[BioPython] Blastall problem w/ restrict_gi

[Roger Barrette]

Thanks for the suggestions Peter.  Once I changed the format of the command
to call the restrict_gi with the \\, it worked fine.  Thanks.

-Roger


On 6/13/07, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> Roger Barrette wrote:
> > Hi Peter,
> >
> > Thank you for the response.  In regards to your questions, I am using
> Python
> > 2.5 w/ biopython v1.43, on a Windows platform (XP).  The specific
> problem I
> > am having occurs when I attempt to run the blastall command from Python
> > through the NCBIStandalone module.  If I run the blastall without the
> > "restrict_gi" option, it gives me  alignment results in the .xml
> > file.  However, when I include the "restrict_gi" option, I get an empty
> .xml
> > result file.  As per your suggestion however, the error file does list
> an
> > error.  The output of this .err file is:
> >
> > [NULL_Caption] ERROR: gi|90968860|gb|DQ443515.1|: Unable to open file
> > .\/BLAST/DATAout/A10241.txt
>
> That is interesting - it tells us that the argument is at least getting
> passed to the blast program (and explains why there is no XML output).
>
> That path is an odd mixture of Unix and Windows style paths, which I
> wouldn't expect to work.
>
> Could you try using \BLAST\DATAout\A10241.txt or
> C:\BLAST\DATAout\A10241.txt instead (both from within Python and from
> the command line).
>
> Remember that slashes are escape characters in python so use either
> r"C:\BLAST\DATAout\A10241.txt" or "C:\\BLAST\\DATAout\\A10241.txt".
>
> > This is odd because when I run the command from the c:\ prompt:
> >  c:\>/BLAST/blastall.exe -p tblastx -d /BLAST/DATAout/VirDBX -i
> > /BLAST/sequencesXX.fasta -m 7 -l .\/BLAST/DATAout/A10241.txt
> >
> > ;it works fine, and I get the alignment results, and no error.
>
> I'm a little surprised that does work to be honest.
>
> I suspect this is something subtle to do with how command line programs
> break up the arguments (which is complicated by quotes and slashes - at
> least you have no spaces in the filenames!).
>
> Note some of ways of getting python to make a system call pass the
> arguments as a long string (as if typed by the user at the command
> prompt) while others are already broken down into the individual terms.
>
> > Because I do not get any results in the xml file when I get this error,
> > running the blast from the python script,  there is nothing to parse,
> > however, when I run the script without the "restrict_gi" option, from
> either
> > the command prompt or my python script, I get results in the xml file,
> and
> > they are able to be parsed.  Any suggestions as to how to fix this
> problem
> > would be greatly appreciated.  Thanks
>
> Fingers crossed using Windows style absolute paths fixes this for you...
>
> Peter
>
>