Perl script to insert the DNA string in genome
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; my $file = $ARGV[0]; # input fasta file (genome file) my $out = $ARGV[1]; # output fasta...2675 days ago
Calculate ATGC percentage in parallel with perl
#!/usr/bin/perl use strict; use Parallel::ForkManager; use Bio::SeqIO; #usage: perl testParallel.pl my %seq...hash to resolve PID's back to child specific information my $pm =...g); my $AT=($DNA=~s/AT/AT/g); my $GCper=($GC/($Total)*100); print"$...2672 days ago
BASH script for SelfBLAST a genome
#!/bin/bash #self BLAST a genome -- Expecting you have blast and samtools installed in your system #Au...DB named $MYDB for you"; makeblastdb -in $FASTAFILE -parse_seqids -dbtype nucl -out $MYDB fi if [ $...2668 days ago
Extract a range from genome file with perl.
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; my $in_file = $ARGV[0]; my $start_pos = $ARGV[1]; my $end_pos = $ARGV[2]; my $in = Bio::SeqIO->new...2643 days ago
Calculate some statistics for a DNA alignment with Perl
use Bio::AlignIO; use Bio::Align::DNAStatistics; my $stats = Bio::Align::DNAStatistics->new(); my $alignin = Bio::AlignIO->new(-format => 'emboss',...2665 days ago
2652 days ago
Check overlapping range with Perl
#!/usr/bin/perl use strict; use warnings; my @ranges = 0; push @ranges, $ranges[-1] + 1 + int rand 200 for 1..10000; my @tests = map int rand $ranges[-1], 0..1000...2643 days ago
Extracting FASTA sequences based on position with perl script !!
#!/usr/bin/env perl #Uses: perl sub-seq.pl input.txt range use strict; use warnings; my $end = pop; my $start = pop; local $/ = '>'; while () { chomp;...2637 days ago
Extract ids from file with perl
#!/usr/bin/perl use strict; use warnings; my $fh=read_fh("fi...################################################ #Open and Read a file sub read_fh...ilehandle; if ($filename =~ /gz$/) { open $filehandle, "gunzip -dc $fi...2624 days ago
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICARD_HOME/pic...1353 days ago