Hehe, we submitted nearly identical solutions at the same moment.
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Lars Juhl Jensen
how to keep fasta based on pattern in header.
Hi, I have a fasta file like this:
>NZ_CP012501.1 Escherichia coli strain 08-00022 plasmid pCFSAN004179G, complete sequence
GTTCTGGACGTACTGTGTCAGTGTGTCGATACCCCGGCGCATATCGACGGGTTTTACGACCAGGAATACG
TTATCAGGCGTCAGCATGGCGAAGAGCCCGGAAAACATCGGTTAACTGAGAAGGCTGGCAGCACATCCGG
ATACCTCCGGGAAGGAAAAGTGTGACAGGCTCATCCGACAATGGTCTGCCATCAGCCATACCGGGAGCGC
CAGACACTGAAACTGGAATAATTTCAGGTGCTCTGGCTCGTTTTTCGGCTTTTGCGACATCCTGCGGCCA
> mus musculus
TTTAAAAAGATATTATATATTA
> or whatever in the header
GGGGATATATTATATATATATAT
I want to keep in a multifasta only sequence belonging to coli. I tried several stuff using SeqIO or awk but it failed each time. Any idea? Thnaks!!!!
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Alex Reynolds
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yreynaud •
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yreynaud •
3 answers
awk '/^>/ {ok=index($0,"Escherichia coli");} {if(ok) print;}' in.fasta
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Pierre Lindenbaum
Thanks guys, it work perfectly!!!
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yreynaud •
You can do it with an awk one-liner if you like:
awk '/^>/{x = /Escherichia coli/;}(x)'
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Lars Juhl Jensen
Mine is smaller ;-) (Things you won't hear T say)
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Lars Juhl Jensen
:-)
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Pierre Lindenbaum
Use the record separator variable RS in awk. For example:
$ awk 'BEGIN{ RS = ">"; } { if ($0 ~ /coli/) { printf ">"$0; } }' input.fa > coli.fa
Or:
$ awk 'BEGIN{ RS = ">"; } { if ($0 ~ /mus/) { printf ">"$0; } }' input.fa > mus.fa
Etc.
If you want to automate this with a shell variable:
$ export NEEDLE="mus"
$ awk -vneedle=${NEEDLE} 'BEGIN{ RS = ">"; } { if ($0 ~ needle) { printf ">"$0; } }' input.fa > needle.fa
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Alex Reynolds
Thanks for your help !!!!!!!
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yreynaud •
You're very welcome!
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