2110 days ago
Install Python locally on shared Linux server !
...thon wget https://www.python.org/ftp/python/2.7.11/Python-2.7.11.tgz tar zxfv P...ng lines: export PATH=$HOME/python/Python-2.7.11/:$PATH export PYTHONPATH=$H...ted in your home directory: ~/python/Python-#2.7.11/python Install pip #Pi...2109 days ago
Perl script to extract sequence by Ids from multifasta file !
...perl -w use strict; my $idsfile = "$ARGV[0]"; my $seqfile = "$ARGV[1]"; my %ids = (); open FILE, $idsfile; while() { chomp; $ids{$_} += 1; } close FILE; local $/...2107 days ago
Installing Busco version 4.0.6
...--------------- _r-mutex-1.0.1 | anacondar_...7.3.0 | h553295d_18 21 KB conda-forge...2.4 MB tktable-2.10 | h14c39...oarch::r-rprojroot-1.3_2-r36h6115d3f_1003 r-rstudioapi...1464 days ago
2086 days ago
2086 days ago
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 or die "Err...2077 days ago
Perl script to break the contigs by 'N'
...sions for (my $i=0;$i=$minNlen) { my $end=$i; my $ini=$end-$n+1; push(@regions,"$ini $en...$n=0; } } #Now, all regions without Ns are in @regions my $cont=1; my $laststart=1; if ($#r...2074 days ago
#Install older version of R Packages !
#Install older version of R Packages ! require(devtools) install_version("IdeoViz", version = "0.9.1", repos = "http://cran.us.r-project.org")2071 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheterozygous3percen...2064 days ago