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PROCH / FASTX-Reader-1.5.1-TRIAL / scripts / Loader.pl 

            

              
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#!/usr/bin/env perl
use 5.010;
use Term::ANSIColor;
use Data::Dumper;
use Carp qw(confess);
use FindBin qw($RealBin);
use lib "$RealBin/../lib/";
use FASTX::Reader;
$Data::Dumper::Terse = 1;
# Print splash screen
print STDERR color('bold'), "TEST FASTA/FASTQ READER\n", color('reset');
print STDERR color('bold'), "Read FASTA/FASTQ files, printing them back to the user\n", color('reset');
print STDERR "Usage: $0 FILE1 FILE2 ... FILEn\n\n";
# Read two samples files if the user didnt provide any filename
push(@ARGV,"$RealBin/../data/test.fastq", "$RealBin/../data/test.fasta" )
  unless ($ARGV[0]);
foreach my $input_file (@ARGV) {
  # Skip non existing files
  if ( not -e "$input_file") {
    print STDERR color('red'), "] Skipping: $input_file (not exists)\n", color('reset');
    next;
  } else {
    my $seq_reader;
    # Allow the user to type "STDIN" or "-" to read from STDIN
    $seq_reader = FASTX::Reader->new({
        filename => "$input_file",
        loadseqs => 'name',
    });
    # Parse the existing files (no check on file type?)
    print STDERR color('yellow'), "* Reading: $input_file\n", color('reset');
    say Dumper [$seq_reader];
  }
}
=head1 NAME
B<Reader.pl and othe scripts> - Demo scripts implementing FASTX::Reader
=head1 USAGE
  reader.pl FILE1 FILE2 ... FILE{n}
If no arguments are supplied, it will parse two test files contained in the script directory
=head1 NOTES
The printed sequences can be slightly different from the input file as the header will be C<{name}{space}{comments}>,
but any white space (including a tab) could be the comment separator
=head1 OTHER SAMPLE SCRIPTS
The C<scripts> directory contains scripts to test the library:
=over 4
=item I<Reader.pl>
This script: a minimal implementation of the FASTX::Reader module to show how to parse a FASTA/FASTQ files.
It will work with demo files if no arguments are supplied.
=item I<FastqReader.pl>
A script to read and print sequences from FASTQ files using the faster C<getFastqRead()> method.
It will work with demo files if no arguments are supplied.
=item I<Counter.pl>
A script to count the number of sequences in both FASTA/FASTQ files. It will work with demo files if no arguments are supplied.
=item I<Stdin.pl>
A script to print sequences from STDIN.
=back
=head1 WEBSITES
=over 4
=item L<https://github.com/telatin/FASTQ-Parser>
The B<GitHub> repository for this module
=item L<https://metacpan.org/pod/FASTX::Reader>
The B<MetaCPAN> page for this module
=back
=head1 AUTHORS
=over 4
=item Andrea Telatin
=item Fabrizio Levorin
=back
=cut