Mercurial > repos > brinkmanlab > make_unique_id
annotate make_unique_id.py @ 3:a2258ce2d58c draft
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 08b7b36e1eba516e4d7eb97086baf7ec8d177c5d"
author | brinkmanlab |
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date | Mon, 15 Jun 2020 19:32:32 -0400 |
parents | c8bda09480ae |
children | f2656e644641 |
rev | line source |
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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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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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10 |
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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13 |
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"
brinkmanlab
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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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17 |
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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22 |
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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27 |
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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30 |
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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a2258ce2d58c
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 08b7b36e1eba516e4d7eb97086baf7ec8d177c5d"
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32 seqlenlen = len(str(len(seq))) |
a2258ce2d58c
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 08b7b36e1eba516e4d7eb97086baf7ec8d177c5d"
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33 newid = seq.id[:26 - seqlenlen] # Genbank has a max length for the id and sequence length number, truncate the sequence id if too long |
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061c3402a977
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit b661895b5e2dff7235eb32476602c3b93411a42e"
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34 count = ids[newid] |
061c3402a977
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit b661895b5e2dff7235eb32476602c3b93411a42e"
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35 ids[newid] += 1 |
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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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36 if count: |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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37 suffix = "_" + str(count) |
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a2258ce2d58c
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 08b7b36e1eba516e4d7eb97086baf7ec8d177c5d"
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38 if len(newid) + len(suffix) + 1 + seqlenlen > 26: |
a2258ce2d58c
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 08b7b36e1eba516e4d7eb97086baf7ec8d177c5d"
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39 newid = newid[:25 - seqlenlen - len(suffix)] |
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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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40 |
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061c3402a977
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit b661895b5e2dff7235eb32476602c3b93411a42e"
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41 newid += suffix |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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42 seq.name += suffix |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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43 |
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061c3402a977
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit b661895b5e2dff7235eb32476602c3b93411a42e"
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44 if seq.id != newid: |
061c3402a977
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit b661895b5e2dff7235eb32476602c3b93411a42e"
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45 print(f"{seq.id}\t{newid}") |
061c3402a977
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit b661895b5e2dff7235eb32476602c3b93411a42e"
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46 |
061c3402a977
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit b661895b5e2dff7235eb32476602c3b93411a42e"
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47 seq.id = newid |
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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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48 return seq |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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49 |
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a2258ce2d58c
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 08b7b36e1eba516e4d7eb97086baf7ec8d177c5d"
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50 |
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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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51 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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52 |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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53 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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54 SeqIO.write( |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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55 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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56 output, |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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57 format |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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58 ) |
a3a09dd8d09a
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e"
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59 |
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a2258ce2d58c
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/make_unique_id commit 08b7b36e1eba516e4d7eb97086baf7ec8d177c5d"
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60 |