Mercurial > repos > stephenshank > abayesqr

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planemo upload commit 4a2876135fca2f46ffa6451e463eb167a0b51b65
author stephenshank
date Thu, 21 Mar 2019 12:47:00 -0400
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1 import os
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3 from Bio.Seq import Seq
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4 from Bio.SeqRecord import SeqRecord
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5 from Bio import SeqIO
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8 def parse_abayesqr_output(input_text, output_fasta):
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9 wd = os.path.join(os.getcwd())
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10 with open(os.path.join(wd, input_text)) as input_file:
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11 lines = input_file.readlines()
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12 records = []
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13 for i, line in enumerate(lines):
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14 if i % 2 == 0:
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15 freq = float(line.split()[-1])
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16 number = int(i/2)+1
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17 header = 'haplotype-%d_freq-%f' % (number, freq)
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18 else:
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19 seq = Seq(line.strip())
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20 record = SeqRecord(seq, id=header, description='')
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21 records.append(record)
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22 SeqIO.write(records, os.path.join(wd, output_fasta), 'fasta')
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25 if __name__ == '__main__':
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26 parse_abayesqr_output("test_ViralSeq.txt", "haplotypes.fasta")
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