Bash script to convert SAM to BAM visualization ready
samtools view -bS file.sam | samtools sort - file_sorted samtools index test_sorted.bam test_sorted.bai2210 days ago
Biological Sequence handling with Perl !
package Sequence::Generic; # File: Sequence/Generic.pm use strict; use Carp; u...$reversed = reverse $self->seq; return $reversed; } # A human-readable description of the object sub asStrin...2208 days ago
Perl script to count number of Ns in a multifasta file !
#!/usr/bin/perl my ($h, $n, $l); open(I,$ARGV[0]) or die($!); while(){ chomp..._END__ Note: Convert sequences in oneline first perl -pe '/^>/ ? print "\n" : chomp' scaffolds_backup.fasta > out.fasta perl c...2171 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, "2171 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 beetwee...l the contigs and scaffolds #Usage: perl clustalReads.pl genome.fa > H...0 $tmpFile > MAFFT_out"); #usage: perl clustalRead.pl MAFFT_out m...2167 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 $seqfile=""; my...2167 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fa...'fasta', -file => ">$ARGV[2].upstream3000.fasta" ); ###### Output type description ###### # cds - translated...2166 days ago
2164 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($_ =~ /^>...2160 days ago
Install Parrot Virtual Machine !
#Parrot is a virtual machine designed to efficiently compile and execute...-Pro-3335-MT:~/Downloads/parrot-8.1.0$ perl Configure.pl Parrot Version...nning this program, you obviously have Perl 5--I'll be pulling some defa...t..........................yes. auto::perldo...1564 days ago