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how to discard same hypothetical protein in 300 strains protein file

Hi, i have almost 990798 hypothetical protein across 300 strains, so my question is how i can remove duplicates from it ? Actually i have try to sort but it gave same number because header is different that's why i think it consider all hypothetical header unique but their sequence must be same for few protein in two different strains.

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Thank you!

annotation fasta
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written by Neel • Neel

Are you interested in removing sequences that have hypothetical word in header or actually sequences that are duplicates (irrespective of what they say in the header).

For first case, you can do (Pierrer's fasta code)

$ awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' your.fa | grep -v "hypothetical" | tr "\t" "\n" | fold -w 80 > clean.fa

for latter, you will need to use a program like cd-hit that actually looks at the sequence.

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written by GenoMax GenoMax

Thank you so much for your reply, actually i want to remove duplicates sequences.

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written by Neel • Neel

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