Results for "bio marker discovery"
Bio-Scripts
# To follow these instructions, we'll assume your system admins have already installed these...Catalyst::Runtime Catalyst::Devel List::Util Test::XML::Simple Test::XPath IO::String Bio::Perl...2133 days ago
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https:/...ext) seqs = seqs['genbank-sequences'] print("got %d sequences" % len(seqs)) from Bio impor...1125 days ago
BioPerl to convert between sequence formats from Fasta to Genbank
#!/usr/local/bin/perl -w # Sequence formats to choose: Fasta, EMBL. GenBank, Swissprot, PIR and GCG use Bio::SeqIO; $inFile = "BRCA2.fa"; $in = Bio::SeqI...2904 days ago
Check if your coputer ready to use BioPerl
#!/usr/bin/perl use strict; use warnings; #bioperl example code use strict; use warnings; #make the bioperl module (class) accessible to your program use Bio::Seq; print"ok - ready to use Bio::Seq";2905 days ago
Blast result parser with Perl and Bioperl
#!/usr/local/bin/perl # # Dr. Xiaodong Bai # It may be freely distributed under GNU G...further analysis. # use strict; use warnings; use Bio::S...@ARGV; print "Parsing the BLAST result ..."; my $in = Bio::Sear...2903 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
#!/usr/bin/perl -w my $usage="\nUsage: $0 [-h] [-m char] [fastaFileName1 ...]\n"....ke STDIN as the input\n"; our($opt_h, $opt_m); use Bio::S...@ARGV; while (my $file = shift) { my $seqio_obj = Bio::SeqI...2903 days ago
Extract a range from genome file with perl.
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; my $in_file = $ARGV[0]; my $start_pos = $ARGV[1]; my $end_pos = $ARGV[2]; my $in = Bio::S...( -file => $in_file, -format => 'fasta'); my $out = Bio::SeqI...2615 days ago
- #! /usr/local/bin/perl5.8.3 -w ### ### Script Name : calcN50.pl ### Description : Thi...nt to STDOUT ### use strict; use Getopt::Long; use Bio::S...### ### Get the length of each sequence: ### my $in = Bio::SeqI...
2693 days ago
Perl script to remove the duplicate sequences from multifasta file
use strict; use Bio::SeqIO; my %unique; my $file = "myseqs.fa"; my $seqio = Bio::SeqIO->new(-file => $file, -format => "fasta"); my $outseq = Bio::SeqI...2678 days ago
Perl script to insert the DNA string in genome
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; my $file = $ARGV[0]; # input fasta file...AAA"; #sequence of the insertion my $seq_in = Bio::S...eq, $pos,$length); my $seq_obj = Bio::Seq-...2647 days ago
