Perl script to extract a sequence from multifasta with range !
# filterfastarange.pl #!/usr/bin/perl use strict; use warnings; #perl filterfastarange.pl 301 600 contigs.fasta > contigs-gt300-lte600.fasta my $minlen = shift...2059 days ago
Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict;...ases are in uppercase #Searches for NNNNN regions (scaffold breaks) #Hash nregions stores a hash from the conti...y $end=$i; my $ini=$end-$n+1; push(@regions,"$ini $end"); } $n=0...2055 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencing data. PROJECT=PRJNA257197 #...samtools view -c -r GROUP-SRR1972919 all.bam # Reverting the process is to extrac...1535 days ago
Perl script to reads and extract webpage contents !
use 5.010; use strict; use warnings; use WWW::Mechanize; my ($url) = @ARGV; die "Usage: $0 URL\n" if not $url; my $w = WWW::Mechanize->new; $w->get($url); say $w->content; #Run #jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ perl web.pl https://bioinformaticsonline.com1506 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-Pro-3335-MT:~/Downloads/...e.com/snippets/view/41440/perl-script-to-reads-and-extract-webpage-contents jit@jit-H...re taxdump files !By Jit 37 days ago extrac...1504 days ago
1395 days ago
Script to extract the cluster detail !
$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 18.04.1 LTS Release: 18.04 Codename: bionic $ cat /proc/cpuinfo | grep -i 'model name' | head -n 1 model name : Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz1371 days ago
Bash script to extract intronic fragments !
#To obtain introns, we simply need the gene and exonic coordinates; #by subtracting the exonic regions from the genic region, we have the intronic region....1358 days ago
Bash script to get intergenic region from genome files !
#For the intergenic region, we will require the size of the chromosomes. wget http://xxx.chrom.sizes cat xxx.chrom.sizes | sed 's/^chr//' | sed 's/Cp/Pt/' > tmp mv tmp xxx.c...1358 days ago
1333 days ago