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annotate glimmerHMM/glimmerhmm_gff_to_sequence.py @ 0:e9ed61e74837 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
author bgruening
date Wed, 13 Jul 2016 10:56:32 -0400
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1 #!/usr/bin/env python
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2 """Convert GlimmerHMM GFF3 gene predictions into protein sequences.
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4 This works with the GlimmerHMM GFF3 output format:
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6 ##gff-version 3
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7 ##sequence-region Contig5.15 1 47390
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8 Contig5.15 GlimmerHMM mRNA 323 325 . + . ID=Contig5.15.path1.gene1;Name=Contig5.15.path1.gene1
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9 Contig5.15 GlimmerHMM CDS 323 325 . + 0 ID=Contig5.15.cds1.1;Parent=Contig5.15.path1.gene1;Name=Contig5.15.path1.gene1;Note=final-exon
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11 http://www.cbcb.umd.edu/software/GlimmerHMM/
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13 Modified version of the converter from Brad Chapman: https://github.com/chapmanb/bcbb/blob/master/biopython/glimmergff_to_proteins.py
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15 Usage:
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16 glimmer_to_proteins.py <glimmer output> <ref fasta> <output file> <convert to protein ... False|True>
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17 """
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18 import sys
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19 import os
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20 import operator
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22 from Bio import SeqIO
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23 from Bio.SeqRecord import SeqRecord
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25 from BCBio import GFF
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27 def main(glimmer_file, ref_file, out_file, to_protein):
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28 with open(ref_file) as in_handle:
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29 ref_recs = SeqIO.to_dict(SeqIO.parse(in_handle, "fasta"))
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31 base, ext = os.path.splitext(glimmer_file)
e9ed61e74837 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
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33 with open(out_file, "w") as out_handle:
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34 SeqIO.write(protein_recs(glimmer_file, ref_recs, to_protein), out_handle, "fasta")
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36 def protein_recs(glimmer_file, ref_recs, to_protein):
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37 """Generate protein records from GlimmerHMM gene predictions.
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38 """
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39 with open(glimmer_file) as in_handle:
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40 for rec in glimmer_predictions(in_handle, ref_recs):
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41 for feature in rec.features:
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42 seq_exons = []
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43 for cds in feature.sub_features:
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44 seq_exons.append(rec.seq[
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45 cds.location.nofuzzy_start:
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46 cds.location.nofuzzy_end])
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47 gene_seq = reduce(operator.add, seq_exons)
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48 if feature.strand == -1:
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49 gene_seq = gene_seq.reverse_complement()
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51 if to_protein:
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52 yield SeqRecord(gene_seq.translate(), feature.qualifiers["ID"][0], "", "")
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53 else:
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54 yield SeqRecord(gene_seq, feature.qualifiers["ID"][0], "", "")
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56 def glimmer_predictions(in_handle, ref_recs):
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57 """Parse Glimmer output, generating SeqRecord and SeqFeatures for predictions
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58 """
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59 for rec in GFF.parse(in_handle, target_lines=1000, base_dict=ref_recs):
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60 yield rec
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61
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62 if __name__ == "__main__":
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63 if len(sys.argv) != 3:
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64 print __doc__
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65 sys.exit()
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66 main(*sys.argv[1:])