# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1390489816 21600
# Node ID 3b526a7808495a85015ad3bca20f7c1798b2b3aa
# Parent  359addb9b9d4c3c952310be84fde727099bea815
Change default seqtype from pep:novel to pep:splice

diff -r 359addb9b9d4 -r 3b526a780849 translate_bed_sequences.py
--- 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' )
diff -r 359addb9b9d4 -r 3b526a780849 translate_bed_sequences.xml
--- 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">