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, '154 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\...154 days ago
Python script for basic stats of the assembled genome !
...for record in SeqIO.parse(input_file, 'fasta'): length = len(record.seq) total_length += length num_contigs += 1 contig_lengths.append(length) # Sort contig...154 days ago
Python script to finds extact similar sequence between two multi fasta files !
from Bio.Blast.Applications import NcbiblastnCommandline import os import sys def perform_local_blast(query_file, subject_file, output_file): # Set up the BLAST co...63 days ago
Python script to parse GFF file
...': fields[7], 'attributes': dict(item.split('=') for item in fields[8].split(';')) } features.append(feature) return feat...99 days ago
Python script to parse a FASTQ file !
...ecord.id, "sequence": str(record.seq), "quality": record.letter_annotations["phred_quality"] } sequences.append(sequence_info) ret...24 days ago