Results for "bio"
Bio-Scripts
...:Autotie Tie::IxHash Log::Log4perl FindBin::Real Getopt::Long Catalyst::Runtime Catalyst::Devel List::Util Test::XML::Simple Test::XPath IO::String Bio::Perl version # Set $PERL5...2155 days ago
Python script to download covid genome !
....nlm.nih.gov/core/assets/genbank/files/ncov-sequences.yaml").text) seqs = seqs['genbank-sequences'] print("got %d sequences" % len(seqs)) from Bio import Entrez allseq = {} f...1147 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"; $in = Bio::SeqIO->newFh('-file' => "$inFile" ,...2927 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";2928 days ago
Blast result parser with Perl and Bioperl
...for browsing and further analysis. # use strict; use warnings; use Bio::SearchIO; # Usage informa...Hits,$outfile) = @ARGV; print "Parsing the BLAST result ..."; my $in = Bio::SearchIO->new(-format => 'bl...2925 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
...iven, it will take STDIN as the input\n"; our($opt_h, $opt_m); use Bio::SeqIO; use Getopt::Std;...V = ('-') unless @ARGV; while (my $file = shift) { my $seqio_obj = Bio::SeqIO->new(-file => $file, -...2925 days ago
Extract a range from genome file with perl.
...sr/bin/perl use strict; use warnings; use Bio::SeqIO; my $in_file = $ARG...$ARGV[1]; my $end_pos = $ARGV[2]; my $in = Bio::SeqIO->new ( -file => $in_file, -format => 'fasta'); my $out = Bio::SeqIO->new( -file => ">$in_f...2638 days ago
- ...this value is sent to STDOUT ### use strict; use Getopt::Long; use Bio::SeqIO; my $fasta_file; m...th !~ /\d+/; ### ### Get the length of each sequence: ### my $in = Bio::SeqIO->new(-file => $fasta_f...
2715 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 $outseq = Bio::SeqIO->new(-file => ">$file....2701 days ago
Perl script to insert the DNA string in genome
.../bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; my $file = $ARGV[0];...#sequence of the insertion my $seq_in = Bio::SeqIO->new( -format => 'fast...pos,$length); my $seq_obj = Bio::Seq->new(-seq => $upstream.$...2670 days ago
