From 3a5401c88a90a2315a2b958d7eb4c119adba158f Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Sun, 24 May 2009 19:49:12 +0000
Subject: [PATCH] migrated split biopieces

git-svn-id: http://biopieces.googlecode.com/svn/trunk@401 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/BioRun.pm | 113 -------------------------------------
 1 file changed, 113 deletions(-)

diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm
index 4863090..32be349 100644
--- a/code_perl/Maasha/BioRun.pm
+++ b/code_perl/Maasha/BioRun.pm
@@ -145,8 +145,6 @@ 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 "fold_seq" )                 { script_fold_seq(                  $in, $out, $options ) }
-    elsif ( $script eq "split_seq" )                { script_split_seq(                 $in, $out, $options ) }
-    elsif ( $script eq "split_bed" )                { script_split_bed(                 $in, $out, $options ) }
     elsif ( $script eq "tile_seq" )                 { script_tile_seq(                  $in, $out, $options ) }
     elsif ( $script eq "invert_align" )             { script_invert_align(              $in, $out, $options ) }
     elsif ( $script eq "patscan_seq" )              { script_patscan_seq(               $in, $out, $options ) }
@@ -408,20 +406,6 @@ sub get_options
             flank|f=s
         );
     }
-    elsif ( $script eq "split_seq" )
-    {
-        @options = qw(
-            word_size|w=s
-            uniq|u
-        );
-    }
-    elsif ( $script eq "split_bed" )
-    {
-        @options = qw(
-            window_size|w=s
-            step_size|s=s
-        );
-    }
     elsif ( $script eq "tile_seq" )
     {
         @options = qw(
@@ -2380,103 +2364,6 @@ sub script_fold_seq
 }
 
 
-sub script_split_seq
-{
-    # Martin A. Hansen, August 2007.
-
-    # Split a sequence in stream into words.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $record, $new_record, $i, $subseq, %lookup );
-
-    $options->{ "word_size" } ||= 7;
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-    {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
-        {
-            for ( $i = 0; $i < length( $record->{ "SEQ" } ) - $options->{ "word_size" } + 1; $i++ )
-            {
-                $subseq = substr $record->{ "SEQ" }, $i, $options->{ "word_size" };
-
-                if ( $options->{ "uniq" } and not $lookup{ $subseq } )
-                {
-                    $new_record->{ "SEQ_NAME" } = $record->{ "SEQ_NAME" } . "[" . ( $i + 1 ) . "-" . ( $i + $options->{ "word_size" } ) . "]";
-                    $new_record->{ "SEQ" }      = $subseq;
-
-                    Maasha::Biopieces::put_record( $new_record, $out );
-
-                    $lookup{ $subseq } = 1;
-                }
-                else
-                {
-                    $new_record->{ "SEQ_NAME" } = $record->{ "SEQ_NAME" } . "[" . ( $i + 1 ) . "-" . ( $i + $options->{ "word_size" } ) . "]";
-                    $new_record->{ "SEQ" }      = $subseq;
-
-                    Maasha::Biopieces::put_record( $new_record, $out );
-                }
-            }
-        }
-        else
-        {
-            Maasha::Biopieces::put_record( $record, $out );
-        }
-    }
-}
-
-
-sub script_split_bed
-{
-    # Martin A. Hansen, June 2008.
-
-    # Split a BED record into overlapping windows.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $record, $new_record, $i );
-
-    $options->{ "window_size" } ||= 20;
-    $options->{ "step_size" }   ||= 1;
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-    {
-        if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
-        {
-            $record->{ "BED_LEN" } = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
-
-            for ( $i = 0; $i < $record->{ "BED_LEN" } - $options->{ "window_size" }; $i += $options->{ "step_size" } )
-            {
-                $new_record->{ "REC_TYPE" } = "BED";
-                $new_record->{ "CHR" }      = $record->{ "CHR" };
-                $new_record->{ "CHR_BEG" }  = $record->{ "CHR_BEG" } + $i;
-                $new_record->{ "CHR_END" }  = $record->{ "CHR_BEG" } + $i + $options->{ "window_size" };
-                $new_record->{ "BED_LEN" }  = $options->{ "window_size" };
-                $new_record->{ "Q_ID" }     = $record->{ "Q_ID" } . "_$i";
-                $new_record->{ "SCORE" }    = $record->{ "SCORE" };
-                $new_record->{ "STRAND" }   = $record->{ "STRAND" };
-
-                Maasha::Biopieces::put_record( $new_record, $out );
-            }
-        }
-        else
-        {
-            Maasha::Biopieces::put_record( $record, $out );
-        }
-    }
-}
-
-
 sub script_tile_seq
 {
     # Martin A. Hansen, February 2008.
-- 
2.39.2