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annotate glimmer_gbk_to_orf.py @ 2:cc51783dc93c draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 274d1f6804bfd0362fdcd2383bfdb32ca8fd634e"
author iuc
date Sun, 20 Mar 2022 10:06:50 +0000
parents 9c195b26a5ac
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9c195b26a5ac 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
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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2
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3 ###################################################################
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4 #
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5 # gbk2orf.py by Errol Strain (estrain@gmail.com)
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6 #
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7 # Read a GenBank file and export fasta formatted amino acid and
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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8 # CDS files
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9 #
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10 ###################################################################
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12 import sys
9c195b26a5ac 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
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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9c195b26a5ac 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
9c195b26a5ac 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
9c195b26a5ac 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
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20 # Command line usage
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21 usage = "usage: %prog -g input.gbk -a aa.fasta -n nuc.fasta"
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22 p = OptionParser(usage)
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23 p.add_option("-t", "--translate", dest="transtabl", type="int", default=11,
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24 help="Translation table used to translate coding regions (default=11)")
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25 p.add_option("-g", "--genbank", dest="gb_file", help="GenBank input file")
9c195b26a5ac 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")
9c195b26a5ac 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")
9c195b26a5ac 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()
9c195b26a5ac 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?
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30 if not opts and not args:
9c195b26a5ac 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")
9c195b26a5ac 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:
9c195b26a5ac 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")
9c195b26a5ac 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
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36 aalist = []
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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37 nuclist = []
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38
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39 # If the CDS does not have a locus tag the name will be assigned using the
9c195b26a5ac 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
9c195b26a5ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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41 feat_count = 0
9c195b26a5ac 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
9c195b26a5ac 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"):
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45 for (index, feature) in enumerate(gb_record.features):
9c195b26a5ac 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":
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47 feat_count = feat_count + 1
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48 gene = feature.extract(gb_record.seq)
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49 if "locus_tag" in feature.qualifiers:
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50 value = feature.qualifiers["locus_tag"][0]
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51 else:
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52 value = "Index_" + str(feat_count)
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53 nuclist.append(SeqRecord(Seq(str(gene)), id=value, name=value))
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54 pro = Seq(str(gene.translate(table=opts.transtabl, to_stop=True)))
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55 aalist.append(SeqRecord(pro, id=value, name=value))
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56
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57 # Write out lists in fasta format
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58 aa_handle = open(opts.aa_file, "w")
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59 SeqIO.write(aalist, aa_handle, "fasta")
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60 aa_handle.close()
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61 orf_handle = open(opts.orf_file, "w")
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62 SeqIO.write(nuclist, orf_handle, "fasta")
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63 orf_handle.close()