '\t' + t_fract + '\t' + \ u_fract + '\t' + v_fract + '\t' + \ w_fract + '\t' + x_fract + '\t' + \ y_fract + '\t' + z_fract + '\t' + \ stop_fract + '\t' + `stop_count` + '\n') ### STRING PROCESSING END ### # print seqs_len if have_seqs != "": out_file.write('>' + proper_id + ' ' + good_name + '\n') out_file.write(have_seqs + '\n') #### END OF SUB_SEQ #### out_tab.write(proper_id + '\t' + `seqs_len` + '\t' + have_seqs + '\n') ########################## have_seqs = "" my_seqs = [] if fasta_match != ">" and fasta_match != "" and dupl_status == "GOOD": proper_id = good_head good_name = long_tail my_seqs.append(t) a_fract_tot = round((a_tot*100.00/tot_len),2) b_fract_tot = round((b_tot*100.00/tot_len),2) c_fract_tot = round((c_tot*100.00/tot_len),2) d_fract_tot = round((d_tot*100.00/tot_len),2) e_fract_tot = round((e_tot*100.00/tot_len),2) f_fract_tot = round((f_tot*100.00/tot_len),2) g_fract_tot = round((g_tot*100.00/tot_len),2) h_fract_tot = round((h_tot*100.00/tot_len),2) i_fract_tot = round((i_tot*100.00/tot_len),2) j_fract_tot = round((j_tot*100.00/tot_len),2) k_fract_tot = round((k_tot*100.00/tot_len),2) l_fract_tot = round((l_tot*100.00/tot_len),2) m_fract_tot = round((m_tot*100.00/tot_len),2) n_fract_tot = round((n_tot*100.00/tot_len),2) o_fract_tot = round((o_tot*100.00/tot_len),2) p_fract_tot = round((p_tot*100.00/tot_len),2) q_fract_tot = round((q_tot*100.00/tot_len),2) r_fract_tot = round((r_tot*100.00/tot_len),2) s_fract_tot = round((s_tot*100.00/tot_len),2) t_fract_tot = round((t_tot*100.00/tot_len),2) u_fract_tot = round((u_tot*100.00/tot_len),2) v_fract_tot = round((v_tot*100.00/tot_len),2) w_fract_tot = round((w_tot*100.00/tot_len),2) x_fract_tot = round((x_tot*100.00/tot_len),2) y_fract_tot = round((y_tot*100.00/tot_len),2) z_fract_tot = round((z_tot*100.00/tot_len),2) stop_fract_tot = round((stop_tot*100.00/tot_len),2) ### at_fract_tot = a_fract_tot + t_fract_tot gc_fract_tot = g_fract_tot + c_fract_tot atgc_fract_tot = a_fract_tot + t_fract_tot + g_fract_tot + c_fract_tot # atgc_fract_tot = round(atgc_fract_tot) atgc_fract_tot = round(atgc_fract_tot,2) ### STRING ### a_fract_tot = str(a_fract_tot) b_fract_tot = str(b_fract_tot) c_fract_tot = str(c_fract_tot) d_fract_tot = str(d_fract_tot) e_fract_tot = str(e_fract_tot) f_fract_tot = str(f_fract_tot) g_fract_tot = str(g_fract_tot) h_fract_tot = str(h_fract_tot) i_fract_tot = str(i_fract_tot) j_fract_tot = str(j_fract_tot) k_fract_tot = str(k_fract_tot) l_fract_tot = str(l_fract_tot) m_fract_tot = str(m_fract_tot) n_fract_tot = str(n_fract_tot) o_fract_tot = str(o_fract_tot) p_fract_tot = str(p_fract_tot) q_fract_tot = str(q_fract_tot) r_fract_tot = str(r_fract_tot) s_fract_tot = str(s_fract_tot) t_fract_tot = str(t_fract_tot) u_fract_tot = str(u_fract_tot) v_fract_tot = str(v_fract_tot) w_fract_tot = str(w_fract_tot) x_fract_tot = str(x_fract_tot) y_fract_tot = str(y_fract_tot) z_fract_tot = str(z_fract_tot) stop_fract_tot = str(stop_fract_tot) at_fract_tot = str(at_fract_tot) gc_fract_tot = str(gc_fract_tot) atgc_fract_tot = str(atgc_fract_tot) ### if seq_type == "DNA": out_stat.write("#TOTAL" + '\t' + `tot_len` + '\t' + a_fract_tot + '\t' + t_fract_tot + '\t' + \ g_fract_tot + '\t' + c_fract_tot + '\t' + at_fract_tot + '\t' + gc_fract_tot + '\t' \ + atgc_fract_tot + '\t' + 'N: ' + n_fract_tot + '\t' + 'X: ' + x_fract_tot + '\n') if seq_type == "prot": out_stat.write("#TOTAL" + '\t' + `tot_len` + '\t' + \ a_fract_tot + '\t' + b_fract_tot + '\t' + \ c_fract_tot + '\t' + d_fract_tot + '\t' + \ e_fract_tot + '\t' + f_fract_tot + '\t' + \ g_fract_tot + '\t' + h_fract_tot + '\t' + \ i_fract_tot + '\t' + j_fract_tot + '\t' + \ k_fract_tot + '\t' + l_fract_tot + '\t' + \ m_fract_tot + '\t' + n_fract_tot + '\t' + \ o_fract_tot + '\t' + p_fract_tot + '\t' + \ q_fract_tot + '\t' + r_fract_tot + '\t' + \ s_fract_tot + '\t' + t_fract_tot + '\t' + \ u_fract_tot + '\t' + v_fract_tot + '\t' + \ w_fract_tot + '\t' + x_fract_tot + '\t' + \ y_fract_tot + '\t' + z_fract_tot + '\t' + \ stop_fract_tot + '\t' + `stop_tot` + '\n') in_file.close() out_file.close() out_stat.close() out_tab.close() out_bin1.close() out_bin2.close() out_dna1.close() out_dna2.close() out_tab3.close() if trans_fr == 1: gl_tr_file1.close() gl_fw_file7.close() gl_rc_file8.close() gl_l0_file9.close() gl_l1_file9.close() gl_s_file10.close() gl_l_file10.close() tab_out1.close() tab_out2.close() out_n2a_frw.close() out_n2a_rev.close() if trans_fr == 3: gl_tr_file1.close() gl_tr_file2.close() gl_tr_file3.close() gl_fw_file7.close() gl_rc_file8.close() gl_l0_file9.close() gl_l1_file9.close() gl_l2_file9.close() gl_l3_file9.close() gl_ls_file9.close() gl_s_file10.close() gl_l_file10.close() tab_out1.close() tab_out2.close() out_n2a_frw.close() out_n2a_rev.close() if trans_fr == 6: gl_tr_file1.close() gl_tr_file2.close() gl_tr_file3.close() gl_tr_file4.close() gl_tr_file5.close() gl_tr_file6.close() gl_fw_file7.close() gl_rc_file8.close() gl_l0_file9.close() gl_l1_file9.close() gl_l2_file9.close() gl_l3_file9.close() gl_l4_file9.close() gl_l5_file9.close() gl_l6_file9.close() gl_ls_file9.close() gl_s_file10.close() gl_l_file10.close() tab_out1.close() tab_out2.close() out_n2a_frw.close() out_n2a_rev.close() print "" print " PROCESSING DONE " print "" ####### MAIN BODY ############## import math import re import sys import string import time if __name__ == "__main__": if len(sys.argv) == 2 and sys.argv[1] == "help": HelpTranslation() sys.exit() if len(sys.argv) <= 5 or len(sys.argv) > 6: print "" print " Program usage: " print " input_file output_file DNA/prot trans_frame[0 1 3 6] genetic_code[1 2 3]" print " Script counts \"ATGC\" content in FASTA file" print " and translate DNA sequence into protein" print " 0 - no translation; 1 - first frame" print " 3 - three frames; 6 - all six frame" print " Genetic Code: 1 - Standard; 2 - Vertebrate Mitochondrial; 3 - Yeast Mitochondrial" print "" print " use argument \"help\" - for help" print "" sys.exit() if len(sys.argv) == 6: in_name = sys.argv[1] out_name = sys.argv[2] seq_type = sys.argv[3] trans_fr = sys.argv[4] gen_code = sys.argv[5] trans_fr = int(trans_fr) gen_code = int(gen_code) if trans_fr != 0 and trans_fr != 1 and trans_fr != 3 and trans_fr != 6: print " TRANSLATION FRAME MUST BE 0 1 3 or 6" sys.exit() if gen_code != 1 and gen_code != 2 and gen_code != 3: print " GENE CODE MUST BE 1 2 or 3" sys.exit() if in_name != out_name: Seqs_Cleaner(in_name, out_name, seq_type, trans_fr, gen_code) else: print "Output should have different name than Input" sys.exit() ######### THE END ############