how to use BlastTextParser

Question

[Kurban]

Hello everybody,

Is there anyone have ever used BlastTextParser before?

I have a blastx output file which is still pretty big (after I have filtered out no hit results from it by using Mr.@RamRS script). Several days ago he also recommend try the parser which could help me to simplify my following work. then I have sent some time to find some information about how to use that module, but still came up with nothing.

So if there is any one here have used that before,cloud u give me some information about how it (as simple as possible)? I am a true rookie.

Thank you

Answer 1

[Michael]

Please see the documentation of http://biopython.org/DIST/docs/api/Bio.SearchIO-module.html

As for other Bio* implementations (perl, java) this parser is not to be invoked directly, instead you need to specify the format as an argument to the constructor (e.g. 'blast-xml', 'blast-text', 'blast-tab'). Use the example code provided in the documentation of Bio.SearchIO

General comment: Next time you run a blastjob, use output format 11 (asn1). After that you can convert the output to any other blast output format including tabular and standard text format using blast_formatter using a single command. This is the only way I know to enable conversion to any other output format using existing code, except for combining BioPerl (supports most formats except binary and writing XML) and BioPython (supports less formats than bioperl but writes XML).