You should probably be using Bio::SeqIO from the BioPerl package. I was able to extract the sequence from your sample GenBank file.
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; my $in = Bio::SeqIO->new( -file => "sample_gb.gb" , -format => 'GenBank'); my $out = Bio::SeqIO->new( -file => '>fasta.dat', -format => 'fasta'); while ( my $seq = $in->next_seq() ) { $out->write_seq($seq); }
Contents of 'fasta.dat' were:
>NC_004905 Influenza A virus (A/Hong Kong/1073/99(H9N2)), complete gen +ome. AGCAGGGTTAATAATCACTCACTGAGTGACATCAACATCATGGCGTCGCAAGGCACCAAA CGATCCTATGAACAGATGGAAACTGGTGGAGAACGCCAGAATGCCACTGAGATCAGGGCA TCTGTTGGAAGAATGGTTGGTGGAATTGGGAGGTTTTACGTACAGATGTGCACTGAACTC AAACTCAGCGACCAAGAAGGAAGGTTGATCCAGAACAGTATAACAATAGAGAGAATGGTT CTCTCCGCATTTGATGAAAGGAGGAACAGGTACCTAGAGGAACATCCCAGTGCGGGGAAG GACCCGAAGAAGACCGGAGGTCCAATCTACCGAAGGAGAGACGGGAAATGGGTGAGAGAG CTGATTCTGTATGACAAAGAGGAGATAAGGAGAATTTGGCGTCAAGCGAACAATGGAGAA GACGCAACTGCTGGTCTCACTCATATGATGATCTGGCATTCCAACCTAAATGATGCCACA TACCAGAGAACAAGAGCCCTCGTGCGGACTGGAATGGACCCCAGAATGTGCTCTCTGATG CAAGGATCAACCCTCCCGAGGAGATCTGGAGCTGCTGGTGCAGCAATAAAGGGAGTCGGG ACAATGGTAATGGAACTAATTCGGATGATAAAGCGAGGCATTAATGACCGGAACTTCTGG AGAGGCGATAATGGACGAAGAACAAGGATTGCATATGAGAGAATGTGCAACATCCTCAAA GGGAAATTTCAAACAGCAGCACAAAGAGCAATGATGGATCAGGTGCGAGAAAGCAGAAAT CCTGGGAATGCTGAAATTGAAGATCTCATCTTTCTGGCACGGTCTGCACTCATCCTGAGA GGATCCGTAGCCCATAAGTCCTGCTTGCCTGCTTGTGTGTACGGGCTCGCTGTGGCCAGT GGATATGATTTTGAGAGGGAAGGGTACTCTCTGGTTGGGATAGATCCTTTCCGTCTGCTT CAGAACAGTCAGGTCTTCAGTCTTATTAGACCAAATGAGAATCCAGCACATAAAAGTCAA TTGGTATGGATGGCATGCCATTCTGCAGCATTTGAGGACCTGAGAGTCTCAAGTTTCATT AGAGGAACAAGAGTGATCCCAAGAGGACAACTATCCACTAGAGGAGTTCAGATTGCTTCA AATGAGAACGTGGAAGCAATGGATTCCAGCACTCTTGAACTGAGAAGCAGATATTGGGCT ATAAGGACCAGGAGTGGAGGAAACACCAATCAACAGAGAGCATCTGCAGGACAAATCAGT GTACAGCCCACTTTCTCAGTACAGAGAAATCTTCCCTTCGAAAGACCGACCATTATGGCT GCGTTTAAGGGGAATACCGAGGGCAGAACATCTGACATGAGGACTGAAATCATAAGGATG ATGGAAAGTGCCAGACCAGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAGCTCTCG GACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGATCTTAT TTCTTCGGAGACAATGCAGAGGAATATGACAATTGAGGAAAAATACCCTTGTTTCTA

In reply to Re: Extracting field information from a GenBank file. by Cristoforo
in thread Extracting field information from a GenBank file. by Anonymous Monk

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