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Fixing line splitting bug in GuidanceWrapper_v2.1.py

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Auden Cote-L'Heureux 2023-08-14 15:01:54 -04:00 committed by GitHub
parent 943bc3461d
commit 366e91256b
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1 changed files with 15 additions and 3 deletions
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18
Utilities/for_fastas/GuidanceWrapper_v2.1.py
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@ -85,8 +85,12 @@ for file in os.listdir(args.input):
#If it ran successfully
if os.path.isfile(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names'):
sep = ' '
if '\t' in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names').readlines()[1]:
sep = '\t'
#Create a record of sequences below the sequence score cutoff
seqs_below = len([line for line in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names').readlines()[1:-1] if float(line.split()[-1]) < args.seq_cutoff])
seqs_below = len([line for line in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names').readlines()[1:-1] if float(line.split(sep)[-1]) < args.seq_cutoff])
#If the number of remaining sequences is less than 4, then stop iterating
if n_recs - seqs_below < 4:
@ -126,13 +130,21 @@ for file in os.listdir(args.input):
#Read in the MAFFT alignment
running_aln = { rec.description : str(rec.seq) for rec in SeqIO.parse(tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_MAFFT_realigned.fasta', 'fasta') }
sep = ' '
if '\t' in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr').readlines()[1]:
sep = '\t'
#Apply residue cutoff per site per sequence
for site in [(int(line.split()[1]), int(line.split()[0]) - 1) for line in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr').readlines()[1:-1] if float(line.split(' ')[-1].strip()) < args.res_cutoff]:
for site in [(int(line.split(sep)[1]), int(line.split(sep)[0]) - 1) for line in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr').readlines()[1:-1] if float(line.split(sep)[-1].strip()) < args.res_cutoff]:
if(orig_seqs[site[0]] in seqs2keep):
running_aln[orig_seqs[site[0]]][site[1]] = 'X'
sep = ' '
if '\t' in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_col.scr').readlines()[1]:
sep = '\t'
#Apply column cutoff per column
cols2remove = [int(line.split()[0]) - 1 for line in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_col.scr').readlines()[1:-1] if float(line.split(' ')[-1].strip()) < args.col_cutoff]
cols2remove = [int(line.split(sep)[0]) - 1 for line in open(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_col.scr').readlines()[1:-1] if float(line.split(sep)[-1].strip()) < args.col_cutoff]
for seq in running_aln:
running_aln[seq] = ''.join([running_aln[seq][i] for i in range(len(running_aln[seq])) if i not in cols2remove])