Mercurial > repos > bgruening > glimmer_not_knowledge_based
annotate glimmer_gbk_to_orf.py @ 2:73c58e2debd0 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 274d1f6804bfd0362fdcd2383bfdb32ca8fd634e"
author | iuc |
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date | Sun, 20 Mar 2022 10:08:30 +0000 |
parents | 4da5f6bdcf12 |
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4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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1 #!/usr/bin/env python |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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2 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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3 ################################################################### |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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4 # |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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5 # gbk2orf.py by Errol Strain (estrain@gmail.com) |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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6 # |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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7 # Read a GenBank file and export fasta formatted amino acid and |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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8 # CDS files |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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9 # |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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10 ################################################################### |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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11 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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12 import sys |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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13 from optparse import OptionParser |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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14 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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15 from Bio import SeqIO |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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16 from Bio.Seq import Seq |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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17 from Bio.SeqRecord import SeqRecord |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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18 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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19 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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20 # Command line usage |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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21 usage = "usage: %prog -g input.gbk -a aa.fasta -n nuc.fasta" |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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22 p = OptionParser(usage) |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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23 p.add_option("-t", "--translate", dest="transtabl", type="int", default=11, |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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24 help="Translation table used to translate coding regions (default=11)") |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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25 p.add_option("-g", "--genbank", dest="gb_file", help="GenBank input file") |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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26 p.add_option("-a", "--amino_acid", dest="aa_file", help="Fasta amino acid output") |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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27 p.add_option("-n", "--nucleotide", dest="orf_file", help="Fasta nucleotide output") |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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28 (opts, args) = p.parse_args() |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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29 # Do I need this next line? |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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30 if not opts and not args: |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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31 p.error("Use --help to see usage") |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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32 if len(sys.argv) == 1: |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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33 p.error("Use --help to see usage") |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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34 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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35 # Lists to hold SeqRecords |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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36 aalist = [] |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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37 nuclist = [] |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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38 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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39 # If the CDS does not have a locus tag the name will be assigned using the |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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40 # order in which it was found |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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41 feat_count = 0 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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42 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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43 # Iterate through genbank records in input file |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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44 for gb_record in SeqIO.parse(open(opts.gb_file, "r"), "genbank"): |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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45 for (index, feature) in enumerate(gb_record.features): |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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46 if feature.type == "CDS": |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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47 feat_count = feat_count + 1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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48 gene = feature.extract(gb_record.seq) |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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49 if "locus_tag" in feature.qualifiers: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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50 value = feature.qualifiers["locus_tag"][0] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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51 else: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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52 value = "Index_" + str(feat_count) |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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53 nuclist.append(SeqRecord(Seq(str(gene)), id=value, name=value)) |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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54 pro = Seq(str(gene.translate(table=opts.transtabl, to_stop=True))) |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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55 aalist.append(SeqRecord(pro, id=value, name=value)) |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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56 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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57 # Write out lists in fasta format |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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58 aa_handle = open(opts.aa_file, "w") |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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59 SeqIO.write(aalist, aa_handle, "fasta") |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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60 aa_handle.close() |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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61 orf_handle = open(opts.orf_file, "w") |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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62 SeqIO.write(nuclist, orf_handle, "fasta") |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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63 orf_handle.close() |