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16 lines
667 B
Python
16 lines
667 B
Python
import os, sys
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from Bio import SeqIO
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score_by_seq = { line.split('\t')[0] : float(line.split('\t')[1]) for line in open('ScoreBySeq.tsv') }
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remove3 = [seq for seq in score_by_seq if score_by_seq[seq] < 0.3]
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remove5 = [seq for seq in score_by_seq if score_by_seq[seq] < 0.5]
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remove7 = [seq for seq in score_by_seq if score_by_seq[seq] < 0.7]
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for clade in os.listdir('GuidanceOutput'):
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if('OG5_' in clade):
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with open('SeqFiltered_ToAlign/Preguidance_0.7/' + clade[:12] + '.fasta', 'w') as o:
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for rec in SeqIO.parse('GuidanceOutput/' + clade + '/Seqs.Orig.fas', 'fasta'):
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if(rec.id not in remove7):
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o.write('>' + rec.id + '\n' + str(rec.seq) + '\n\n') |