Extract the values between to user defined string with Perl
#!/usr/bin/perl -w use strict; while () { pro...^\s*START/; } sub process_record { my $line; while (defined ($line = ) and $line !~ /^\s*END/)...XXXX YYYY START These are the first set of lines which are to be extracted...2314 days ago
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Estimate Genome Size with Jellyfish and R
jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? /common/Tutorial/Genome_estimation/sample_read_1.fastq /common/Tutorial/Genome_estimation/sample_rea...2267 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...2242 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number o...r codon my %pcodons; my ($codon,$freq); my $line; # for each line in the file (tableofcodons) d...e close(SEQUENCE); # concat every segment (line) in the array into the var $s...2177 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2166 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; $| = 1;...sh @allIds, $seqid; } else { chomp $line; $sequences{$seqid}{seq} .= $line; $sequences{$seq...2162 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; # Flush output my $outfile_cds = Bio::SeqIO->new( -form...2160 days ago
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