Mercurial > repos > dfornika > micall_lite

annotate amino2consensus.py @ 29:4ff24c044fed draft default tip

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
author dfornika
date Thu, 27 Feb 2020 22:31:32 +0000
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4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
dfornika
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1 #!/usr/bin/env python
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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3 from __future__ import print_function
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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dfornika
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5 import argparse
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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6 import csv
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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8
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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9 AMINO_ACIDS = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y', '*']
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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12 def determine_amino(amino_counts, threshold):
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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13 amino = ""
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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14 total_count = sum(amino_counts.values())
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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15 amino_with_max_counts = sorted(amino_counts, key=amino_counts.get, reverse=True)[0]
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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16 if total_count == 0:
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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17 amino = "#"
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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18 elif (amino_counts[amino_with_max_counts] / float(total_count)) > threshold:
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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19 amino = amino_with_max_counts
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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20 else:
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21 amino = "@"
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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22 return amino
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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25 def determine_first_region(amino_file):
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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26 with open(amino_file) as f:
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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27 reader = csv.DictReader(f)
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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28 row = next(reader)
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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29 region = row['region']
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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30 return region
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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33 def main(args):
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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34 current_region = determine_first_region(args.amino)
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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35 seq = []
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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36 with open(args.amino) as f:
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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37 reader = csv.DictReader(f)
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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38 for row in reader:
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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39 if row['region'] == current_region:
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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40 amino_counts = {}
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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41 for amino_acid in AMINO_ACIDS:
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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42 amino_counts[amino_acid] = int(row[amino_acid])
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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43 amino = determine_amino(amino_counts, args.threshold)
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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44 seq.append(amino)
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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45 else:
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46 print(">" + current_region)
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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47 print(''.join(seq))
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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48 current_region = row['region']
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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49 seq = []
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50 amino_counts = {}
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51 for amino_acid in AMINO_ACIDS:
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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52 amino_counts[amino_acid] = int(row[amino_acid])
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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53 amino = determine_amino(amino_counts, args.threshold)
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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54 seq.append(amino)
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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55 print(">" + current_region)
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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56 print(''.join(seq))
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57
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58
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59 if __name__ == '__main__':
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60 parser = argparse.ArgumentParser()
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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61 parser.add_argument("amino", help="MiCall amino.csv output file")
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62 parser.add_argument("--threshold", default=0.15, type=float, help="Threshold for calling")
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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63 args = parser.parse_args()
4ff24c044fed "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9d563c366233a5de79429ac1fa8f994f5d8f785d-dirty"
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64 main(args)