[Bioperl-guts-l] bioperl-live/scripts/seq extract_feature_seq.PLS, 1.2, 1.3 make_mrna_protein.PLS, 1.1, 1.2 seqconvert.PLS, 1.3, 1.4 split_seq.PLS, 1.2, 1.3 translate_seq.PLS, 1.4, 1.5 unflatten_seq.PLS, 1.4, 1.5

Jason Stajich jason at pub.open-bio.org
Tue Apr 26 11:08:45 EDT 2005


Update of /home/repository/bioperl/bioperl-live/scripts/seq
In directory pub.open-bio.org:/tmp/cvs-serv868

Modified Files:
	extract_feature_seq.PLS make_mrna_protein.PLS seqconvert.PLS 
	split_seq.PLS translate_seq.PLS unflatten_seq.PLS 
Log Message:
obscure emails, standardize perl at header


Index: extract_feature_seq.PLS
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/scripts/seq/extract_feature_seq.PLS,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** extract_feature_seq.PLS	3 Feb 2005 15:04:58 -0000	1.2
--- extract_feature_seq.PLS	26 Apr 2005 15:08:42 -0000	1.3
***************
*** 37,41 ****
  =head1 AUTHOR
  
!  Jason Stajich <jason at bioperl.org>
  
  =cut
--- 37,41 ----
  =head1 AUTHOR
  
!  Jason Stajich E<lt>jason-at-bioperl-dot-orgE<gt>
  
  =cut
***************
*** 81,82 ****
--- 81,84 ----
      }
  }
+ 
+ __END__

Index: make_mrna_protein.PLS
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/scripts/seq/make_mrna_protein.PLS,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** make_mrna_protein.PLS	26 Apr 2005 01:47:40 -0000	1.1
--- make_mrna_protein.PLS	26 Apr 2005 15:08:42 -0000	1.2
***************
*** 1,3 ****
! #!/usr/bin/perl -w
  # $Id$
  #
--- 1,3 ----
! #!perl -w
  # $Id$
  #
***************
*** 29,33 ****
  =head1 AUTHOR - Jason Stajich
  
!   Email jason at chg.mc.duke.edu
  
  =cut
--- 29,33 ----
  =head1 AUTHOR - Jason Stajich
  
!   Email jason-at-bioperl-dot-org
  
  =cut
***************
*** 89,94 ****
  
  while( my $seq = $in->next_seq ) {
! 	my $protseq = $seq->translate($termchar,$unknownProt, $frame,$codontable,
! 											$fullCDS, $throw_on_Incomp_CDS);
! 	$out->write_seq($protseq);
  }
--- 89,96 ----
  
  while( my $seq = $in->next_seq ) {
!     my $protseq = $seq->translate($termchar,$unknownProt, $frame,$codontable,
! 				  $fullCDS, $throw_on_Incomp_CDS);
!     $out->write_seq($protseq);
  }
+ 
+ __END__

Index: seqconvert.PLS
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/scripts/seq/seqconvert.PLS,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** seqconvert.PLS	9 Mar 2004 19:57:32 -0000	1.3
--- seqconvert.PLS	26 Apr 2005 15:08:42 -0000	1.4
***************
*** 51,59 ****
  =head1 DESCRIPTION
  
! This script gives command line interface to BioPerl Bio::SeqIO.
  
  =head1 SEE ALSO
  
  L<Bio::SeqIO>
  
  =head1 FEEDBACK
--- 51,60 ----
  =head1 DESCRIPTION
  
! This script gives command line interface to BioPerl Bio::SeqIO. 
  
  =head1 SEE ALSO
  
  L<Bio::SeqIO>
+ L<bp_sreformat.PLS> for similar functionality which also supports AlignIO.
  
  =head1 FEEDBACK
***************
*** 71,83 ****
  
  Report bugs to the Bioperl bug tracking system to help us keep track
! of the bugs and their resolution. Bug reports can be submitted via
! email or the web:
  
-   bioperl-bugs at bioperl.org
    http://bugzilla.bioperl.org/
  
  =head1 AUTHOR - Philip Lijnzaad
  
! Email p.lijnzaad at med.uu.nl
  
  =cut
--- 72,85 ----
  
  Report bugs to the Bioperl bug tracking system to help us keep track
! of the bugs and their resolution. Bug reports can be submitted via the
! web:
  
    http://bugzilla.bioperl.org/
  
  =head1 AUTHOR - Philip Lijnzaad
  
! Email E<lt>p.lijnzaad-at-med.uu.nlE<gt>
  
  =cut
+ 
+ __END__

Index: unflatten_seq.PLS
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/scripts/seq/unflatten_seq.PLS,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** unflatten_seq.PLS	8 Sep 2004 22:04:19 -0000	1.4
--- unflatten_seq.PLS	26 Apr 2005 15:08:43 -0000	1.5
***************
*** 2,6 ****
  use strict;
  # $Id$
! # Author Chris Mungall <cjm at bioperl.org>
  
  =head1 NAME
--- 2,6 ----
  use strict;
  # $Id$
! # Author Chris Mungall <cjm-at-bioperl.org>
  
  =head1 NAME
***************
*** 161,165 ****
  =head1 AUTHOR
  
!  Chris Mungall <cjm at bioperl.org>
  
  =cut
--- 161,165 ----
  =head1 AUTHOR
  
!  Chris Mungall E<lt>cjm-at-bioperl.orgE<gt>
  
  =cut
***************
*** 251,252 ****
--- 251,254 ----
  
  }
+ 
+ __END__

Index: split_seq.PLS
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/scripts/seq/split_seq.PLS,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** split_seq.PLS	27 Oct 2004 19:38:03 -0000	1.2
--- split_seq.PLS	26 Apr 2005 15:08:42 -0000	1.3
***************
*** 3,7 ****
  # $Id$
  
- 
  =head1 NAME
  
--- 3,6 ----
***************
*** 30,35 ****
  
  Report bugs to the Bioperl bug tracking system to help us keep track
! of the bugs and their resolution. Bug reports can be submitted via
! email or the web:
  
   http://bugzilla.bioperl.org/
--- 29,34 ----
  
  Report bugs to the Bioperl bug tracking system to help us keep track
! of the bugs and their resolution. Bug reports can be submitted via the
! web:
  
   http://bugzilla.bioperl.org/
***************
*** 37,41 ****
  =head1 AUTHOR
  
!   Ewan Birney <birney at ebi.ac.uk>
  
  =cut
--- 36,40 ----
  =head1 AUTHOR
  
!   Ewan Birney E<lt>birney-at-ebi.ac.ukE<gt>
  
  =cut
***************
*** 73,74 ****
--- 72,75 ----
     }
  }
+ 
+ __END__

Index: translate_seq.PLS
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/scripts/seq/translate_seq.PLS,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** translate_seq.PLS	24 Jan 2005 02:31:57 -0000	1.4
--- translate_seq.PLS	26 Apr 2005 15:08:43 -0000	1.5
***************
*** 3,7 ****
  # $Id$
  
- 
  =head1 NAME
  
--- 3,6 ----
***************
*** 61,62 ****
--- 60,63 ----
  	$seqout->write_seq($pseq);
  }
+ 
+ __END__



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