Question: tabular blast output file
0
gravatar for vmicrobio
2.7 years ago by
vmicrobio240
vmicrobio240 wrote:

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?

alignment • 1.5k views
ADD COMMENTlink modified 2.7 years ago by st.ph.n2.5k • written 2.7 years ago by vmicrobio240
3
gravatar for Jean-Karim Heriche
2.7 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche20k wrote:

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.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Jean-Karim Heriche20k
2

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

ADD REPLYlink written 2.7 years ago by genomax71k

Thanks, just found it again while you were writing.

ADD REPLYlink written 2.7 years ago by Jean-Karim Heriche20k
0
gravatar for vmicrobio
2.7 years ago by
vmicrobio240
vmicrobio240 wrote:

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?

ADD COMMENTlink written 2.7 years ago by vmicrobio240
0
gravatar for st.ph.n
2.7 years ago by
st.ph.n2.5k
Philadelphia, PA
st.ph.n2.5k wrote:

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.

ADD COMMENTlink written 2.7 years ago by st.ph.n2.5k
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