1180 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## u...eq) = ($lSeq, $sSeq); } my $doRC = ($strand eq "-"); if($doRC){...) { # target sequence is assumed to be forward strand $lSeq = rc($l...2271 days ago
Plot custom gene density with R
library(karyoploteR) pp2213 days ago
Install grabseqs using conda !
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1017 days ago
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker;..._result->start(); my $rm_end = $rm_result->end(); my $rm_strand = $rm_result->strand(); if ($rm_clas...388 days ago
Python script to parse GFF file
def parse_gff(gff_file): features = [] with open(gff_file, 'r') as f: for line in f:...int(fields[4]), 'score': fields[5], 'str...yesterday