[Bioperl-guts-l] bioperl-live/scripts/tree nexus2nh.PLS, 1.1, 1.2 tree2pag.PLS, 1.1, 1.2

Heikki Lehvaslaiho heikki at pub.open-bio.org
Tue Dec 7 08:03:50 EST 2004


Update of /home/repository/bioperl/bioperl-live/scripts/tree
In directory pub.open-bio.org:/tmp/cvs-serv22054/core/scripts/tree

Modified Files:
	nexus2nh.PLS tree2pag.PLS 
Log Message:
POD and doc formating fixes


Index: nexus2nh.PLS
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/scripts/tree/nexus2nh.PLS,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** nexus2nh.PLS	25 Jun 2004 15:34:18 -0000	1.1
--- nexus2nh.PLS	7 Dec 2004 13:03:48 -0000	1.2
***************
*** 10,19 ****
  
   # OR pipe in through STDIN
!  
   cat file.nexus | nexus2nh > file.nh
  
   # OR specify an output
  
!  nexus2nh -o file.nh file.nexus 
  
  =head1 DESCRIPTION
--- 10,19 ----
  
   # OR pipe in through STDIN
! 
   cat file.nexus | nexus2nh > file.nh
  
   # OR specify an output
  
!  nexus2nh -o file.nh file.nexus
  
  =head1 DESCRIPTION

Index: tree2pag.PLS
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/scripts/tree/tree2pag.PLS,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** tree2pag.PLS	16 Jul 2004 15:37:52 -0000	1.1
--- tree2pag.PLS	7 Dec 2004 13:03:48 -0000	1.2
***************
*** 10,19 ****
  
   # OR pipe in through STDIN, and use newick format instead
!  
   cat file.newick | tree2pag -if newick > file.nh
  
   # OR specify an output and input
  
!  tree2pag -o file.pag -i file.newick 
  
  =head1 DESCRIPTION
--- 10,19 ----
  
   # OR pipe in through STDIN, and use newick format instead
! 
   cat file.newick | tree2pag -if newick > file.nh
  
   # OR specify an output and input
  
!  tree2pag -o file.pag -i file.newick
  
  =head1 DESCRIPTION
***************
*** 21,25 ****
  Convert TreeIO parseable files into Pagel format tree files.  Be
  warned that pagel format only really supports a single tree per file
! so.  Also Pagel parsing is not yet available in bioperl. 
  
  =cut
--- 21,25 ----
  Convert TreeIO parseable files into Pagel format tree files.  Be
  warned that pagel format only really supports a single tree per file
! so.  Also Pagel parsing is not yet available in bioperl.
  
  =cut



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