Perl script to remove fasta sequences in multifasta file with certain length threshold
#!/usr/bin/perl use strict; use warnings; my $minlen = shift or die "Error: `minlen` parameter not provided\n"; { local $/=">"; while() { cho...2265 days ago
Perl script to convert fastq to fasta file
...ctory::EMBOSS; my $usage = "perl $0 in.fq out.fa"; my $infile = shift or die $usage; my $outfile = shift or die $usage; my...Run::EMBOSSApplication object $seqret->run({-sequence => $infile, -sformat1 =>...2265 days ago
Plot custom gene density with R
library(karyoploteR) pp2264 days ago
Estimate Genome Size with Jellyfish and R
...-m -mer-len=unit32 Length of the k-mer #-s -size=unit32 Hash size / memory allocation #-o -output=string Output file name #--min-quality-char...2260 days ago
Perl script to read multi fasta sequence one by one
...gs; #USAGE #perl rohanRun.pl seq.fa my $outfile='tmp.fa'; my $fastaSeq_ref =...h my $key ( keys %fastaSeq) { open (OUT, ">$outfile") or die "couldn't open the f...q{$key}\n"; } sub readfasta { (my $file)=@_; my %sequence; my $he...2235 days ago
Perl script to extract the uniq Ids
#!/usr/bin/perl -w use strict; use warnings; use List::Uniq ':all'; open(my $val, "2253 days ago
Perl script to count the number of files in a directory with regex
...,"_A23_","_B34_","_B38_","_E3B2_","_E3T1_","_HPRIM14_","_H158_"); my @files = glob("*.scf *.SCF"); fore...h my $name (@allNames) { my $nName=lc ($name); my $cnt=0; foreach my $file (@files) { #print "$file =~...2251 days ago
Perl script to find palindromic regions in DNA sequences
use strict; use warnings; my $pp = qr/(?: (\w) (?1) \g{-1} | \w? )/ix; my $filename = $ARGV[0]; open(my $fh, '2168 days ago
Installing Busco version 4.0.6
...inux-64::perl-extutils-manifest-1.72-pl526_0 perl-extutils-par~ bioconda/linux-64::perl-extutils-parsexs-3.35-pl526_0 perl-file-path bioconda/linux-64::perl-file-path-2.16-pl526_0 perl-fil...1467 days ago
Perl script to find coding regions in DNA sequences
...it(1); } # create two vars contaning the filenames my $filecodontable = $ARGV[0]; my $fi...$freq); my $line; # for each line in the file (tableofcodons) do while (..._END__ To test the program, save this two files in your current working dire...2169 days ago