Mercurial > repos > dfornika > micall_lite

annotate amino2consensus.py @ 18:43a987c03ec5 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit 822e7e1c2de31a72c2a13bcc15b9df06b699561f-dirty
author dfornika
date Wed, 25 Sep 2019 18:28:54 -0400
parents 61667ff2c8b5
children 8e6d3de9c7fa
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1 #!/usr/bin/env python
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3 from __future__ import print_function
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5 import csv
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6 import argparse
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8 AMINO_ACIDS = ['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y','*']
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10 def determine_amino(amino_counts, threshold):
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11 amino = ""
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12 total_count = sum(amino_counts.values())
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13 amino_with_max_counts = sorted(amino_counts, key=amino_counts.get, reverse=True)[0]
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14 if total_count == 0:
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15 amino = "#"
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16 elif (amino_counts[amino_with_max_counts] / total_count) > threshold:
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17 amino = amino_with_max_counts
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18 else:
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19 amino = "@"
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20 return amino
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22 def determine_first_region(amino_file):
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23 with open(amino_file) as f:
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24 reader = csv.DictReader(f)
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25 row = next(reader)
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26 region = row['region']
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27 return region
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29 def main(args):
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30 current_region = determine_first_region(args.amino)
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31 seq = []
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32 with open(args.amino, newline='') as f:
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33 reader = csv.DictReader(f)
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34 for row in reader:
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35 if row['region'] == current_region:
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36 amino_counts = {}
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37 for amino_acid in AMINO_ACIDS:
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38 amino_counts[amino_acid] = int(row[amino_acid])
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39 amino = determine_amino(amino_counts, args.threshold)
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40 seq.append(amino)
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41 else:
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42 print(">" + current_region)
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43 print(''.join(seq))
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44 current_region = row['region']
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45 seq = []
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46 amino_counts = {}
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47 for amino_acid in AMINO_ACIDS:
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48 amino_counts[amino_acid] = int(row[amino_acid])
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49 amino = determine_amino(amino_counts, args.threshold)
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50 seq.append(amino)
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51 print(">" + current_region)
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52 print(''.join(seq))
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53
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54
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55 if __name__ == '__main__':
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56 parser = argparse.ArgumentParser()
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57 parser.add_argument("amino", help="MiCall amino.csv output file")
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58 parser.add_argument("--threshold", default=0.15, help="Threshold for calling")
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59 args = parser.parse_args()
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60 main(args)