[Bioperl-guts-l] bioperl-live/scripts/Bio-DB-GFF genbank2gff3.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/Bio-DB-GFF
In directory pub.open-bio.org:/tmp/cvs-serv22054/core/scripts/Bio-DB-GFF

Modified Files:
	genbank2gff3.PLS 
Log Message:
POD and doc formating fixes


Index: genbank2gff3.PLS
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/scripts/Bio-DB-GFF/genbank2gff3.PLS,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** genbank2gff3.PLS	5 Oct 2004 01:44:53 -0000	1.1
--- genbank2gff3.PLS	7 Dec 2004 13:03:48 -0000	1.2
***************
*** 7,11 ****
  =head1 NAME 
  
! bp_genbank2gff3.pl -- Genbank->gbrowse-friendly GFF3
  
  =head1 SYNOPSIS
--- 7,11 ----
  =head1 NAME 
  
! bp_genbank2gff3.pl -- Genbank-E<gt>gbrowse-friendly GFF3
  
  =head1 SYNOPSIS
***************
*** 40,75 ****
  
  This script uses Bio::SeqFeature::Tools::Unflattener and
! Bio::Tools::GFF to convert GenBank flatfiles to GFF3 with
! gene containment hierarchies mapped for optimal display in
! gbrowse.
  
! The input files are assumed to be gzipped GenBank flatfiles
! for refseq contigs.  The files may contain multiple GenBank records.
! Either a single file or an entire directory can be processed.  
! By default, the DNA sequence is embedded in the GFF but it can be saved 
! into seperate fasta file with the --split(-y) option.
  
- If an input file contains multiple records, the default behaviour is 
- to dump all GFF and sequence to a file of the same name (with .gff appended).
- Using the 'nolump' option will create a seperate file for each 
- genbank record.  Using the 'split' option will create seperate 
- GFF and Fasta files for each genbank record.  
  
  
  =head3 Note1:
  
! In cases where the input files contain many GenBank records
! (for example, the chromosome files for the mouse genome build), 
! a very large number of output files will be produced 
! if the 'split' or 'nolump' options are selected.  
! If you do have lists of files > 6000, use the --long_list option
! in bp_bulk_load_gff.pl or bp_fast_load_gff.pl to load the gff and/
! or fasta files.
  
! =head3 Note2: 
  
! This script is designed for refseq genomic sequence entries.  
! It may work for third party annotations but this has not 
! been tested.
  
  =head1 AUTHOR 
--- 40,74 ----
  
  This script uses Bio::SeqFeature::Tools::Unflattener and
! Bio::Tools::GFF to convert GenBank flatfiles to GFF3 with gene
! containment hierarchies mapped for optimal display in gbrowse.
  
! The input files are assumed to be gzipped GenBank flatfiles for refseq
! contigs.  The files may contain multiple GenBank records.  Either a
! single file or an entire directory can be processed.  By default, the
! DNA sequence is embedded in the GFF but it can be saved into seperate
! fasta file with the --split(-y) option.
! 
! If an input file contains multiple records, the default behaviour is
! to dump all GFF and sequence to a file of the same name (with .gff
! appended).  Using the 'nolump' option will create a seperate file for
! each genbank record.  Using the 'split' option will create seperate
! GFF and Fasta files for each genbank record.
  
  
+ =head2 Notes
  
  =head3 Note1:
  
! In cases where the input files contain many GenBank records (for
! example, the chromosome files for the mouse genome build), a very
! large number of output files will be produced if the 'split' or
! 'nolump' options are selected.  If you do have lists of files E<gt> 6000,
! use the --long_list option in bp_bulk_load_gff.pl or
! bp_fast_load_gff.pl to load the gff and/ or fasta files.
  
! =head3 Note2:
  
! This script is designed for refseq genomic sequence entries.  It may
! work for third party annotations but this has not been tested.
  
  =head1 AUTHOR 



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