From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 23 Jul 2009 11:42:25 +0000 (+0000)
Subject: added verbose stuff to format_genome
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=034eccf0eb61729674184cd5898b11041a626e15;p=biopieces.git

added verbose stuff to format_genome

git-svn-id: http://biopieces.googlecode.com/svn/trunk@582 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
index 9fbdcb8..9972bf5 100755
--- a/bp_bin/format_genome
+++ b/bp_bin/format_genome
@@ -109,12 +109,16 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
 foreach $format ( @{ $options->{ 'formats' } } )
 {
+    print STDERR qq(Creating format: $format for $genome ... ) if $options->{ 'verbose' };
+
     if    ( $format =~ /^fasta$/i )     { Maasha::Fasta::fasta_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/fasta/$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 ( $format =~ /^vmatch$/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 ( $format =~ /^phastcons$/i ) { Maasha::UCSC::phastcons_index( "$genome.pp", $phastcons_dir ) }
+
+    print STDERR qq(done.\n) if $options->{ 'verbose' };
 }
 
 close $fh_out if $fh_out;