[Biopython-dev] [Bug 2496] Bio.Blast.NCBIWWW.qblast() does not support RUN_PSIBLAST option

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2496





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-05-08 07:58 EST -------
Created an attachment (id=918)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=918&action=view)
Patch to Bio/Blast/NCBIWWW.py

This seems to work, however there is another problem in the XML parser.  e.g.

from Bio.Blast.NCBIWWW import qblast
#gi|160837788|ref|NP_075631.2| actin related protein 2/3 complex, subunit 1B
sequence = \
"MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGAKWNKVHELKEHNGQVTGIDWAPESNRIVTC" \
+ "GTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNENKFAVGSGSRVISICYFEQENDWWVCKHIKKP" \
+ "IRSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCF" \
+ "SASGSRVAWVSHDSTVCLVDADKKMAVATLASETLPLLAVTFITENSLVAAGHDCFPVLFTYDNAAVTLS" \
+ "FGGRLDVPKQSSQRGMTARERFQNLDKKASSEGGAATGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGM" \
+  "DGGMSIWDVKSLESALKDLKIK"
result_handle1 = qblast('blastp', 'nr', sequence, expect=0.001)
result_handle2 = qblast('blastp', 'nr', sequence, i_thresh=0.05, expect=10,
run_psiblast="on")


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