Generate hashes for all sequences in a FASTA file
Hello!
I am working on novel transcripts assembled from RNA-Seq data, using Stringtie. However, since stringtie "MSTRG" ids are poorly conserved across runs, I wanted to implement a strategy that converts all transcript sequences in a FASTA file to a sequence-specific hash, which can then be used as part of the header for identification of the transcripts. Any and all help is appreciated.
Thanks!
1 answer
linearize, get the md5sum for each sequence.
cat input.fasta | awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' | while read T S ; do echo -e "${T}" | cut -c2- | tr "\n" "\t" && echo -n "${S}" | md5sum ; done | sed 's/ -$//'
gi|27592135 45fd3018a37826799cf5ceb93189e62e
gi|13675786 51e96c6ff43eb067a0204ce2f82e9d92
gi|13675777 5a4679ce61c2e2110a7f9bec1084e65b
gi|84131965 71fcfc75699ccf252e0ce65e434a1c24
gi|66260449 6b148daa7379b2822ca3ef9455b78bc6
gi|33609016 71034abc928ac29402bc33d724b431bc
(....)
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Pierre Lindenbaum
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