How To Get Fasta Source File From Blast Csv Format?

Question

[elmore.nathan]

I am currently writing a library that uses the -outfmt 10 option of Blast, which give you a CSV instead of the pretty human readable format.

Like

tblastn -db dmel_a -query somequery.faa -outfmt 10

The problem is, I want to access the db source file so I can extract some sequences after processing. The only way I know how to do this, is to use the remove -outfmt 10 and run the blast twice. Then I parse the human readable output for the line that says:

Database: Source.fas

This only works if the user does not use the title option in makeblastdb. The stitle option of outfmt 10 gives the fasta header line. I cannot just look for the database name and then a .fna, .fas, .faa because you can name the database differently than the source file.

Is there another way to extract the fasta source file from the blast database name? I do not see one in the list of outfmt options. Or am I blind today?

Answer 1

[Michael]

Not so sure, what you exactly want to do, but blastdbcmd from blast+ has the entry and entry_batch option to extract sequences. The default output format is fasta and can be controlled with -outfmt. If you want to extract only sequences with hits, then you can extract the id column from your blast output using unix cmd cut and use that as input to -entry_batch (one identifier per line).

Answer 2

[Manu Prestat]

Take a look at the blastdbcmd tool (part of the blast+ suite).