v0.21

lskatz · Jul 19, 2017 · e426b4e · e426b4e
1 parent 909752f
commit e426b4e
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Showing 2 changed files with 14 additions and 7 deletions.
diff --git a/bin/mashtree.pl b/bin/mashtree.pl
@@ -18,7 +18,7 @@
 
 use FindBin;
 use lib "$FindBin::RealBin/../lib";
-use Mashtree qw/logmsg @fastqExt @fastaExt @richseqExt _truncateFilename createTreeFromPhylip $MASHTREE_VERSION/;
+use Mashtree qw/logmsg @fastqExt @fastaExt @mshExt @richseqExt _truncateFilename createTreeFromPhylip $MASHTREE_VERSION/;
 use Mashtree::Db;
 use Bio::Tree::DistanceFactory;
 use Bio::Matrix::IO;
@@ -156,7 +156,7 @@ sub mashSketch{
   my @msh;
   # $fastq is a misnomer: it could be any kind of accepted sequence file
   for my $fastq(@$genomeArr){
-    my($fileName,$filePath,$fileExt)=fileparse($fastq,@fastqExt,@fastaExt,@richseqExt);
+    my($fileName,$filePath,$fileExt)=fileparse($fastq,@fastqExt,@fastaExt,@richseqExt,@mshExt);
 
     # Unzip the file. This temporary file will
     # only exist if the correct extensions are detected.
@@ -179,7 +179,7 @@ sub mashSketch{
 
     if($was_unzipped){
       $fastq=$unzipped;
-      ($fileName,$filePath,$fileExt)=fileparse($fastq,@fastqExt,@fastaExt,@richseqExt);
+      ($fileName,$filePath,$fileExt)=fileparse($fastq,@fastqExt,@fastaExt,@richseqExt,@mshExt);
     }
 
     # If we see a richseq (e.g., gbk or embl), then convert it to fasta
@@ -213,17 +213,23 @@ sub mashSketch{
       $sketchXopts.="-m $minDepth -g $$settings{genomesize} ";
     } elsif(grep {$_ eq $fileExt} @fastaExt) {
       $sketchXopts.=" ";
+    } elsif(grep {$_ eq $fileExt} @mshExt){
+      $sketchXopts.=" ";
     } else {
       logmsg "WARNING: I could not understand what kind of file this is by its extension ($fileExt): $fastq";
     }
 
-    my $outPrefix="$sketchDir/".basename($fastq);
+    my $outPrefix="$sketchDir/".basename($fastq, @mshExt);
 
     # See if the user already mashed this file locally
     if(-e "$fastq.msh"){
       logmsg "Found locally mashed file $fastq.msh. I will use it.";
       copy("$fastq.msh","$outPrefix.msh");
     }
+    if(grep {$_ eq $fileExt} @mshExt){
+      logmsg "Input file is a sketch file itself and will be used as such: $fastq";
+      copy($fastq, "$outPrefix.msh");
+    }
 
     if(-e "$outPrefix.msh"){
       logmsg "WARNING: ".basename($fastq)." was already mashed.";

diff --git a/lib/Mashtree.pm b/lib/Mashtree.pm
@@ -15,7 +15,7 @@ use Bio::Matrix::IO;
 
 our @EXPORT_OK = qw(
            logmsg openFastq _truncateFilename distancesToPhylip createTreeFromPhylip sortNames
-           @fastqExt @fastaExt @bamExt @vcfExt @richseqExt
+           @fastqExt @fastaExt @bamExt @vcfExt @richseqExt @mshExt
            $MASHTREE_VERSION
          );
 
@@ -24,12 +24,13 @@ local $0=basename $0;
 ######
 # CONSTANTS
 
-our $VERSION = "0.20";
+our $VERSION = "0.21";
 our $MASHTREE_VERSION=$VERSION;
 our @fastqExt=qw(.fastq.gz .fastq .fq .fq.gz);
-our @fastaExt=qw(.fasta .fna .faa .mfa .fas .fa);
+our @fastaExt=qw(.fasta .fna .faa .mfa .fas .fsa .fa);
 our @bamExt=qw(.sorted.bam .bam);
 our @vcfExt=qw(.vcf.gz .vcf);
+our @mshExt=qw(.msh);
 # Richseq extensions were obtained mostly from bioperl under
 # the genbank, embl, and swissprot entries, under
 # the source for Bio::SeqIO