From be204f3b0d9d30364db3a5b125877e0180db08b9 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 28 May 2009 09:43:48 +0000
Subject: [PATCH] migrated patscan_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@435 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/BioRun.pm | 115 -------------------------------------
 1 file changed, 115 deletions(-)

diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm
index 1f2ffeb..33884c4 100644
--- a/code_perl/Maasha/BioRun.pm
+++ b/code_perl/Maasha/BioRun.pm
@@ -136,7 +136,6 @@ sub run_script
     elsif ( $script eq "get_genome_align" )         { script_get_genome_align(          $in, $out, $options ) }
     elsif ( $script eq "get_genome_phastcons" )     { script_get_genome_phastcons(      $in, $out, $options ) }
     elsif ( $script eq "tile_seq" )                 { script_tile_seq(                  $in, $out, $options ) }
-    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 "write_bed" )                { script_write_bed(                 $in, $out, $options ) }
     elsif ( $script eq "write_psl" )                { script_write_psl(                 $in, $out, $options ) }
@@ -332,17 +331,6 @@ sub get_options
             supress_indels|s
         );
     }
-    elsif ( $script eq "patscan_seq" )
-    {
-        @options = qw(
-            patterns|p=s
-            patterns_in|P=s
-            comp|c
-            max_hits|h=s
-            max_misses|m=s
-            genome|g=s
-        );
-    }
     elsif ( $script eq "soap_seq" )
     {
         @options = qw(
@@ -1747,109 +1735,6 @@ sub script_tile_seq
 }
 
 
-sub script_patscan_seq
-{
-    # Martin A. Hansen, August 2007.
-
-    # Locates patterns in sequences using scan_for_matches.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $genome_file, @args, $arg, $type, $seq_file, $pat_file, $out_file, $fh_in, $fh_out, $record, $patterns, $pattern, $entry, $result, %head_hash, $i );
-
-    if ( $options->{ "patterns" } ) {
-        $patterns = Maasha::Patscan::parse_patterns( $options->{ "patterns" } );
-    } elsif ( -f $options->{ "patterns_in" } ) {
-        $patterns = Maasha::Patscan::read_patterns( $options->{ "patterns_in" } );
-    }
-
-    $genome_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna" if $options->{ 'genome' };
-
-    push @args, "-c"                            if $options->{ "comp" };
-    push @args, "-m $options->{ 'max_hits' }"   if $options->{ 'max_hits' };
-    push @args, "-n $options->{ 'max_misses' }" if $options->{ 'max_hits' };
-
-    $seq_file = "$BP_TMP/patscan.seq";
-    $pat_file = "$BP_TMP/patscan.pat";
-    $out_file = "$BP_TMP/patscan.out";
-
-    $fh_out = Maasha::Common::write_open( $seq_file );
-
-    $i = 0;
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-    {
-        if ( $record->{ "SEQ" } and $record->{ "SEQ_NAME" } )
-        {
-            $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
-
-            Maasha::Fasta::put_entry( [ $i, $record->{ "SEQ" } ], $fh_out );
-
-            $head_hash{ $i } = $record->{ "SEQ_NAME" };
-
-            $i++;
-        }
-    }
-
-    close $fh_out;
-
-    $arg  = join " ", @args;
-    $arg .= " -p" if $type eq "protein";
-
-    foreach $pattern ( @{ $patterns } )
-    {
-        $fh_out = Maasha::Common::write_open( $pat_file );
-
-        print $fh_out "$pattern\n";
-
-        close $fh_out;
-
-        if ( $options->{ 'genome' } ) {
-            `scan_for_matches $arg $pat_file < $genome_file > $out_file`;
-            # Maasha::Common::run( "scan_for_matches", "$arg $pat_file < $genome_file > $out_file" );
-        } else {
-            `scan_for_matches $arg $pat_file < $seq_file > $out_file`;
-            # Maasha::Common::run( "scan_for_matches", "$arg $pat_file < $seq_file > $out_file" );
-        }
-
-        $fh_in = Maasha::Common::read_open( $out_file );
-
-        while ( $entry = Maasha::Fasta::get_entry( $fh_in ) )
-        {
-            $result = Maasha::Patscan::parse_scan_result( $entry, $pattern );
-
-            if ( $options->{ 'genome' } )
-            {
-                $result->{ "CHR" }     = $result->{ "S_ID" };
-                $result->{ "CHR_BEG" } = $result->{ "S_BEG" }; 
-                $result->{ "CHR_END" } = $result->{ "S_END" }; 
-
-                delete $result->{ "S_ID" };
-                delete $result->{ "S_BEG" };
-                delete $result->{ "S_END" };
-            }
-            else
-            {
-                $result->{ "S_ID" } = $head_hash{ $result->{ "S_ID" } };
-            }
-
-            Maasha::Biopieces::put_record( $result, $out );
-        }
-
-        close $fh_in;
-    }
-
-    unlink $pat_file;
-    unlink $seq_file;
-    unlink $out_file;
-}
-
-
 sub script_soap_seq
 {
     # Martin A. Hansen, July 2008.
-- 
2.39.5