X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fformat_genome;h=9b3e4fe81790b7ea159efaad477bb5d87922dbad;hb=2f0fd91b461033529a4a72e161bd133252a22eb6;hp=9fbdcb859d7e1f93be37fd1ca9a6a5aff2b9b026;hpb=1f203b5788a335b1e17f540fa52709ac63c35520;p=biopieces.git

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
index 9fbdcb8..9b3e4fe 100755
--- a/bp_bin/format_genome
+++ b/bp_bin/format_genome
@@ -30,6 +30,8 @@ use warnings;
 use strict;
 use Maasha::Fasta;
 use Maasha::Biopieces;
+use Maasha::Bowtie;
+use Maasha::BWA;
 use Maasha::NCBI;
 use Maasha::Match;
 use Maasha::UCSC;
@@ -43,7 +45,7 @@ my ( $default, $formats, $options, $in, $out, $record, $data_out, $entry,
 
 $tmp_dir = Maasha::Biopieces::get_tmpdir();
 $default = $ENV{ 'BP_DATA' };
-$formats = 'fasta,blast,vmatch,bowtie,phastcons';
+$formats = 'fasta,blast,vmatch,bowtie,bwa,phastcons';
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -63,7 +65,7 @@ $genome = $options->{ 'genome' };
 Maasha::Filesys::dir_create_if_not_exists( "$dir/genomes" );
 Maasha::Filesys::dir_create_if_not_exists( "$dir/genomes/$genome" );
 
-if ( grep { $_ =~ /fasta|blast|vmatch|bowtie/i } @{ $options->{ "formats" } } )
+if ( grep { $_ =~ /fasta|blast|vmatch|bowtie|bwa/i } @{ $options->{ "formats" } } )
 {
     if ( -f "$dir/genomes/$genome/fasta/$genome.fna" )
     {
@@ -93,7 +95,7 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     {
         Maasha::Fasta::put_entry( $entry, $fh_out );
     }
-    elsif ( $fh_out and $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "STEP" } and $record->{ "VALS" } )
+    elsif ( $fh_out and $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "STEP" } and $record->{ "VALS" } )  # TODO: clean this!
     {
         print $fh_out "fixedStep chrom=$record->{ 'CHR' } start=$record->{ 'CHR_BEG' } step=$record->{ 'STEP' }\n";
 
@@ -107,47 +109,27 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
 }
 
+close $fh_out if $fh_out;
+
 foreach $format ( @{ $options->{ 'formats' } } )
 {
-    if    ( $format =~ /^fasta$/i )     { Maasha::Fasta::fasta_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/fasta/$genome.index" ) }
+    print STDERR qq(Creating format: $format for $genome ... ) if $options->{ 'verbose' };
+
+    if    ( $format =~ /^fasta$/i )     { Maasha::Fasta::fasta_index( "$fasta_dir/$genome.fna", $fasta_dir, "$genome.index" ) }
     elsif ( $format =~ /^blast$/i )     { Maasha::NCBI::blast_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/blast", "dna", $genome ) }
-    elsif ( $format =~ /^blat$/i )      { warn "BLAT FORMAT NOT IMPLEMENTED" }
+    elsif ( $format =~ /^blat$/i )      { warn "BLAT FORMAT NOT IMPLEMENTED\n" }
     elsif ( $format =~ /^vmatch$/i )    { Maasha::Match::vmatch_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/vmatch", $tmp_dir ) }
-    elsif ( $format =~ /^bowtie$/i )    { bowtie_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bowtie", $genome, $options->{ 'verbose' } ) }
+    elsif ( $format =~ /^bowtie$/i )    { Maasha::Bowtie::bowtie_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bowtie", $genome, $options->{ 'verbose' } ) }
+    elsif ( $format =~ /^bwa$/i )       { Maasha::BWA::bwa_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bwa", $genome, $options->{ 'verbose' } ) }
     elsif ( $format =~ /^phastcons$/i ) { Maasha::UCSC::phastcons_index( "$genome.pp", $phastcons_dir ) }
-}
 
-close $fh_out if $fh_out;
+    print STDERR qq(done.\n) if $options->{ 'verbose' };
+}
 
 Maasha::Biopieces::close_stream( $in );
 Maasha::Biopieces::close_stream( $out );
 
 
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-sub bowtie_index
-{
-    # Martin A. Hansen, July 2009.
-    
-    # Create a bowtie index for fast sequence mapping.
-
-    my ( $src_file,   # filename of source file
-         $dst_dir,    # destination dir to store index
-         $base_name,  # base name of index
-         $verbose,    # verbose flag
-       ) = @_;
-
-    Maasha::Filesys::dir_create_if_not_exists( $dst_dir );
-
-    if ( $verbose ) {
-        Maasha::Common::run( "bowtie-build", "$src_file $dst_dir/$base_name" );
-    } else {
-        Maasha::Common::run( "bowtie-build", "$src_file $dst_dir/$base_name > /dev/null 2>&1" );
-    }
-}
-
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<