/usr/bin/bp_seqretsplit is in bioperl 1.6.924-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 | #!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
#
=head1 NAME
bp_seqretsplit - split a sequence (or stream) into a single file per sequence
=head1 SYNOPSIS
bp_seqretsplit file1 file2 ..
# or
bp_seqretsplit < file1
=head1 DESCRIPTION
The script will split all sequences from fasta file(s) (or stdin) to
individual files. The filename is the sequence ID (everything before
the 1st whitespace in a FASTA header). Currently it doesn't check to
see that it isn't overwriting an existing file so IDs should be unique
This is inspired by EMBOSS seqretsplit tool.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Reporting Bugs
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:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR
Jason Stajich E<lt>jason_AT_bioperl_DOT_orgE<gt>
=cut
use strict;
use warnings;
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-format => 'fasta',
-fh => \*ARGV);
while( my $s = $in->next_seq ) {
Bio::SeqIO->new(-format => 'fasta',
-file => ">".$s->id.".fa")->write_seq($s);
}
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