Results for "PE"
Bio-Scripts
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if (!defined(@$aux)); return if ($aux->[1]); if (!defined($...2201 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if...esequence = $ARGV[1]; # open the first file: table of cod...on usage frequencies if (!open(PROPCODONS,"< $filecodontabl...######################### # open the DNA sequence (second fil...of a real exon and intron, respectively. Extremely different v...2202 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
...map.py) for obtaining sorted and indexed BAM files with BWA-mem or BWA-sampe in one go. An example call fo...h/to/lib1_B.fq /path/to/contigs.fasta --threads N where N is an integer specifying how many threads BWA-m...2171 days ago
- ...ilter git:(master) swig -Wall -c++ -perl5 BloomFilter.i Unable to f...re && make checking build system type... x86_64-pc-linux-gnu check...ude used by make... GNU checking dependency style of g++... gcc3 c...ude used by make... GNU checking dependency style of g++... gcc3 c...
2198 days ago
- ...' sudo yum install -y expat-devel openssl-devel mysql-devel libxml2...where you want to install different Perls, and cd into it: # Note t...erl-5.24.1.tar.gz cd src tar -zxf perl-5.24.1.tar.gz # Configur...:Simple Test::XPath IO::String Bio::Perl version # Set $PERL5LIB...
2191 days ago
Perl script to count number of Ns in a multifasta file !
#!/usr/bin/perl my ($h, $n, $l); open(I,$ARGV[0]) or die($!); while(){ chomp;..._ Note: Convert sequences in oneline first perl -pe '/^>/ ? print "\n" : chomp' scaffolds_backup.fasta > out.fasta perl countN.pl scaff.fa Resul...2191 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2191 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings;...contigs and scaffolds #Usage: perl clustalReads.pl genome.fa > HammingDist.txt #Dependancy: MAFFT my ($refSeq,...pFile > MAFFT_out"); #usage: perl clustalRead.pl MAFFT_out...$filename =~ /gz$/) { open $filehandle, "gunzip -dc $fi...2187 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 analysi...[1] eq "ids") { my $idFile="palindrome_ids.txt"; open my $handle, '2187 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings;...2].cds.fasta" ); my $outfile_pep = Bio::SeqIO->new( -format =...'fasta', -file => ">$ARGV[2].pep.fasta" ); my $outfile_cdna....fasta" ); ###### Output type description ###### # cds - t...my $mRNA_name; my $frame; open GFF, "...2186 days ago
