migrated add_ident

[biopieces.git] / code_perl / Maasha / BioRun.pm

diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm
index ecf32f239eeb714f125983b859fd20b63209073f..ebbd3c53578deafe5451648d72596112021a580f 100644 (file)
--- a/code_perl/Maasha/BioRun.pm
+++ b/code_perl/Maasha/BioRun.pm
@@ -133,7 +133,6 @@ sub run_script
     elsif ( $script eq "assemble_tag_contigs" )     { script_assemble_tag_contigs(      $in, $out, $options ) }
     elsif ( $script eq "length_seq" )               { script_length_seq(                $in, $out, $options ) }
     elsif ( $script eq "uppercase_seq" )            { script_uppercase_seq(             $in, $out, $options ) }
-    elsif ( $script eq "shuffle_seq" )              { script_shuffle_seq(               $in, $out, $options ) }
     elsif ( $script eq "analyze_seq" )              { script_analyze_seq(               $in, $out, $options ) }
     elsif ( $script eq "analyze_tags" )             { script_analyze_tags(              $in, $out, $options ) }
     elsif ( $script eq "complexity_seq" )           { script_complexity_seq(            $in, $out, $options ) }
@@ -176,7 +175,6 @@ sub run_script
     elsif ( $script eq "merge_records" )            { script_merge_records(             $in, $out, $options ) }
     elsif ( $script eq "compute" )                  { script_compute(                   $in, $out, $options ) }
     elsif ( $script eq "flip_tab" )                 { script_flip_tab(                  $in, $out, $options ) }
-    elsif ( $script eq "add_ident" )                { script_add_ident(                 $in, $out, $options ) }
     elsif ( $script eq "count_records" )            { script_count_records(             $in, $out, $options ) }
     elsif ( $script eq "random_records" )           { script_random_records(            $in, $out, $options ) }
     elsif ( $script eq "sort_records" )             { script_sort_records(              $in, $out, $options ) }
@@ -660,13 +658,6 @@ sub get_options
             eval|e=s
         );
     }
-    elsif ( $script eq "add_ident" )
-    {
-        @options = qw(
-            prefix|p=s
-            key|k=s
-        );
-    }
     elsif ( $script eq "count_records" )
     {
         @options = qw(
@@ -1845,29 +1836,6 @@ sub script_length_seq
 }
 
 
-sub script_shuffle_seq
-{
-    # Martin A. Hansen, December 2007.
-
-    # Shuffle sequences in stream.
-
-    my ( $in,    # handle to in stream
-         $out,   # handle to out stream
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $record );
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-    {
-        $record->{ "SEQ" } = Maasha::Seq::seq_shuffle( $record->{ "SEQ" } ) if $record->{ "SEQ" };
-
-        Maasha::Biopieces::put_record( $record, $out );
-    }
-}
-
-
 sub script_analyze_seq
 {
     # Martin A. Hansen, August 2007.
@@ -4147,37 +4115,6 @@ sub script_flip_tab
 }
 
 
-sub script_add_ident
-{
-    # Martin A. Hansen, May 2008.
-
-    # Add a unique identifier to each record in stream.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $record, $key, $prefix, $i );
-
-    $key    = $options->{ "key" }    || "ID";
-    $prefix = $options->{ "prefix" } || "ID";
-
-    $i = 0;
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-    {
-        $record->{ $key } = sprintf( "$prefix%08d", $i );
-
-        Maasha::Biopieces::put_record( $record, $out );
-
-        $i++;
-    }
-}
-
-
 sub script_count_records
 {
     # Martin A. Hansen, August 2007.