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 $seqobj = $fast...2057 days ago
Perl script to run in parellel !
.../bin/perl use strict; use warnings; use Parallel::ForkManager; use Bio::SeqIO; my ($sequence_data...my $file=shift; my (%sequence_data); my $file_content = new Bio::SeqIO(-format => 'fasta',-fi...1680 days ago
1508 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)1209 days ago
1209 days ago
Parse the NCBI taxonomy database with Perl !
use Bio::DB::Taxonomy; use warnings; my $s...om 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::Tree::Tree; my $tree_functi...1166 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::DB::Taxonomy->new(-source...1158 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...le', 'Try::Tiny', 'Data::Dumper', 'File::Basename', 'Bio::SeqIO', 'FindBin',...ong', 'Statistics::R', 'Math::Round', 'File::Find', 'Bio::DB::Taxonomy', 'Pod::Us...1154 days ago
1152 days ago
Perl script to check modules installed !
...le', 'Try::Tiny', 'Data::Dumper', 'File::Basename', 'Bio::SeqIO', 'FindBin',...ong', 'Statistics::R', 'Math::Round', 'File::Find', 'Bio::DB::Taxonomy', 'Pod::Us...1149 days ago