Extracting fasta file according to Ids
Hello,
I have a huge Fasta file. I would like to extract all the sequences with id such that the ids start from NM?
I tried following two commands which did not work for me.
awk‘BEGIN{RS=”>”}/NM/{print“>”$0}’huge.fasta
grep '^>NM' -B 1 huge.fasta > Nm.fasta
Could someone help me with a better solution. thank you in advance.
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James Ashmore
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KVC_bioinfo
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KVC_bioinfo
1 answer
Index your FASTA file:
samtools faidx input.fasta
Then get ids which start with "NM" and pipe them into samtools faidx to retrieve only those sequences:
cut -f 1 input.fasta.fai | egrep "^NM" | xargs samtools faidx input.fasta > result.fasta
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is your huge fasta a multi-line fasta or single line fasta?
multi-line fasta file
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