$ python Python_CAP3_ContigExtractor_Feb_27_2004.py
What type of output do you want? (1/2): 2
Enter the SOURCE file name: tomato_ABC.cap3.out
Enter the DESTINATION directory with alignments: tomato_alignments
Default contig file extension is ali
Enter the contig file extension :aln
Default contig file name prefix is Contig
Enter the contig file name prefix:L_ABC_Contig

Upon execution, a new directory "tomato_alignments" will be created and files with ".aln" extention will be generated for every contig in the assembly. The example of an "Alignment File" fragment is shown below:


[text in red and dot actually are not displayed in the "Alignment File". We need some extra steps to find polymorphic sites]