Results for "R"
Bio-Scripts
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number of input arguments is lower t...ence\n"; exit(1); } # create two vars contaning the fi...s{$codon}=$freq; } close(PROPCODONS); ################...m/.../g); # the likelihood ratio is for a current triplet,...2157 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 aligner + samtools can be...to obtain such files. Read pairs needs to be aligned in paire...o_ctg_map.py) for obtaining sorted and indexed BAM files with...ll to use BWA-sampe as the paired read alignment pipeline....2126 days ago
- ➜ Tools git:(master) ✗ git clone git://github.com/bcgsc/bloomfilter.git Cloning into 'bloomfilter'... remote: Counting objects...onfig.status config.status: creating Makefile config.status...y '/home/urbe/Tools/bloomfilter/Tests/AdHoc' make[2]: Enteri...
2153 days ago
- # To follow these instructions, we'll assume your system admins have already in...ysqlclient-dev libxml2-dev # RHEL/CentOS system admins shoul...l-5.24.1 ./Configure -des -Dprefix=$PERL_BASE/perl-5.24.1 -D...hose 2 lines to the end of your `~/.bashrc` to make it persis...
2146 days ago
Perl script to count number of Ns in a multifasta file !
#!/usr/bin/perl my ($h, $n, $l); open(I,$ARGV[0]) or die($!); while(){ ch...f /^$/; if(/^>/){ $h=substr($_,1); }else{ $n=($_=...N/nN/); $l=length($_); print $h,"\t",$l,"\t",$n,"\t",$n...sta perl countN.pl scaff.fa Result ➜ SSPACED_P2 perl coun...2146 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2146 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 beetwe...my $tmpFile="tmpOutfile"; foreach my $chr (@$SeqIds) { my...cnt]}{seq}\n"; close $ofh or die "Could not close file '$t...val\n"; }} until($value= $trimLen2) {$val = $trimLen1; } e...2142 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 here my $seqfile=...genome my $tarfile = "renamedAdinetaV2.fa"; #Ur target file my $satsumaLoc="...2142 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::...ile_cds = Bio::SeqIO->new( -format => 'fasta', -file => ">$AR...ile_pep = Bio::SeqIO->new( -format => 'fasta', -file => ">$AR...rmat => 'fasta', -file => ">$ARGV[2].gene.fasta" ); my $outf...ding UTRs and introns) # upstream3000 - the 3000 upstream re...2141 days ago
- #!/bin/bash #set the path export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/bin export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/scripts...rbe/Tools/augustus-3.2.3/config #run BUSCO python BUSCO.py -i /...BUSCO python BUSCO_plot.py -wd GRAALHaploid_BUSCO...
2139 days ago
