parsing tabular blast output
Hello to all!
I have seen that Biopython recommend xml output to parse blast file. I need however to do my blast in -outfmt 7
How to parse my file having a tabular output? What I want is to associate queries (end of line) to each organism hits: input
Query= R1_sam10_filt_denovo_18-02-17_c1 cov=4.55 len=204 gc=41.67 nseq=6
ref|XR_001550329.1| PREDICTED: Oryza brachyantha beta-glucosidas... 53.6 0.002
ref|XR_001550328.1| PREDICTED: Oryza brachyantha beta-glucosidas... 53.6 0.002
ref|XM_006654251.2| PREDICTED: Oryza brachyantha beta-glucosidas... 53.6 0.002
ref|XM_006654251.1| PREDICTED: Oryza brachyantha beta-glucosidas... 53.6 0.002
emb|LN590686.1| Cyprinus carpio genome assembly common carp geno... 48.2 0.064
Query= R1_sam10_filt_denovo_18-02-17_c2 cov=4.54 len=198 gc=52.78 nseq=6
emb|LN590686.1| Cyprinus carpio genome assembly common carp geno... 48.2 0.064
output
emb|LN590686.1| Cyprinus carpio genome assembly common carp geno... c1 c2
ref|XR_001550329.1| PREDICTED: Oryza brachyantha beta-glucosidas... c1
Thanks for your answers!
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Pierre Lindenbaum
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nh75 •
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nh75 •
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not the output you asked (but anyway, this is a bad output :-) )
$ awk '/^Query=/ {n=split($2,a,/_/);Q=a[n];next;} {print $1,$2, Q;} ' input.blast
ref|XR_001550329.1| PREDICTED: c1
ref|XR_001550328.1| PREDICTED: c1
ref|XM_006654251.2| PREDICTED: c1
ref|XM_006654251.1| PREDICTED: c1
emb|LN590686.1| Cyprinus c1
emb|LN590686.1| Cyprinus c2
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Pierre Lindenbaum
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Pierre Lindenbaum
ok with groupby
bedtools groupby -i output.txt -grp 1 -c 2 -o collapse
what will be the command in awk?
other question related to the output file :
- how to have tabulation between fields?
- how to print query information (cov=4.55 len=204 gc=41.67 nseq=6) into a new file?
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