Biological Sequence handling with Perl !
...lass; if (ref($sequence)) { croak "Can't initialize sequence from non-Sequence object.\n" u...unless $sequence=~/^[gactnu\s]+$/i; $self->{'data'} = $self->_canonicalize($sequence); $sel...2236 days ago
Perl script to find coding regions in DNA sequences
...$filecodontable")) { print "dnaloglkh.pl: the file $filecodontable can not be opened\n"; exit(1); }...E,"< $filesequence")) { print "dnaloglkh.pl: the file $filesequence can not be opened\n"; exit(1); }...2210 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
...py /path/to/lib1_A.fq /path/to/lib1_B.fq /path/to/contigs.fasta --threads N where N is an integer specifying how many threads BWA-mem should use. --nomem can be specified to the ab...2179 days ago
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2199 days ago
Perl script to count number of Ns in a multifasta file !
...r($_,1); }else{ $n=($_=~tr/nN/nN/); $l=length($_); print $h,"\t",$l,"\t",$n,"\t",$n/($l-$n),"\n"; } } close(I); __END__ Note: Convert sequences in oneli...2199 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...gs and scaffolds #Usage: perl clustalReads.pl genome.fa > HammingDist.txt #Depe...qIds[$cnt]}{seq}\n"; close $ofh or die "Could not close file '$tmpFile' $!";...s/[^atgc]/N/ig; $sequences{$seqid}{nonatgc} += ($line =~ tr/N/N/);...2195 days ago
Perl script to run SATSUMA in loop !
...ge perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name here my $seqfile=""; my $queryfile = "genome.fasta"; # Ur query genome my $tarfile = "renamedAdin...2195 days ago
Perl script to convert GFF 2 FASTA !
...ion of the gene (likely including the promoter) ### First, index the genome my $file_fasta = $ARGV[0]; my $db = Bio::DB::Fasta->new($file_fasta); print ("Genome fasta parsed\n"); ##...2194 days ago
2192 days ago