Results for "IT"
Bio-Scripts
Biological Sequence handling with Perl !
...my $self = bless {},$class; if (ref($sequence)) { croak "Can't initialize sequence from non-Seque...e),$l-($l-abs($frame)+1)%3); my $s = $seq->seq; $s=~tr/T/U/; # put it in RNA mode $s =~ s/(\S{3}...2240 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if (!defined(@$aux)); return if ($aux->[1]); if (!de...2213 days ago
Perl script to find coding regions in DNA sequences
....pl codontable DNAsequence\n"; exit(1); } # create two vars c...dontable can not be opened\n"; exit(1); } # load the freque...extract the two values or columns with a regular expression # A g...in # the input DNA sequence. To split the sequence in segments of l...2214 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
...red read mode. BESST provides a script (https://github.com/ksahlin/BESST/blob/mas....py) for obtaining sorted and indexed BAM files with BWA-mem or BWA-sampe in one...the paired read alignment pipeline. https://github.com/ksahlin/BESST/blob/mas...2183 days ago
- ➜ Tools git:(master) ✗ git clone git://github.com/bcgsc/bloomfilter.git...nfig.status: creating Tests/Unit/Makefile config.status: crea...nfig.status: creating Tests/Unit/Makefile config.status: crea...m Tests ➜ bloomfilter git:(master) ✗
2210 days ago
- ...eate a folder where you want to install different Perls, and cd into it: # Note that it doesn't need to be your home...ode File::Copy::Recursive Perl::OSType Module::Metadata Statistics::Lite Tie::Autotie Tie::IxHash Log...
2203 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...my $value=scalar(@$SeqIds); do{{ $value=$value-1; my $ofh = write_fh($tmpFile); next if $ch...t close file '$tmpFile' $!"; $cnt++; system ("mafft --retree 1 --maxiterate 0 --thread 40 $tmpFile >...2199 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name he...2199 days ago
Perl script to convert GFF 2 FASTA !
...at => 'fasta', -file => ">$ARGV[2].upstream3000.fasta" ); ###### Output type description ###### # cds - translated sequence (starting with ATG and ending with a stop codon included) # cd...2198 days ago
Long reads mapper bash script !
...rip to map your long reads and make it visualization ready !" #L...2 ref.fa reads.fa/fq 48 ont" exit 1 fi fileName=$(basename...== "bwa" ]; then echo "Mapping with $toolName" $bwaMemLoc in..."ngmlr" ]; then echo "Mapping with $toolName" if [ $readsType...2181 days ago
