X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fget_genome_seq;h=e219c5188a993fd54e0af1b2c363abbb45ba9720;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=5292b72f58efe1f98933e11b19a44d5c7e3a4193;hpb=5aed4676ad1bf35abbade6215ac90ee591e6d8fe;p=biopieces.git

diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
index 5292b72..e219c51 100755
--- a/bp_bin/get_genome_seq
+++ b/bp_bin/get_genome_seq
@@ -26,9 +26,12 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
+use Data::Dumper;
 use Maasha::Biopieces;
 use Maasha::Filesys;
+use Maasha::Fasta;
 use Maasha::Seq;
 
 
@@ -36,7 +39,7 @@ use Maasha::Seq;
 
 
 my ( $options, $in, $out, $record, $genome_file, $index_file, $fh, $genome,
-     $beg, $end, $len, $index_beg, $index_len, @begs, @lens, $index, $seq, $i, %lookup_hash );
+     $beg, $end, $len, $index_beg, $index_len, @begs, @lens, $index, $seq, $i );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -64,13 +67,9 @@ if ( $options->{ "genome" } )
     $fh          = Maasha::Filesys::file_read_open( $genome_file );
     $index       = Maasha::Fasta::index_retrieve( $index_file );
 
-    shift @{ $index }; # Get rid of the file size info
-
-    map { $lookup_hash{ $_->[ 0 ] } = [ $_->[ 1 ], $_->[ 2 ] ] } @{ $index };
-
-    if ( defined $options->{ "chr" } and exists $lookup_hash{ $options->{ "chr" } } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
+    if ( defined $options->{ "chr" } and exists $index->{ $options->{ "chr" } } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
     {
-        ( $index_beg, $index_len ) = @{ $lookup_hash{ $options->{ "chr" } } };
+        ( $index_beg, $index_len ) = @{ $index->{ $options->{ "chr" } } };
 
         $beg = $index_beg + $options->{ "beg" } - 1;
 
@@ -89,7 +88,9 @@ if ( $options->{ "genome" } )
             $beg = $index_beg;
         }
 
-        $len = $index_beg + $index_len - $beg if $beg + $len > $index_beg + $index_len;
+        if ( $beg + $len > $index_beg + $index_len ) {
+            $len = $index_beg + $index_len - $beg;
+        }
 
         next if $beg > $index_beg + $index_len;
 
@@ -108,30 +109,30 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 {
     if ( $options->{ "genome" } and not $record->{ "SEQ" } )
     {
-        if ( $record->{ "REC_TYPE" } eq "BED" and exists $lookup_hash{ $record->{ "CHR" } } )
+        if ( $record->{ "REC_TYPE" } eq "BED" and exists $index->{ $record->{ "CHR" } } )
         {
-            ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "CHR" } } };
+            ( $index_beg, $index_len ) = @{ $index->{ $record->{ "CHR" } } };
         
             $beg = $record->{ "CHR_BEG" } + $index_beg;
             $len = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
         }
-        elsif ( $record->{ "REC_TYPE" } eq "PSL" and exists $lookup_hash{ $record->{ "S_ID" } } )
+        elsif ( $record->{ "REC_TYPE" } eq "PSL" and exists $index->{ $record->{ "S_ID" } } )
         {
-            ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "S_ID" } } };
+            ( $index_beg, $index_len ) = @{ $index->{ $record->{ "S_ID" } } };
         
             $beg = $record->{ "S_BEG" } + $index_beg;
             $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
         }
-        elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and exists $lookup_hash{ $record->{ "S_ID" } } )
+        elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and exists $index->{ $record->{ "S_ID" } } )
         {
-            ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "S_ID" } } };
+            ( $index_beg, $index_len ) = @{ $index->{ $record->{ "S_ID" } } };
         
             $beg = $record->{ "S_BEG" } + $index_beg;
             $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
         }
-        elsif ( $record->{ "REC_TYPE" } eq "BLAST" and exists $lookup_hash{ $record->{ "S_ID" } } )
+        elsif ( $record->{ "REC_TYPE" } eq "BLAST" and exists $index->{ $record->{ "S_ID" } } )
         {
-            ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "S_ID" } } };
+            ( $index_beg, $index_len ) = @{ $index->{ $record->{ "S_ID" } } };
         
             $beg = $record->{ "S_BEG" } + $index_beg;
             $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;