Mercurial > repos > jjohnson > translate_bed_sequences
changeset 3:3b526a780849
Change default seqtype from pep:novel to pep:splice
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 23 Jan 2014 09:10:16 -0600 |
| parents | 359addb9b9d4 |
| children | aa93f7910259 |
| files | translate_bed_sequences.py translate_bed_sequences.xml |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/translate_bed_sequences.py Thu Jan 09 14:24:41 2014 -0600 +++ b/translate_bed_sequences.py Thu Jan 23 09:10:16 2014 -0600 @@ -118,7 +118,7 @@ def get_seq_id(self,seqtype='unk:unk',reference='',frame=None): ## Ensembl fasta ID format # >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT - # >ENSP00000328693 pep:novel chromosome:NCBI35:1:904515:910768:1 gene:ENSG00000158815:transcript:ENST00000328693 gene_biotype:protein_coding transcript_biotype:protein_coding + # >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1 gene:ENSG00000158815:transcript:ENST00000328693 gene_biotype:protein_coding transcript_biotype:protein_coding frame_name = '' chromStart = self.chromStart chromEnd = self.chromEnd @@ -160,7 +160,7 @@ parser.add_option( '-i', '--input', dest='input', help='BED file (tophat junctions.bed) with sequence column added' ) parser.add_option( '-o', '--output', dest='output', help='Translations of spliced sequence') parser.add_option( '-b', '--bed_format', dest='bed_format', action='store_true', default=False, help='Append translations to bed file instead of fasta' ) - parser.add_option( '-S', '--seqtype', dest='seqtype', default='pep:novel', help='SEQTYPE:STATUS for fasta ID line' ) + parser.add_option( '-S', '--seqtype', dest='seqtype', default='pep:splice', help='SEQTYPE:STATUS for fasta ID line' ) parser.add_option( '-R', '--reference', dest='reference', default=None, help='Genome Reference Name for fasta ID location ' ) parser.add_option( '-Q', '--score_name', dest='score_name', default=None, help='include in the fasta ID line score_name:score ' ) parser.add_option( '-l', '--leading_bp', dest='leading_bp', type='int', default=None, help='leading number of base pairs to ignore when filtering' )
--- a/translate_bed_sequences.xml Thu Jan 09 14:24:41 2014 -0600 +++ b/translate_bed_sequences.xml Thu Jan 23 09:10:16 2014 -0600 @@ -44,7 +44,7 @@ <param name="reference" type="text" value="" optional="true" label="Genome reference name" help="By default, the database metadata will be used."/> <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines" - help="For example: pep:novel"/> + help="For example: pep:splice"/> <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name" help="For example: with the tag name 'depth' and bed score 12: depth:12"/> <conditional name="filter">