Extract the values between to user defined string with Perl
#!/usr/bin/perl -w use strict; while () { process_record() if /^\s*START/; } sub process_record { my $line; while (defined ($line = ) and $line !~ /^...2344 days ago
Perl script to remove fasta sequences in multifasta file with certain length threshold
#!/usr/bin/perl use strict; use warnings; my $minlen = shift or die "Error: `minlen` parameter not provided\n"; { local $/=">"; while() { chomp;...2303 days ago
Perl script to convert fastq to fasta file
#!/usr/bin/env perl use strict; use warnings; use Bio::Factory::EMBOSS; my $usage = "perl $0 in.fq out.fa"; my $infile...2303 days ago
Perl script to read multi fasta sequence one by one
#!/usr/bin/env perl use strict; use warnings; #USAGE #perl rohanRun.pl seq.fa my $outfile='tmp.fa'; my $fastaSeq_ref = readfasta ("$ARGV[0]"); my %fastaSeq = %$fastaSeq_ref; foreach my $...2273 days ago
Perl script to extract the uniq Ids
#!/usr/bin/perl -w use strict; use warnings; use List::Uniq ':all'; open(my $val, "2291 days ago
Perl script to find missing and move to desire folder
#!/usr/bin/perl -w use strict; use warnings; open(my $ids, "2291 days ago
Perl script to count the number of files in a directory with regex
#!/usr/bin/perl use strict; use warnings; my @allNames=("_D14_","_B14_","_B15_","_C1T1_","_C3T3_","_D12_","_D13_","_E1B1_","_E1B3_","_H001_","_H3-03_","_H3-04_","_HB0_",...2289 days ago
Perl script to find palindromic regions in DNA sequences
use strict; use warnings; my $pp = qr/(?: (\w) (?1) \g{-1} | \w? )/ix; my $filename = $ARGV[0]; open(my $fh, '2206 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if (!defined(@$aux)); return if ($aux->[1]); if (!defined($a...2206 days ago
Installing Busco version 4.0.6
(base) jit@jit-HP-Pro-3335-MT: conda inst...5 KB bioconda perl-cpan-meta-requirements-2.140|...64 KB conda-forge r-withr-2.2.0 | r36h...inux-64::openblas-0.2.20-8 perl-app-cpanminus bioconda/linux-...e-0.3.0-r36h6115d3f_1003 r-withr conda-forge/noarc...1505 days ago