more read_ tools migrated

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

diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm
index 7b5a9da0fa38ffcf0277a15fa2d685fed7ce1b96..5383aa3d8bac76256e89838d65046fba88c90e0b 100644 (file)
--- a/code_perl/Maasha/BioRun.pm
+++ b/code_perl/Maasha/BioRun.pm
@@ -113,8 +113,6 @@ sub run_script
     if    ( $script eq "print_usage" )              { script_print_usage(               $in, $out, $options ) }
     elsif ( $script eq "read_psl" )                 { script_read_psl(                  $in, $out, $options ) }
     elsif ( $script eq "read_fixedstep" )           { script_read_fixedstep(            $in, $out, $options ) }
-    elsif ( $script eq "read_blast_tab" )           { script_read_blast_tab(            $in, $out, $options ) }
-    elsif ( $script eq "read_embl" )                { script_read_embl(                 $in, $out, $options ) }
     elsif ( $script eq "read_stockholm" )           { script_read_stockholm(            $in, $out, $options ) }
     elsif ( $script eq "read_phastcons" )           { script_read_phastcons(            $in, $out, $options ) }
     elsif ( $script eq "read_soft" )                { script_read_soft(                 $in, $out, $options ) }
@@ -174,23 +172,6 @@ sub get_options
             num|n=s
         );
     }
-    elsif ( $script eq "read_blast_tab" )
-    {
-        @options = qw(
-            data_in|i=s
-            num|n=s
-        );
-    }
-    elsif ( $script eq "read_embl" )
-    {
-        @options = qw(
-            data_in|i=s
-            num|n=s
-            keys|k=s
-            feats|f=s
-            quals|q=s
-        );
-    }
     elsif ( $script eq "read_stockholm" )
     {
         @options = qw(
@@ -569,157 +550,6 @@ sub script_read_fixedstep
 }
 
 
-sub script_read_blast_tab
-{
-    # Martin A. Hansen, September 2007.
-
-    # Read tabular BLAST output from NCBI blast run with -m8 or -m9.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $file, $line, @fields, $strand, $record, $data_in, $num );
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) {
-        Maasha::Biopieces::put_record( $record, $out );
-    }
-
-    $num = 1;
-
-    foreach $file ( @{ $options->{ "files" } } )
-    {
-        $data_in = Maasha::Common::read_open( $file );
-
-        while ( $line = <$data_in> )
-        {
-            chomp $line;
-
-            next if $line =~ /^#/;
-
-            @fields = split /\t/, $line;
-
-            $record->{ "REC_TYPE" }   = "BLAST";
-            $record->{ "Q_ID" }       = $fields[ 0 ];
-            $record->{ "S_ID" }       = $fields[ 1 ];
-            $record->{ "IDENT" }      = $fields[ 2 ];
-            $record->{ "ALIGN_LEN" }  = $fields[ 3 ];
-            $record->{ "MISMATCHES" } = $fields[ 4 ];
-            $record->{ "GAPS" }       = $fields[ 5 ];
-            $record->{ "Q_BEG" }      = $fields[ 6 ] - 1; # BLAST is 1-based
-            $record->{ "Q_END" }      = $fields[ 7 ] - 1; # BLAST is 1-based
-            $record->{ "S_BEG" }      = $fields[ 8 ] - 1; # BLAST is 1-based
-            $record->{ "S_END" }      = $fields[ 9 ] - 1; # BLAST is 1-based
-            $record->{ "E_VAL" }      = $fields[ 10 ];
-            $record->{ "BIT_SCORE" }  = $fields[ 11 ];
-
-            if ( $record->{ "S_BEG" } > $record->{ "S_END" } )
-            {
-                $record->{ "STRAND" } = '-';
-
-                ( $record->{ "S_BEG" }, $record->{ "S_END" } ) = ( $record->{ "S_END" }, $record->{ "S_BEG" } );
-            }
-            else
-            {
-                $record->{ "STRAND" } = '+';
-            }
-
-            Maasha::Biopieces::put_record( $record, $out );
-
-            goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
-            $num++;
-        }
-
-        close $data_in;
-    }
-
-    NUM:
-
-    close $data_in if $data_in;
-}
-
-
-sub script_read_embl
-{
-    # Martin A. Hansen, August 2007.
-
-    # Read EMBL format.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( %options2, $file, $data_in, $num, $entry, $record );
-
-    map { $options2{ "keys" }{ $_ } = 1 }  @{ $options->{ "keys" } };
-    map { $options2{ "feats" }{ $_ } = 1 } @{ $options->{ "feats" } };
-    map { $options2{ "quals" }{ $_ } = 1 } @{ $options->{ "quals" } };
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) {
-        Maasha::Biopieces::put_record( $record, $out );
-    }
-
-    $num = 1;
-
-    foreach $file ( @{ $options->{ "files" } } )
-    {
-        $data_in = Maasha::Common::read_open( $file );
-
-        while ( $entry = Maasha::EMBL::get_embl_entry( $data_in ) ) 
-        {
-            $record = Maasha::EMBL::parse_embl_entry( $entry, \%options2 );
-
-            my ( $feat, $feat2, $qual, $qual_val, $record_copy );
-
-            $record_copy = dclone $record;
-
-            delete $record_copy->{ "FT" };
-
-            Maasha::Biopieces::put_record( $record_copy, $out );
-
-            delete $record_copy->{ "SEQ" };
-
-            foreach $feat ( keys %{ $record->{ "FT" } } )
-            {
-                $record_copy->{ "FEAT_TYPE" } = $feat;
-
-                foreach $feat2 ( @{ $record->{ "FT" }->{ $feat } } )
-                {
-                    foreach $qual ( keys %{ $feat2 } )
-                    {
-                        $qual_val = join "; ", @{ $feat2->{ $qual } };
-
-                        $qual =~ s/^_//;
-                        $qual = uc $qual;
-
-                        $record_copy->{ $qual } = $qual_val;
-                    }
-
-                    Maasha::Biopieces::put_record( $record_copy, $out );
-                }
-            }
-
-            goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
-            $num++;
-        }
-
-        close $data_in;
-    }
-
-    NUM:
-
-    close $data_in if $data_in;
-}
-
-
 sub script_read_stockholm
 {
     # Martin A. Hansen, August 2007.