Extract the values between to user defined string with Perl
#!/usr/bin/perl -w use strict; while () { process_record() if /^\s*START/;...ne; while (defined ($line = ) and $line !~ /^\s*END/) { print "$line"...the first set of lines which are to be extracted END ST...2306 days ago
Plot the density of genes in R
#column1 = chromosome name and column2 = start position of the gene # check if ggplot2 is installed, if so, l...import a text file with gene positions # columns should be: chr, position (no end or gen...2298 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, '2168 days ago
2223 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligne...to obtain such files. Read pairs needs to be aligned in pai...be specified to the above call to use BWA-sampe as the paired rea...2138 days ago
Biological Sequence handling with Perl !
package Sequence::Generic; # File: Sequence/Generic.pm use strict; use Carp;...ate { my $self = shift; my ($new_seq,$prepend) = @_; my ($to_append); if (ref($new_seq)) {...ub subseq { my $self = shift; my ($start,$end) = @_;...2195 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; #Script to see the distance beetween...s and scaffolds #Usage: perl clustalReads.pl genome.fa > HammingDist.txt #Dependancy: M...2154 days ago
Install Parrot Virtual Machine !
#Parrot is a virtual machine designed to efficiently compile and execute bytecode for...Compute native byteorder for wordsize.....little-endian. auto::va_ptr - Te...--gc-debug --leak-test|--destroy-at-end -...1551 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Porechop.git Cloni...riting porechop.egg-info/PKG-INFO writing dependency_links to porechop.egg-info/dependency_links.txt writing entry...th their start and end (defau...2120 days ago
2089 days ago