Mercurial > repos > brinkmanlab > make_unique_id

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 669399887aebfe546eae29022f446664d9b52d44"
author brinkmanlab
date Sat, 05 Sep 2020 04:20:01 +0000 (2020-09-05)
parents f2656e644641
children
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a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
brinkmanlab
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1 #!/usr/bin/env python
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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2 import sys
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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3 from Bio import SeqIO
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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4 from collections import defaultdict
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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5
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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6 usage = """
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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7 make_unique_id
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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8 Makes all record ids unique across all input data.
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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9 All input data must be the same format.
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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11 Use: make_unique_id.py [-v] <format> <input1> <output1> [<input2> <output2> ... <inputn> <outputn>]
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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12 \t-v Print version and exit
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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14 Valid formats: clustal, embl, fasta, fasta-2line, fastq-sanger, fastq, fastq-solexa, fastq-illumina, genbank, gb, imgt,
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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15 nexus, phd, phylip, pir, seqxml, sff, stockholm, tab, qual
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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16 """
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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18 if __name__ == '__main__':
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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19 if '-v' in sys.argv:
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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20 print('1.0')
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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21 exit(0)
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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23 if len(sys.argv) < 4:
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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24 print("Missing arguments", file=sys.stderr)
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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25 print(usage, file=sys.stderr)
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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26 exit(1)
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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28 format = sys.argv[1]
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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29 ids = defaultdict(int)
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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31 def makeUnique(seq):
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f2656e644641 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit e3bef6bd24b0d0bf5645a5d1083c1fa886c19e4a"
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32 count = ids[seq.id]
f2656e644641 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit e3bef6bd24b0d0bf5645a5d1083c1fa886c19e4a"
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33 ids[seq.id] += 1
0
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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34 if count:
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f2656e644641 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit e3bef6bd24b0d0bf5645a5d1083c1fa886c19e4a"
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35 oldid = seq.id
0
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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36 suffix = "_" + str(count)
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f2656e644641 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit e3bef6bd24b0d0bf5645a5d1083c1fa886c19e4a"
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37 seq.id += suffix
0
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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38 seq.name += suffix
4
f2656e644641 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit e3bef6bd24b0d0bf5645a5d1083c1fa886c19e4a"
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39 print(f"{oldid}\t{seq.id}")
0
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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41 return seq
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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3
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0
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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44 paths = iter(sys.argv[2:])
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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46 for input, output in zip(paths, paths):
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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47 SeqIO.write(
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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48 map(makeUnique, SeqIO.parse(input, format)),
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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49 output,
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50 format
a3a09dd8d09a "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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51 )
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3
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