107 days ago
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....107 days ago
Raku script to find overlaps between two bed files !
...n the first BED file for my $line1 (@bed1) { my @fields1 = $line1.split("\t"); my $chr1 = @field...ond BED file for my $line2 (@bed2) { my @fields2 = $line2.split("\t"); my $chr2 = @f...107 days ago
Perl script to find overlaps between two bed files !
#!/usr/bin/perl use strict; use warnings; # Check if the correct number of arguments are provided if (@ARGV != 2) { die "Usage: $0 file1.bed file2.bed\n"; } # Read the contents of the two BED files my $file1 = shift @ARGV; my $file2 = shift @ARGV; open my $fh1, '107 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 @AR...107 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...107 days ago
Python script to parse GFF file
...th('#'): # Ignore comment lines fields = line.strip().split('\t') featur...'phase': fields[7], 'attributes': dict(item.split('=') for item in fields[8].sp...51 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 = fie...16 days ago