Edit Software to change blast output

Question

[dllopezr]

Hi community

I am working with a software called SWeBLAST, which produce custom subsequences of a fasta format and blast them.

The problem is that the blast output of this program by default is the format number 8, and for my work the query cover parameter is important, so the blastn format customized by this way : 6 -outfmt "6 length mismatch gapope qcovs evalue bitscore" is the appropriate for me.

I am searching across the code of the two scripts of the program to see if this option can be change there but maybe for my poor knowledge i don't find the way.

The scripts SWeBLAST.py and SWeBLAST_parser.py are in this web page (I don't put the whole codes here because maybe could be astonishing, even when the code is not too big)

https://github.com/4ment/SWeBLAST

Could someone help me with that?

[lakhujanivijay]

Hello dllopezr

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[5heikki]

If you are doing remote queries, you could use blast_formatter with rid(s) to convert the output(s) to your desired format without changing any code (other than adding the line to deal with this). I think..