-#!/usr/bin/env perl
+#!/usr/bin/env perl -w
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Create a Vmatch index from sequences in stream for use with [vmatch_seq].
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Common;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::Seq;
+use Maasha::Fasta;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $default, $formats, $options, $in, $out, $record, $file_tmp, $fh_tmp, $type, $entry );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'prefix_length', short => 'p', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$file_tmp = $options->{ 'index_name' };
+$fh_tmp = Maasha::Filesys::file_write_open( $file_tmp );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
+ {
+ Maasha::Fasta::put_entry( $entry, $fh_tmp );
+
+ $type = Maasha::Seq::seq_guess_type( $record->{ 'SEQ' } ) if not defined $type;
+ }
+
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+close $fh_tmp;
+
+if ( $type eq "protein" ) {
+ Maasha::Common::run( "mkvtree", "-db $file_tmp -protein -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" );
+} else {
+ Maasha::Common::run( "mkvtree", "-db $file_tmp -dna -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" );
+}
+
+unlink $file_tmp;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ $run_time_beg = Maasha::Biopieces::run_time();
+
+ Maasha::Biopieces::log_biopiece();
+}
+
+END
+{
+ Maasha::Biopieces::close_stream( $in );
+ Maasha::Biopieces::close_stream( $out );
+
+ $run_time_end = Maasha::Biopieces::run_time();
+
+ Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
+
-use Maasha::BioRun;
elsif ( $script eq "patscan_seq" ) { script_patscan_seq( $in, $out, $options ) }
elsif ( $script eq "soap_seq" ) { script_soap_seq( $in, $out, $options ) }
elsif ( $script eq "match_seq" ) { script_match_seq( $in, $out, $options ) }
- elsif ( $script eq "create_vmatch_index" ) { script_create_vmatch_index( $in, $out, $options ) }
elsif ( $script eq "write_bed" ) { script_write_bed( $in, $out, $options ) }
elsif ( $script eq "write_psl" ) { script_write_psl( $in, $out, $options ) }
elsif ( $script eq "write_fixedstep" ) { script_write_fixedstep( $in, $out, $options ) }
direction|d=s
);
}
- elsif ( $script eq "create_vmatch_index" )
- {
- @options = qw(
- index_name|i=s
- prefix_length|p=s
- no_stream|x
- );
- }
elsif ( $script eq "write_bed" )
{
@options = qw(
}
Maasha::Common::error( qq(no --database specified) ) if $script eq "remove_ucsc_tracks" and not $options{ "database" };
- Maasha::Common::error( qq(no --index_name specified) ) if $script =~ /create_vmatch_index/ and not $options{ "index_name" };
Maasha::Common::error( qq(no --in_file or --genome specified) ) if $script eq "soap_seq" and not $options{ "genome" } and not $options{ "in_file" };
Maasha::Common::error( qq(both --in_file and --genome specified) ) if $script eq "soap_seq" and $options{ "genome" } and $options{ "in_file" };
Maasha::Common::error( qq(no --genome specified) ) if $script =~ /get_genome_align|get_genome_phastcons|plot_phastcons_profiles|plot_karyogram/ and not $options{ "genome" };
}
-sub script_create_vmatch_index
-{
- # Martin A. Hansen, January 2008.
-
- # Create a vmatch index from sequences in the stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $file_tmp, $fh_tmp, $type, $entry );
-
- if ( $options->{ "index_name" } )
- {
- $file_tmp = $options->{ 'index_name' };
- $fh_tmp = Maasha::Common::write_open( $file_tmp );
- }
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- if ( $options->{ "index_name" } and $entry = Maasha::Fasta::biopiece2fasta( $record ) )
- {
- Maasha::Fasta::put_entry( $entry, $fh_tmp );
-
- $type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not defined $type;
- }
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- if ( $options->{ "index_name" } )
- {
- close $fh_tmp;
-
- if ( $type eq "protein" ) {
- Maasha::Common::run( "mkvtree", "-db $file_tmp -protein -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" );
- } else {
- Maasha::Common::run( "mkvtree", "-db $file_tmp -dna -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" );
- }
-
- unlink $file_tmp;
- }
-}
-
-
sub script_write_bed
{
# Martin A. Hansen, August 2007.
projects / biopieces.git / commitdiff