added create_bowtie_index

[biopieces.git] / bp_bin / bowtie_seq

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index aedf02ad3edce43918f4eb460846e9407060f98e..f7229f106fba9abe71105bd6adca0758237c9848 100755 (executable)
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -42,18 +42,26 @@ my ( $options, $in, $out, $index, $tmp_dir, $tmp_in, $tmp_out, $fh_in, $fh_out,
 
 $options = Maasha::Biopieces::parse_options(
     [
-        { long => 'genome',      short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef,     disallowed => undef },
-        { long => 'mismatches',  short => 'm', type => 'uint',   mandatory => 'no',  default => 0,     allowed => "0,1,2,3", disallowed => undef },
-        { long => 'max_hits',    short => 'h', type => 'uint',   mandatory => 'no',  default => undef, allowed => undef,     disallowed => 0     },
-        { long => 'seed_length', short => 's', type => 'uint',   mandatory => 'no',  default => 28,    allowed => undef,     disallowed => 0     },
-        { long => 'cpus',        short => 'c', type => 'uint',   mandatory => 'no',  default => 1,     allowed => undef,     disallowed => 0     },
+        { long => 'genome',      short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef,     disallowed => undef },
+        { long => 'index_name',  short => 'i', type => 'string', mandatory => 'no', default => undef, allowed => undef,     disallowed => undef },
+        { long => 'mismatches',  short => 'm', type => 'uint',   mandatory => 'no', default => 0,     allowed => "0,1,2,3", disallowed => undef },
+        { long => 'max_hits',    short => 'h', type => 'uint',   mandatory => 'no', default => undef, allowed => undef,     disallowed => 0     },
+        { long => 'seed_length', short => 's', type => 'uint',   mandatory => 'no', default => 28,    allowed => undef,     disallowed => 0     },
+        { long => 'cpus',        short => 'c', type => 'uint',   mandatory => 'no', default => 1,     allowed => undef,     disallowed => 0     },
     ]   
 );
 
+Maasha::Common::error( qq(both --index_hame and --genome specified) ) if     $options->{ "genome" } and     $options->{ "index_name" };
+Maasha::Common::error( qq(no --index_name or --genome specified) )    if not $options->{ "genome" } and not $options->{ "index_name" };
+
 $in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 
-$index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/bowtie/$options->{ 'genome' }";
+if ( defined $options->{ 'genome' } ) {
+    $index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/bowtie/$options->{ 'genome' }";
+} elsif (defined $options->{ 'index_name' } ) {
+    $index = $options->{ 'index_name' };
+}
 
 $tmp_dir = Maasha::Biopieces::get_tmpdir();
 $tmp_in  = "$tmp_dir/bowtie.seq";