Merge branch 'JABAWS_Release_2_5' into develop

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

diff --git a/binaries/src/jpred/lib/Index/EMBOSS.pm b/binaries/src/jpred/lib/Index/EMBOSS.pm
new file mode 100644 (file)
index 0000000..484c4f1
--- /dev/null
+++ b/binaries/src/jpred/lib/Index/EMBOSS.pm
@@ -0,0 +1,53 @@
+package Index::EMBOSS;
+
+use strict;
+use warnings;
+use Carp;
+
+use POSIX qw(WIFEXITED WEXITSTATUS WIFSIGNALED WTERMSIG);
+use IPC::Open3;
+
+use base qw(Root);
+
+use FASTA::File;
+
+sub read_index { 1 }
+
+sub get_sequence {
+  my ( $self, $key ) = @_;
+  croak "No value for get_sequence" unless $key;
+
+  my @cmd = split / /, "seqret -filter $key";
+
+  my $pid = open3( undef, \*RD, \*ERR, @cmd );
+
+  my $seqs = 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 $seqs }
+
+  # Non-zero exit
+  elsif ( WIFEXITED($?) and WEXITSTATUS($?) ) {
+    carp "seqret had a problem: $?; $!";
+    carp @err;
+  }
+
+  # Was it stopped by an external program
+  elsif ( WIFSIGNALED($?) ) {
+    carp "seqret halted by external signal " . WTERMSIG($?);
+  } else {
+    carp "seqret suffered from a random pantwetting event";
+  }
+
+  return undef;
+}
+
+1;