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  • Extract sequences from fasta in Windows

    Hello everyone,
    I'm a very beginner at bioinformatics and I got a terrible score in a programming exam while I was an undergrad...

    I've been trying to extract some sequences from large fasta file using the script below;
    (source: https://www.biostars.org/p/1195/ )

    #!/usr/bin/perl

    use Bio::Perl;
    use Bio::SeqIO;
    use IO::String;
    use Bio::SearchIO;

    #you can input you genes' name in the array or read it from other files.

    my @genes_name=qw(FGSG_01562 FGSG_02646 FGSG_05604 FGSG_05896 FGSG_06871 FGSG_07409 FGSG_07952 FGSG_08962 FGSG_09852 FGSG_09945 FGSG_10286 FGSG_11792);

    my $filename='fusarium_graminearum_3_proteins.fasta';

    my $gb = Bio::SeqIO->new(-file => "<$filename",
    -format => "fasta");
    my $fa = Bio::SeqIO->new(-file => ">gball.fa",
    -format => "fasta",
    -flush => 0); # go as fast as we can!

    while($seq = $gb->next_seq) {

    #Sorry! Here would be with problem, if we use this "if (grep {$_=$seq->id} @genes_name;"

    $fa->write_seq($seq) if (grep {$_ eq $seq->id} @genes_name);

    }
    It just creates a 0 KB empty file "xxx.fa (gball.fa in this example)".

    I'm working on Windows so I changed the "#!/usr/bin/perl" part but it didn't work.

    Actually the name of my contigs are little long, like

    IonXpressRNA_001.R_2014_06_11_02_20_24_user_xx--58-20140610 (single) trimmed contig 10001
    IonXpressRNA_001.R_2014_06_11_02_20_24_user_xx--58-20140610 (single) trimmed contig 100137
    ...

    Will it be a problem?

    Any advice would be appreciated. Thank you in advance.

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