Biopython NCBIXML Parsing - Field Parameter

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6.2 years ago

maximilian.mayerhofer ▴ 30

Hey,

I want to extract the

 <Iteration_query-def>

from my blast Output (outfmt 5). According to the source code ( http://biopython.org/DIST/docs/api/Bio.Blast.NCBIXML-pysrc.html) it should be something like

blast.query

But

NameError: name 'blast' is not defined

Is there a complete and up to date list what Parameter refers to ist field?

Best regards,

Max

biopython NCBIXML Parse XML • 1.5k views

ADD COMMENT • link 6.2 years ago by maximilian.mayerhofer ▴ 30

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could it be as simple as you need a B in blast? modules are case sensetive

ADD REPLY • link 6.2 years ago by Joe 21k

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Nope. Just tried that.

ADD REPLY • link 6.2 years ago by maximilian.mayerhofer ▴ 30

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I think we need to see more of your code to be any help.

ADD REPLY • link 6.2 years ago by Joe 21k

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I did a workaround. with blast_record.query , I got the line I wanted.

ADD REPLY • link 6.2 years ago by maximilian.mayerhofer ▴ 30

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