Fill up the form and blast with perl
...quence = 'GCCCGCGGTCTCAGAGATCTCGATATATTATA'; $mech->get('http://www.arabidopsis.org/Blast/'); $mech->submit_form( form_name => 'myForm', fields => { 'Algorithm' => 'bla...2322 days ago
Create genome scaffolding with Perl
...-separated values, got %d)", scalar(@fields)), -verbose =...e) ? 1 : 0; my $longTarget = (1 - $shortTarget); my $sName = $fields[9 + ($shortTarget * 4)];...2305 days ago
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Perl and BioPerl script to extract protein sequences using GFF file !
#!/usr/bin/perl use strict; use warnings; use Bio::DB::Fasta; use Bio::SeqIO; # Paths to your GFF file and genome FASTA file my $gff_file = 'path/to/your/file.g...91 days ago
Perl script to parse VCF file !
#!/usr/bin/perl use strict; use warnings; # Usage: ./parse_vcf.pl input.vcf die "Usage: ./parse_vcf.pl input.vcf\n" unless @ARGV; my $vcf_file = shift @ARG...91 days ago
Perl script to parse blast results and plot basic stats !
#!/usr/bin/perl use strict; use warnings; use List::Util qw(sum); # Usage: ./parse_blast.pl blast_result.txt die "Usage: ./parse_blast.pl blast_result.txt\n"...91 days ago
Python script to parse GFF file
...'#'): # Ignore comment lines fields = line.strip().split('\t')...feature = { 'seqid': fields[0], 'sou...int(fields[4]), 'score': fields[5], 'str...36 days ago
Python script to finds extact similar sequence between two multi fasta files !
...Parse BLAST results with open(output_file, "r") as result_handle: for line in result_handle: fields = line.strip().split('\t') qseq = fields[0] # Extract the aligned que...8 hours ago