Perl script to check fastq reads qualities !
...t; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [...ux->[1] = 1; return; } } my $name = /^.(\S+)/? $1 : '';...urn ($name, $seq) if ($c ne '+'); my $qual = ''; while () { c..., $slen, $qlen), "\n"; __END__ my @aux = undef; # this is for k...2206 days ago
Perl script to find coding regions in DNA sequences
...create two vars contaning the filenames my $filecodontable = $ARGV[0]; my $filesequence = $ARGV[1];...ed by a triplet of nucleotides or codon my %pcodons; my ($codon,$freq);...GACTGACTTAC # AGACTGACTTAC # AGACTGAC my $iden = ; # reading the head...2207 days ago
2196 days ago
Perl script to count number of Ns in a multifasta file !
#!/usr/bin/perl my ($h, $n, $l); open(I,$ARGV[0]) or die($!); while(){ chomp; next if /^$/; if(/^>/){ $h=substr($_,1); }else{ $n=($_=~tr/nN/nN/);...2196 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2196 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...HammingDist.txt #Dependancy: MAFFT my ($refSeq, $SeqIds) = fastafile2hash($ARGV[0]); my $tmpFile="tmpOutfile"; forea...age: perl clustalRead.pl MAFFT_out my ($seqRef, $ids) = fastafile2h...s, \@allIds; } sub read_fh { my $filename = shift @_; my...2192 days ago
Perl script to run SATSUMA in loop !
...lysis # User need to set the reference multifasta file name here my $seqfile=""; my $queryfile = "genome.fasta";..."/home/urbe/Tools/SATSUMA/satsuma-code-0"; # Location of ur SATSUMA my $maxSize = 5000; my $resol...2192 days ago
Perl script to convert GFF 2 FASTA !
...asta; $| = 1; # Flush output my $outfile_cds = Bio::SeqIO->ne...-file => ">$ARGV[2].cds.fasta" ); my $outfile_pep = Bio::SeqIO->ne...-file => ">$ARGV[2].cdna.fasta" ); my $outfile_gene = Bio::SeqIO->n...er) ### First, index the genome my $file_fasta = $ARGV[0]; my $...2191 days ago
2189 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 $...2185 days ago