[Bioperl-l] StandAloneBlast.pm, bl2seq() and tempfiles on Win32/cygwin

Brian Osborne brian_osborne at cognia.com
Tue Feb 24 10:22:13 EST 2004


Because he's using the BLAST Win binaries which don't understand Cygwin

Meaning these work:

blastall -i test.fa -d testdb.fa -p blastn

blastall -i e:/cygwin/home/bosborne/test.fa -d test.fa -p blastn

But this doesn't:

blastall -i /home/bosborne/test.fa -d test.fa -p blastn


Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Aaron J. Mackey
Sent: Monday, February 23, 2004 4:11 PM
To: Bioperl list
Cc: Sushma Parankush Das
Subject: [Bioperl-l] StandAloneBlast.pm,bl2seq() and tempfiles on

A colleague of mine is frustrated by attempting to use
Bio::Tools::Run::StandAloneBlast to run bl2seq (Perl 5.8.2, bioperl
1.4, windows XP, CygWin, etc.):

# synopsis:
$seq1 = $seqio->next_seq;
$seq2 = $seqio->next_seq;
$factory->bl2seq($seq1, $seq2);

StandAloneBlast successfully writes two temp files in /tmp, which have
the sequence data and can be read by "less" or "cat" in another open
window (with the main program suspended in debugger); however, if
either the program code or I at the command line attempt to run bl2seq,
it dies with "Cannot open file /tmp/7aasd78asd".  If I "cp" the temp
files into new files, it runs fine.  Or, if I call
$factory->bl2seq($file1, $file2) with filenames instead of seq objects,
it also works fine.  I have tried various incarnations of closing the
filehandles and Bio::SeqIO objects that StandAloneBlast.pm is using to
generate these temp files, but to no avail (and of course, the
tempfiles disappear upon program completion).

This is not the "failed to open tempfile; too many files open" error
seen previously, and I also expect a fair number of "works for me"
responses - please save your breath.

Thanks for any input,


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