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- seq2fasta.pl script:
- use Bio::SeqIO;
- my $in = Bio::SeqIO->new (-fh => \*STDIN);
- # output in Fasta format
- my $out = Bio::SeqIO->new (-format => 'Fasta');
- while (my $seq = $in->next_seq) {
- $out->write_seq($seq);
- }
- sequence file:
- >Contig1244/1236-2383 2383 Weight: 1.02
- ACCCAGGCCAATGTATAGTGCACATACGCAAATAAGACATTATAAAAAGGTTCATCGCATACTAACATTCGGACTTGCAT
- ACAAACCTATAGCAGTGGCTAGAACAGGACCACCAGCATACTCAGATGTGTTTATGATGACTTCACTTGCACATATTCCT
- ATAGAATATCCATTCATGTATTTGAATCCATCAGAATTTGCTTTATTACCACCAGGCTCTAAAGTTAAACGTGTTTTAAG
- CAGAGTAAAAGCTGAAAAGGTTCGTGTTGCATTTCCAACTAACTCTACAGATAATAATTTGGCTACATTACATACAAACA
- GCTTCTTGAGAGTTGGAATTAATTTAAATCAAAAGATTCAATCAGTCAACGCTCAACCAGGTGGATTTGCTGCTGCTCAA
- CCTATGATAGCCACTTCTATTACACCATTTGATGCAAAAAATTATCAATTTTGGATTGATAATTTTTATGGTGTTCCAAA
- CAATGATAATAAAGATCCAGATCAATTTACAACTCAAACTCCAAGACATCAATTCGGTATACCATGGGTAGCTCAACATT
- ACTGTTGTCCAGTTTCTCAAACTAACGACCCTACTAATAGTGGATGGGAAGATTTTCAAGCTCACTTGGAAGAAATTAAA
- GTAGATGGACCTAGCGGATATATCGCTGAAATAGAATATTCACCAGCTATGGGATTATTAAAAGCACCAATTCAAGGTAT
- ATGGACTGGATTGCCTAGTGTAGCTACCCCTGGAACAGCTAGAAGCATTCCCGTAAATACTGGAGCAGGAAACACTCAAC
- ATAGAAGAATTGAAGCATCCGTGACAAATTCTCTTAATACTGGCATAACAGAAGTAACATCAAACTTTAACAGACAACCA
- ACAGCAGAAAACTTTACATTGTTAACTCCTATTGAAAAAAATCAGAGAATTTGTGCAGGAATAACTCCTGAATATTTTGC
- AAAGTCACAACCTACATTACATGTTGGAGTAATGCCAGTTCCAGCTTTAACAACATCAGCAATTGATAACGTTACAAACA
- ACAGTTCATTTACTGACGCTCAAGCATATTTTGAAATAACATGTGAAATGGAAGTAGAATGTGCTTTCCCTACACGCAGA
- GCATTAGCTACAATTGCAAAAACAACTG
- testing:
- OK
- $ seq2fasta.pl < SEQFILE
- not OK
- $ cat SEQFILE | seq2fasta.pl
- ------------- EXCEPTION: Bio::Root::Exception -------------
- MSG: Failed resetting the filehandle; IO error occurred
- STACK: Error::throw
- STACK: Bio::Root::Root::throw /home/lupey/downloads/bioperl/bioperl-live/Bio/Roo
- t/Root.pm:472
- STACK: Bio::Tools::GuessSeqFormat::guess /home/lupey/downloads/bioperl/bioperl-l
- ive/Bio/Tools/GuessSeqFormat.pm:507
- STACK: Bio::SeqIO::new /home/lupey/downloads/bioperl/bioperl-live/Bio/SeqIO.pm:3
- 75
- STACK: ./seq2fasta.pl:5
- -----------------------------------------------------------
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