Perl script to find coding regions in DNA sequences
...ontable = $ARGV[0]; my $filesequence = $ARGV[1]; # open the first file: table of codon usage frequencies if (!open(PROPCODONS,"< $filecodontable...##################################################### # open the DNA sequence (second file...2150 days ago
Perl script to count number of Ns in a multifasta file !
#!/usr/bin/perl my ($h, $n, $l); open(I,$ARGV[0]) or die($!); while(){ chomp; next if /^$/; if(/^>/){ $h=substr($_,1); }else{ $n=($_=~tr/nN/nN/); $l=l...2139 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, "2139 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...= shift @_; my $filehandle; if ($filename =~ /gz$/) { open $filehandle, "gunzip -dc $filename |" or die $!; } else { open $filehandle, "$filename" or d...2135 days ago
Perl script to run SATSUMA in loop !
...my $resolution = 5000; my $dotsize = 1; my $cpu=40; my @ids; #Store the ids if ($ARGV[1] eq "ids") { my $idFile="palindrome_ids.txt"; open my $handle, '...2135 days ago
Perl script to convert GFF 2 FASTA !
...:DB::Fasta->new($file_fasta); print ("Genome fasta parsed\n"); ### Second, parse the GFF3 my %CDS; my %CDNA; my $mRNA_name; my $frame; open GFF, "2134 days ago
Perl subroutine to read genome/reads fasta file !
sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while(){ chomp; if($_ =~ /^>/){ if(defined $id && def...2128 days ago
Perl script to merge LastZ overlaps
#!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '2121 days ago
Installing Porechop on Ubuntu !
...coring_scheme SCORING_SCHEME Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend (default: 3,-6,-5...2101 days ago
Install Python locally on shared Linux server !
...-certificate https://bootstrap.pypa.io/get-pip.py -O - | python - --user #After finishing the installation, we need to update our PATH variable. Open ~/.bashrc_profile and add the...2093 days ago