Results for "Exome Seq"
Bio-Scripts
Convert fastq to fasta in Perl
use Bio::SeqIO; #convert .fastq.gz to .fasta open my $zcat, 'zcat seq.fastq.gz |' or die $!; my $in=Bio::SeqIO->new(-fh=>$zcat, -format=>'fastq'); my $out=Bio::SeqIO->new(-file=>'>seq.fasta',...2329 days ago
Insert the sequence at desire location in multi-fasta file with Perl
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; use File::Copy; #ARGV[0] should be in following format --- Keep the coordinate sorted by name+location #GenomechrName lo...2312 days ago
Create genome scaffolding with Perl
...: $b); } sub rc { my ($seq) = @_; $seq =~ tr/ACGTUYRSWMKDVHBXN-/TGCA...=> 0, # contig file for query sequences "prefix" => "psl_sc...print(STDERR "Loading query sequences into memory..."); open...= $lBlStarts[0]; my $alSeqS = ""; my $alSeqL = ""...2306 days ago
Plot the clock using Lastz -gerenal outfile
use strict; use warnings; use Statistics::R ; use List::Util qw(sum); #Usage perl clockPlot.pl Palindrome.palfc 1500 my $R = Statistics::R->new() ; $R->start...2297 days ago
- # bash cat INFILE.fastq | paste - - - - |cut -f 1, 2| sed 's/@/>/'g | tr -s "/t" "...4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}' > file.fa #seqtk seqtk seq -a input.fastq > output...
848 days ago
Perl script to read multi fasta sequence one by one
#!/usr/bin/env perl use strict; use...ngs; #USAGE #perl rohanRun.pl seq.fa my $outfile='tmp.fa'; my $fastaSeq_ref = readfasta ("$ARGV[0]");...ef; foreach my $key ( keys %fastaSeq) { open (OUT, ">$outfile") o...ose fasta files contains multiple sequences; open (IN, "2219 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warn...my $name = /^.(\S+)/? $1 : ''; my $seq = ''; my $c; $aux->[0] =...eq '>' || $c eq '@' || $c eq '+'); $seq .= $_; } $aux->[0] = $_;..., \@aux)) { ++$n; $slen += length($seq); $qlen += length($qual) if...2152 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict;...nt "dnaloglkh.pl codontable DNAsequence\n"; exit(1); } #...odontable = $ARGV[0]; my $filesequence = $ARGV[1]; # open...############## # open the DNA sequence (second file) if (!op...ne) in the array into the var $seq my $i=0; while ($i < sc...2153 days ago
Biological Sequence handling with Perl !
package Sequence::Generic; # File: Sequence/Generic.pm use strict...ef($self)," must override the seq() method"; } # Return the t...lass) if ref($class); my ($sequence,$type) = @_; my $se...my $self = shift; my $seq = shift; $seq = $seq->se...2179 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 s...Outfile"; foreach my $chr (@$SeqIds) { my $cnt=0; my $valu...alRead.pl MAFFT_out my ($seqRef, $ids) = fastafile2hash('M...c} = $2; push @allIds, $seqid; } else {...2138 days ago
