[Bioperl-guts-l] bioperl-live/scripts/seq seqconvert.PLS,1.4,1.5

[Chris Mungall]

Update of /home/repository/bioperl/bioperl-live/scripts/seq
In directory pub.open-bio.org:/tmp/cvs-serv23779/scripts/seq

Modified Files:
	seqconvert.PLS 
Log Message:
Unflattener:

 now less strict about ordering of exons in a transcript - this
 allows us to process the trans-spliced transcripts in NC_001284
 (if exons are not in order a severity-3 problem is thrown, which
  can be ignored by user if their threshold is high enough)

chaos.pm:

 uses derives_from instead of produced_by for mRNA to pp relation

seqconvert:

 added chaos and chadoxml as file formats


Index: seqconvert.PLS
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/scripts/seq/seqconvert.PLS,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** seqconvert.PLS	26 Apr 2005 15:08:42 -0000	1.4
--- seqconvert.PLS	30 Aug 2005 17:43:11 -0000	1.5
***************
*** 13,17 ****
  my @known_formats=
    qw(gcg fasta ace raw fastq phd pir scf swiss genbank locuslink
!      embl game qual bsml tab raw abi chado alf ctf exp ztr pln);
  
  my $script=substr($0, 1+rindex($0,'/'));
--- 13,18 ----
  my @known_formats=
    qw(gcg fasta ace raw fastq phd pir scf swiss genbank locuslink
!      embl game qual bsml tab raw abi chado alf ctf exp ztr pln
!      chaosxml chadoxml yaml);
  
  my $script=substr($0, 1+rindex($0,'/'));