Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / binaries / src / jpred / lib / Index / FastaCMD.pm

diff --git a/binaries/src/jpred/lib/Index/FastaCMD.pm b/binaries/src/jpred/lib/Index/FastaCMD.pm
new file mode 100644 (file)
index 0000000..d937b8b
--- /dev/null
+++ b/binaries/src/jpred/lib/Index/FastaCMD.pm
@@ -0,0 +1,85 @@
+package Index::FastaCMD;
+
+our $VERSION = '0.2';
+
+=head1 NAME
+
+Index::FastaCMD - module to use the fastacmd program to read BLAST formatted databases
+
+=head1 DESCRIPTION
+
+This module was written as a replacement for Index::EMBOSS as Emboss needed to be statically 
+linked to libgd, whcih was is a very sysadmin-friendly way of installing the software. 
+As BLAST is pretty ubiquitous the fastacmd was deemed to be a better option. Copied heavily 
+from Index::EMBOSS.
+
+=head1 SYNOPSIS
+
+=head1 CHANGES
+
+=over 8
+
+=item 0.2
+
+Added 'use Path' module to ensure that the correct fastacmd binary is used. Previously on the 
+cluster the wrong fastacmd was used, which resulted in a failure. Now is more robust although 
+the path to fastacmd is hardcoded in Paths.pm
+
+=head1 AUTHOR
+
+Chris Cole <christian@cole.name>
+
+=cut
+
+use strict;
+use warnings;
+
+use Carp;
+use POSIX qw(WIFEXITED WEXITSTATUS WIFSIGNALED WTERMSIG);
+use IPC::Open3;
+
+use base qw(Root);
+
+use FASTA::File;
+use Paths qw($fastacmd);
+
+sub get_sequence {
+  my ( $self, $key, $db ) = @_;
+
+  croak "No sequence code given for get_sequence" unless $key;
+  croak "No database given for get_sequence"      unless $db;
+
+  my @cmd = split / /, "$fastacmd -s $key -d $db";
+
+  my $pid = open3( undef, \*RD, \*ERR, @cmd );
+
+  my $seq = FASTA::File->new( read => \*RD );
+  my @err = <ERR>;
+
+  pop @err;
+  pop @err;
+
+  close RD;
+  close ERR;
+  waitpid $pid, 0;
+
+  # Everything was okay...
+  if ( WIFEXITED($?) and not WEXITSTATUS($?) ) { return $seq }
+
+  # Non-zero exit
+  elsif ( WIFEXITED($?) and WEXITSTATUS($?) ) {
+    carp "Command: '@cmd' had a problem: $?; $!";
+    carp @err;
+  }
+
+  # Was it stopped by an external program
+  elsif ( WIFSIGNALED($?) ) {
+    carp "$fastacmd halted by external signal " . WTERMSIG($?);
+  } else {
+    carp "$fastacmd suffered from a random pantwetting event";
+  }
+
+  return undef;
+}
+
+1;