long fasta headers break igblast parser ?

[Former user]

works: MakeDb.py igblast -o test/IG.igblast.fmt7 -s test/IG.fasta --outdir=test

does not work; index error MakeDb.py igblast -o test/IG_headerlen-gt65.igblast.fmt7 -s test/IG_headerlen-gt65.fasta --outdir=test

Actually i'm not sure what the deal is here. if you do a diff on the fmt7 files, it doesn't seem like this should be creating an issue. We use fmt3 as well and there the issue is truncation /splitting of long (>~65char) query headers by igblast, which is why i tried to break your code this way.

[Namita Gupta]

The problem with the long header is actually that it isn't in proper pRESTO header formatting. After the last pipe, the code to parse headers looks for FIELDNAME=FIELD and doesn't find that equals sign, hence the issue. If you just change the header to fit presto formatting it should work just fine...except now I see that even though I am parsing the header, the extra columns are not in the output!

[Namita Gupta]

I fixed the header parsing issue, so this should all be resolved!

[Former user]

ah! ok!