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Update and rename faralog.py to gappiness.py

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Auden Cote-L'Heureux 2023-12-19 13:28:40 -05:00 committed by GitHub
parent 25b41672b3
commit c655354a42
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Utilities/for_MSAs/faralog.py → Utilities/for_MSAs/gappiness.py
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@ -38,7 +38,7 @@ def faralog_gaps():
split = [] split = []
#reading the fasta files with Biopython (looping each sequence in a file and populating the empty name and seq lists). #reading the fasta files with Biopython (looping each sequence in a file and populating the empty name and seq lists).
for x in SeqIO.parse(args.alignment + '/' + file, "fasta"): for x in SeqIO.parse(args.alignment + '/' + file, "fasta"):
if x.id.startswith(args.code): if (args.code != None and x.id.startswith(args.code)) or args.code == None:
name.append(x.id) name.append(x.id)
seq.append(x.seq) seq.append(x.seq)
seq_len.append(len(x.seq)) seq_len.append(len(x.seq))