Results for "End of Evolution"
Bio-Scripts
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 S...2333 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 ge...2325 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, '2195 days ago
- # get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam...ome bowtie2-inspect -s refgenome | awk '{ FS = "\t" } ; BEGIN{L=0}; {L=L+$3}; END{print...
2251 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) = @_...2222 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:...2181 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...1578 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 (defa...2147 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/b...d [346889796/346889796] jitendra@jitendra-UNLOCK-INSTALL[gat...h space-separated values. jitendra@jitendra-UNLOCK-INSTALL[gat...BAM file. CollectIndependentReplicateMetrics (Picard)...SAM/BAM, soft-clipping beyond-end-of-re...
2116 days ago
Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict; my $fasta = Bio::SeqIO->n...#Each region is represented as a pair "$ini $end" indicating that start and #the end of the NNNNN region in the co...q($pseqobj); print SCAFF "$new_id $cini $cend\n";...2104 days ago
