Question: (Closed) Converting Blast CSV or TSV output to regular pairwise output
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gravatar for novice
4.6 years ago by
novice970
United States
novice970 wrote:

How can I convert one format of Blast output to another? I wrote a couple of scripts to manipulate and filter the Blast TSV output according to what I need. Now I'd like to turn this output into pairwise hits (Blast's default output). Blast includes a tool called blast_formatter takes an archive format and converts into any format. Is there a similar tool out there that allows me to specify the input format? 

blast csv • 1.4k views
ADD COMMENTlink written 4.6 years ago by novice970

it sounds like "I want to create a cow from a steak". You'd better re-run your blast queries.

ADD REPLYlink written 4.6 years ago by Pierre Lindenbaum129k

That is not possible. The tabular format is a dead end because it contains less information than ASN1, default text and XML format. You'd be better of using ASN1 format all the time. Otherwise BioPerl and BioPython can convert between most blast formats.

ADD REPLYlink written 4.6 years ago by Michael Dondrup47k

Hello rajeha!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 4.6 years ago by Michael Dondrup47k
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