in reply to Re^3: Command or Perl script for changing headers of multiple FASTA files in a specific order listed in a txt file
in thread Command or Perl script for changing headers of multiple FASTA files in a specific order listed in a txt file

The mapping of names in Headers.txt and the FASTA files can work. 

 Chimpanzee_AMY2B_CDS.fasta                 MP.C_AMY2B
Human_AMY2B_CDS.fasta                      FP.H_AMY2B

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Following solution worked for my problem.

create a folder called test (in the same folder where fasta files are located) and run the command:

$ mkdir test

execute:

 for i in $(seq 1 $(ls *.fasta |wc -l)); do sed -n "$i"p headers.txt| sed 's/^/>/'> test/$(ls *.fasta| sed -n "$i"p); cat $(ls *.fasta| sed -n "$i"p)| sed '1d' >>test/$(ls *.fasta| sed -n "$i"p); done

Cheers.. :)

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