tabular blast output file

Question

[vmicrobio]

Hi all!

I'm doing local blasts on contigs and I'm looking for results with a tabular output. I have already tried -outfmt with 6, 7 or 10, playing with different output format options. However I'm looking for something like this (obtained with blastn -query inputContigs.fasta -db nt -task blastn > output.txt) but with tabulation between references/organisms/bits/evalues:

Query= ha-1_denovo_c1    cov=5.25 len=454 gc=23.79
nseq=16

Length=454
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

gb|AC270265.1|  Homo sapiens chromosome 8 clone CH17-194A21, comp...  57.2    3e-04
gb|KP249663.1|  Eucommia ulmoides microsatellite EU-IV43S4101EQ75...  57.2    3e-04
ref|XM_010093073.1|  Morus notabilis Ethylene-responsive transcri...  57.2    3e-04
emb|LL711914.1|  Elaeophora elaphi genome assembly E_elaphi ,scaf...  57.2    3e-04

Does anybody knows how to solve my problem?

Answer 1

[Jean-Karim Heriche]

I am not sure I get what you're trying to achieve but it may be that what you're missing is simply the custom formatting option for the tabular output. Have a look at blastn -help. Alternatively, you can try the xml output and reformat it to tabular output using XSLT

Edit: (there was a previous post on this but I can't seem to find it). here is Pierre Lindenbaum's post with his blast2tsv stylesheet.

[GenoMax]

This post A: Blast+ results file parsing to fasta file ?

[Jean-Karim Heriche]

Thanks, just found it again while you were writing.

Answer 2

[vmicrobio]

Thank you for your answer, it works either with blast2tsv.xsl or blast_xml_parse.py!

However, it stops when my file is too big. So I split my files. I was also thinking about filtering my input file, something like grep -e Homo -e Query= file.txt > filt_file.txt It works with my original input file but not with xml. How can I filter such a file?

Answer 3

[st.ph.n]

You can do -outfmt 6, then on the command-line do cut -f 1,2,11,12 output.txt > output2.txt to get the query, subject, e-val, and bit score columns.