Extract header from fasta file
Hello, How can I extract the id from the Orffinder fasta file result?
>lcl|ORF2_TRINITY_DN74698_c0_g1_i1:302:0 unnamed protein product, partial
MRIRSVVFTLRPRAKWMAPSSGMRLLLMFRSSSVLLCLSASSRATAPSLPRPLYDKSRVRKKIFPSRPLAAMAPFPRMQFQARLSDFIPAFSAIAAPRIS
I need to extract the id like this, Kindly let me know.
>TRINITY_DN74698_c0_g1_i1
2 answers
A seqkit answer. You may need to tweak the regex depending on the variability in the naming scheme.
seqkit replace -p ".*ORF\d+_([^:]+).*" -r "\$1" test.fasta
>TRINITY_DN74698_c0_g1_i1
MRIRSVVFTLRPRAKWMAPSSGMRLLLMFRSSSVLLCLSASSRATAPSLPRPLYDKSRVR
KKIFPSRPLAAMAPFPRMQFQARLSDFIPAFSAIAAPRIS
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$ awk -F "_|:" -v OFS="_" '/^>/{print ">"$2,$3,$4,$5,$6};!/>/' test.fa
>TRINITY_DN74698_c0_g1_i1
MRIRSVVFTLRPRAKWMAPSSGMRLLLMFRSSSVLLCLSASSRATAPSLPRPLYDKSRVRKKIFPSRPLAAMAPFPRMQFQARLSDFIPAFSAIAAP
$ sed -r '/^>/ s/.*ORF2_/>/;s/:.*//' test.fa
>TRINITY_DN74698_c0_g1_i1
MRIRSVVFTLRPRAKWMAPSSGMRLLLMFRSSSVLLCLSASSRATAPSLPRPLYDKSRVRKKIFPSRPLAAMAPFPRMQFQARLSDFIPAFSAIAAP
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