Results for "Param Bio Blaze"
Bio-Scripts
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; $|...# Flush output my $outfile_cds = Bio::SeqIO->new( -format => 'fast....pep.fasta" ); my $outfile_cdna = Bio::SeqIO->new( -format => 'fast...$file_fasta = $ARGV[0]; my $db = Bio::...2136 days ago
Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict; my $fasta = Bio::SeqIO->new( -file => "$ARGV[0].parts.fasta",-format=>'fasta'); open(SCAFF,">$ARGV[0].parts.scaff"); while ( my $...2060 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManager; use Bio::SeqIO; my ($sequence_data_ref)...nt "starting XFOIL instance with parameters $chr_set!\n"; tou...); print "finished run with parameters $chr_set!\n"; } su...ta); my $file_content = new Bio::...1683 days ago
- # uninstall_perl_module.pl from PerlTricks.com use 5.14.2; use ExtUtils::Installed; use ExtUtils::Packlist;...warn "could not remove $dir: $!\n"; } #Run #perl uninstall_perl_module.pl Bio::...
1511 days ago
Python script to check sequence length in multifasta file
#!/usr/bin/python from Bio import SeqIO import sys cmdargs = str(sys.argv) for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): output_line = '%s\t%i' % \ (seq_record.id, len(seq_record)) print(output_line)1212 days ago
- (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve....
1212 days ago
Parse the NCBI taxonomy database with Perl !
use Bio::DB::Taxonomy; use warnings; my $sps="human"; # Get one from a NCBI taxonomy database my $dbh = Bio::DB::Taxonomy->new(-source...$nam); #print $ancestor_taxon; use Bio::Tree::Tree; my $tree_functi...{ my ($lineageId,$classNode)=@_; use Bio::...1169 days ago
Perl script to get all the descendent in a tree !
use warnings; use Bio::DB::Taxonomy; #Rotifera 10190 # Get one from a NCBI taxonomy database my $dbh = Bio::...1161 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtils::Installed; use LWP::Simple; use Archive::E...', 'Data::Dumper', 'File::Basename', 'Bio::SeqIO', 'FindBin',...cs::R', 'Math::Round', 'File::Find', 'Bio::...1157 days ago
- #use strict; use warnings; use ExtUtils::Installed; use LWP::Simple; use Archive::...', 'Data::Dumper', 'File::Basename', 'Bio::SeqIO', 'FindBin',...cs::R', 'Math::Round', 'File::Find', 'Bio::...
1155 days ago
