Question

Invalid Api For Biopython'S Blast?

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12.5 years ago

Jesse J ▴ 150

According to BioPython's API, Bio.Blast.NCBIWWW.qblast() should have a parameter of specifying megablast to be true or false. When I set my qblast as

result_handle = NCBIWWW.qblast("blastn", "nr", fasta_string, megablast=True)

then I get the error of

TypeError: qblast() got an unexpected keyword argument 'megablast'

What gives? Am I doing something wrong, or does BioPython not actually have that option?

biopython • 2.4k views

ADD COMMENT • link updated 12.5 years ago by Peter 6.0k • written 12.5 years ago by Jesse J ▴ 150

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Are you using the latest version of Biopython?

ADD REPLY • link 12.5 years ago by Niek De Klein ★ 2.6k

score 4 · Answer 1 · 2011-10-12

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12.5 years ago

Peter 6.0k

The megablast argument was added to the qblast function in October 2010, so you need at least Biopython 1.56 which was released in November 2010. Please upgrade, the current release is Biopython 1.58 released August 2011.

ADD COMMENT • link 12.5 years ago by Peter 6.0k

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Huh...turns out I do have an older version. Which is weird considering I installed Biopython only a few weeks ago.

ADD REPLY • link 12.5 years ago by Jesse J ▴ 150

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If you got it on Linux via the distribution's package manager, they often don't have the latest release.

ADD REPLY • link 12.5 years ago by Peter 6.0k