I'm trying to write a bash script to use bioperl bash command bp_fetch and return a CDS list in fasta format. I have installed bioperl and bp_fetch works as intended: xxxx@xxxx:~/Documents$ bp_fetch net::embl:AAA24658.1
AAA24658 Escherichia coli hypothetical protein ATGGAACGTTGCGGCTGGGTGAGTCAGGACCCGCTTTATATTGCCTACCATGATAATGAG TGGGGCGTGCCTGAAACTGACAGTAAAAAACTGTTCGAAATGATCTGCCTTGAAGGGCAG CAGGCTGGATTATCGTGGATCACCGTCCTCAAAAAACGCGAAAACTATCGCGCCTGCTTT CATCAGTTCGATCCGGTGAAGGTCGCAGCAATGCAGGAAGAGGATGTCGAAAGACTGGTA CAGGACGCCGGGATTATCCGCCATCGAGGGAAAATTCAGGCAATTATTGGTAATGCGCGG GCGTACCTGCAAATGGAACAGAACGGCGAACCGTTTGTCGACTTTGTCTGGTCGTTTGTA AATCATCAGCCACAGGTGACACAAGCCACAACGTTGAGCGAAATTCCCACATCTACGTCC GCCTCCGACGCCCTATCTAAGGCACTGAAAAAACGTGGTTTTAAGTTTGTCGGCACCACA ATCTGTTACTCCTTTATGCAGGCATGTGGGCTGGTGAATGATCATGTGGTTGGCTGCTGT TGCTATCCGGGAAATAAACCATGA
The problem is that i have a file with long list of acession numbers, and i'm trying to do a bash script to run "bp_fetch net::" with every line of the file (each line has an acession number) and output the list of FASTA CDS's in a txt file. I have tried something like:
for line in $file do bp_fetch net::$line
But i'm having no sucess. Can i get some help? Thanks in advance.