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Merge pull request #15 from adsj/master

Supply TEMPLATE and SUFFIX for temporary query sequence files.
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commit dc0a3a529af588b381501aabce77457ceb262d46 2 parents 4bf5e9b + a191cfa
@cjfields cjfields authored
Showing with 4 additions and 4 deletions.
  1. +4 −4 lib/Bio/Tools/Run/StandAloneBlast.pm
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8 lib/Bio/Tools/Run/StandAloneBlast.pm
@@ -477,7 +477,7 @@ sub _setinput {
# $input may be an array of BioSeq objects...
if (ref($input1) =~ /ARRAY/i ) {
- ($fh,$infilename1) = $self->io->tempfile();
+ ($fh,$infilename1) = $self->io->tempfile(TEMPLATE=>'blastquery-XXXXXX', SUFFIX=>'.fasta');
$temp = Bio::SeqIO->new(-fh=> $fh, -format => 'fasta');
foreach $seq (@$input1) {
unless ($seq->isa("Bio::PrimarySeqI")) {return 0;}
@@ -491,7 +491,7 @@ sub _setinput {
# $input may be a single BioSeq object...
elsif ($input1->isa("Bio::PrimarySeqI")) {
- ($fh,$infilename1) = $self->io->tempfile();
+ ($fh,$infilename1) = $self->io->tempfile(TEMPLATE=>'blastquery-XXXXXX', SUFFIX=>'.fasta');
# just in case $input1 is taken from an alignment and has spaces (ie
# deletions) indicated within it, we have to remove them - otherwise
@@ -517,7 +517,7 @@ sub _setinput {
last SWITCH2;
}
if ($input2->isa("Bio::PrimarySeqI") && $executable eq 'bl2seq' ) {
- ($fh,$infilename2) = $self->io->tempfile();
+ ($fh,$infilename2) = $self->io->tempfile(TEMPLATE=>'blastquery-XXXXXX', SUFFIX=>'.fasta');
$temp = Bio::SeqIO->new(-fh=> $fh, '-format' => 'Fasta');
$temp->write_seq($input2);
@@ -529,7 +529,7 @@ sub _setinput {
# Option for using psiblast's pre-alignment "jumpstart" feature
elsif ($input2->isa("Bio::SimpleAlign") && $executable eq 'blastpgp' ) {
# a bit of a lie since it won't be a fasta file
- ($fh,$infilename2) = $self->io->tempfile();
+ ($fh,$infilename2) = $self->io->tempfile(TEMPLATE=>'blastquery-XXXXXX', SUFFIX=>'.fasta');
# first we retrieve the "mask" that determines which residues should
# by scored according to their position and which should be scored
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