gap_sequences

Gap the sequences in a FASTA file, using the closest sequence in a gapped reference set as template.

The tool will only use as a template those sequences in the reference set that are complete at the 5’ end and extend at least to the second cysteine. Any others will not be used as a template, and neither will any that are apparently non-functional. Warnings will be given of any sequences with these issues. In most circumstances (that is, if they are only a small fraction of the total sequences in the reference set), these warnings can be ignored.

Gap the sequences in a FASTA file, using the closest sequence in a gapped reference set as template

usage: gap_sequences [-h] inferred_file ref_file out_file

Positional Arguments

inferred_file

ungapped inferred sequences (fasta)

ref_file

gapped reference set (fasta)

out_file

output file containing gapped inferred sequences