Mercurial > repos > iuc > ivar_removereads

annotate prepare_amplicon_info.py @ 6:61507c9d063e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
author iuc
date Thu, 10 Jun 2021 22:05:18 +0000
parents 75c279fa403a
children ee29337f905c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
diff changeset
1 #!/usr/bin/env python
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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2
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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3 # extends ivar trim's amplicon info parsing abilities
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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4 # to include calculation of amplicon regions from
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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5 # sets of nested (more than two) primers
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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6
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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7 import sys
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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8
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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9
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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10 # parse primers and their start positions from BED file
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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11 primer_starts = {}
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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12 with open(sys.argv[1]) as i:
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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13 for line in i:
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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14 f = line.strip().split('\t')
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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15 try:
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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16 if f[5] == '+':
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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17 primer_starts[f[3]] = int(f[1])
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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18 elif f[5] == '-':
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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19 primer_starts[f[3]] = int(f[2]) - 1
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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20 else:
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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21 raise ValueError()
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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22 except (IndexError, ValueError):
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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23 sys.exit(
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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24 'Primer BED file needs to be TAB-separated with the '
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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25 'following columns: '
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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26 'chrom, chromStart, chromEnd, name, score, strand, '
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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27 'where "chromStart", "chromEnd" need to be integer values '
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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28 'and "strand" needs to be either "+" or "-".'
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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29 )
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
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30
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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31 # parse amplicon info and record outer primer names
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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32 with open(sys.argv[2]) as i:
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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33 ret_lines = []
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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34 for line in i:
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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35 first = last = None
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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36 for pname in line.strip().split('\t'):
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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37 try:
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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38 primer_start = primer_starts[pname]
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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39 except KeyError:
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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40 sys.exit(
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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41 'Amplicon info with primer name not found in '
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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42 f'primer BED file: "{pname}"'
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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43 )
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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44 if first is None or primer_start < primer_starts[first]:
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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45 first = pname
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
parents:
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46 if last is None or primer_start > primer_starts[last]:
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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47 last = pname
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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48 if first == last:
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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49 sys.exit(
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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50 line
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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51 + 'is not a proper amplicon info line.'
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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52 )
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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53 ret_lines.append(f'{first}\t{last}\n')
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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54
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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55 # write amended amplicon info
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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56 with open(sys.argv[3], 'w') as o:
75c279fa403a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a5ff06c631a2a5a0d5d44edd6cb58a599d50918b"
iuc
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57 o.writelines(ret_lines)