BOL

Hi All,

I am new to bioinformatics, recently dived into it. I would like to know which type of works, bioinformatics knowledge gonna offer me in near future.  

I am new to bioinformatics and bit confused regarding future. It looks to me that bioinformatics sector have limited opportunity. Need your suggestions and comments.

I have one big file with lots of fasta sequences. I would like to separate the sequences by their name in files. Can anyone please help me to do so. Thanks for your time.

Sample fasta sequences in file:

>SBI_03055_PP_HisKa|Streptomyces bingchenggensis BCW-1
MSSSDAARTGSAEGARDSKRVRTRRTLRDWIVDVCCISLAALFSLTASESMATDPSVSDE
ALFADLMAGVVACLALWLRRRRPVELALVLLAAGVVSYYVAGPLLVALFTVAVHRPLRTV
AWVGGAALAQIFAAPAVHPDPDLDYIGDVLLGALLVSGAIGWGMFVRSRRLLLESLRERA
ARAEAEAALRAERTQRLTRERIAREMHDVLAHRLSLLSVHAGALEYRADASPQEVAEAAG
VIRSSAHQALQDLREVIGVLRAPDSDATAEGSPPDRPQPTLADLPRLVEESRRAGMRVTL
SDEAGVAGADA
>SBI_03056_RR_NarL|Streptomyces bingchenggensis BCW-1
VSSSPPESTDPAPAPTPTPPAPDPAPTPTPGSGPSLTPIRLLVVDDDPLVRAGLRLMLGG
ASSGIEIVGEASDGAEVAALVDRHSPDVVLMDIRMPTVDGLTATEQLRQREPAPEVVVLT
TFNADEHVLRALRAGAAGFVLKDTPPADLVAAVRRVAAGEPVLSPTVTQQLIEHVAGSGR
DARQERARALLDQLNDREREVAVAVGEGKSNAEISAGLFMSVATVKTHVSRILTKLDLNN
RVQIALLAHDAGLLE

Hi Bioinformaticians, 

I am new to bioinformatics and Perl. So, please execuse me if I disturb you all with newbie question.

I am strugling to find a specific files (cattle_genome.fasta) from a folder and sub folders, and read it. I got some of the help form this website http://stackoverflow.com/questions/5651659/read-all-files-in-a-directory-in-perl in which they explain the extraction method using opendir function. It is suitable only when we have know directory name and depth of the folder.

Can you please suggest me any other method to find the file recursively and read or write the specific fasta file. 

Hi All,
Recently I started working on severs/clusters for my biological analysis. I am struggling to find the operating system(OS) detail information before running my scripts. Can you please tell me how to find OS name using perl script?

Hi Bioinformatician, I am working on a small script which read a file and extract the gene coordinates. It works fine when I run on linux OS but in Window OS it print some weird sign, and also does not print the expected result. Following are the code for your reference.

#!/usr/bin/perl
use strict;
use warnings;

    my $fileIn = $ARGV[0];
    my $OutFile = $ARGV[1];
    open my $fh, '<', $fileIn or die "could not open $fileIn for read\n";
    open OUTFILE, ">" , $OutFile or die "$0: open $OutFile: $!";
    while (<$fh>) {
    chomp $_;
    my $line=trim($_);
    $line =~ s/(\.\.|\s+)/\t/g;
    $line =~ s/\(|\)/\t/g;
    my $number=$.;
    my @tmp=split /\t/, $line;
    if($tmp[2] ne 'complement') {
        my @newtmp = split(/gene/, $line);
        my $newline=$newtmp[1];
        my @tmp2=split /\t/, $newline;
        my $head="gene";
        print OUTFILE "$number\t$head\t\t$tmp2[1]\t$tmp2[2]\n";
        }
    else {
        print OUTFILE "$number\t$tmp[1]\t$tmp[2]\t$tmp[3]\t$tmp[4]\n";
        }
}

# Perl trim function to remove whitespace from the start and end of the string
sub trim($) {
    my $string = shift;
    $string =~ s/^[\t\s]+//;
    $string =~ s/[\t\s]+$//;
    return $string;
}

We always need to keep track of all the Perl modules, and install new one if required. Generally, whenever we run the Perl script it flash error message with the name of module not installed. I would like to know the quicker way to check the installed modules on any system/server.