This post A: Blast+ results file parsing to fasta file ?
tabular blast output file
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?
3 answers
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.
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Jean-Karim Heriche
Thanks, just found it again while you were writing.
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Jean-Karim Heriche
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?
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