bin/bp_seqretsplit

   1 #!/usr/bin/perl
   2 #
   3 =head1 NAME
   4
   5 bp_seqretsplit - split a sequence (or stream) into a single file per sequence
   6
   7 =head1 SYNOPSIS
   8
   9   bp_seqretsplit file1 file2 ..
  10   # or
  11   bp_seqretsplit < file1
  12
  13 =head1 DESCRIPTION
  14
  15 The script will split all sequences from fasta file(s) (or stdin) to
  16 individual files. The filename is the sequence ID (everything before
  17 the 1st whitespace in a FASTA header).  Currently it doesn't check to
  18 see that it isn't overwriting an existing file so IDs should be unique
  19
  20 This is inspired by EMBOSS seqretsplit tool.
  21
  22 =head1 FEEDBACK
  23
  24 =head2 Mailing Lists
  25
  26 User feedback is an integral part of the evolution of this and other
  27 Bioperl modules. Send your comments and suggestions preferably to
  28 the Bioperl mailing list.  Your participation is much appreciated.
  29
  30   bioperl-l@bioperl.org                  - General discussion
  31     http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  32
  33 =head2 Reporting Bugs
  34
  35 Report bugs to the Bioperl bug tracking system to help us keep track
  36 of the bugs and their resolution. Bug reports can be submitted via
  37 email or the web:
  38
  39 https://github.com/bioperl/bioperl-live/issues
  40
  41 =head1 AUTHOR
  42
  43 Jason Stajich E<lt>jason_AT_bioperl_DOT_orgE<gt>
  44
  45 =cut
  46
  47 use strict;
  48 use warnings;
  49 use Bio::SeqIO;
  50 my $in = Bio::SeqIO->new(-format => 'fasta',
  51                          -fh   => \*ARGV);
  52 while( my $s = $in->next_seq ) {
  53     Bio::SeqIO->new(-format => 'fasta',
  54                     -file   => ">".$s->id.".fa")->write_seq($s);
  55 }
  56