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Reverse Complement of each coding regions

I have a fasta file which contains coding sequences as like this

>Seq1
ATGAATGACAAAATTAA
GTTATATTTAAA 
TCCTTAATAACTTACCAGAAGAGACTAATGA
CATCTCATGCCATGAAG

I need to find Reverse Complement of each line and concatenate as like this

>Seq1
TTAATTTTGTCATTCATTTTAAATATAACTCATTAGTCTCTTCTGGTAAGTTATTAAGGACTTCATGGCATGAGATG

Normally "cat fasta |tr ACGTacgt TGCAtgca | rev" will Reverse Complement but here I need to find for each CDS

sequence fasta reverse complement

How is this relevant for the original question @Pierre? OP is asking for reverse-complementing individual chunks of sequence on each line and then catting them together? It seems to be an odd/very specific request.

Complement but here I need to find for each CDS

I understand the question as :" I want to find all the ORFs in the reverse complement."

I see. You included that as final solution assuming this is done first.

I need to find Reverse Complement of each line and concatenate as like this

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