Perl script to insert the DNA string in genome
...= "AAAA"; #sequence of the insertion my $seq_in = Bio::SeqIO->new( -format => 'fasta',-file => $file); my $seq_out = Bio::SeqIO->new( -format => 'fasta',-file => ">".$out)...2702 days ago
Calculate ATGC percentage in parallel with perl
...l my %sequences; my $seqio = Bio::SeqIO->new(-file => "$ARGV[0]", -format => "fasta"); while(my$seqobj...keys %sequences; # hash to resolve PID's back to child specific information my $pm = new Parallel:...2699 days ago
Calculate some statistics for a DNA alignment with Perl
...= Bio::Align::DNAStatistics->new(); my $alignin = Bio::AlignIO->new(-format => 'emboss',...nymous /nonsynonymous substitutions ## my $in = Bio::AlignIO->new(-format => 'fasta',...2692 days ago
2555 days ago
Convert newline formated sequence into fasta format with perl
use strict; use warnings; my $filename = $ARGV[0]; open(my $fh, '2413 days ago
Convert fastq to fasta in Perl
...die $!; my $in=Bio::SeqIO->new(-fh=>$zcat, -format=>'fastq'); my $out=Bio::SeqIO->new(-file=>'>seq.fasta', -format=>'fasta'); while (my $seq=$i...2373 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+locatio...2357 days ago
Perl script to find coding regions in DNA sequences
...d file) if (!open(SEQUENCE,"< $filesequence")) { print "dnaloglkh.pl: the file $filesequence can not be opened\n"; exit(1); } # FASTA format: # >header containing a des...2198 days ago
Perl script to convert GFF 2 FASTA !
...sh output my $outfile_cds = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[...fasta" ); my $outfile_pep = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[...asta" ); my $outfile_gene = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[...2182 days ago
2169 days ago