Blast result parser with Perl and Bioperl
#!/usr/local/bin/perl # # Dr. Xiaodong Bai # It may be freely distributed under GNU General Public License. # This script will parse a NCBI blastx output file and out...2924 days ago
Read a tab delimited file and search with perl
use strict; use warnings; use Data::Dumper; use Text::CSV; use IO::Handle; my $file = "/home/urbe/Tools/Alienomics_v0.1/Alienomics/output/intermediate_files/rRNA/refGene.megablast"; open my $fh, "[0]\n"; warn Dumper $row; # To see the structure }2535 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## uses pod documentation in usage code use Getopt::Long qw(:config auto_version auto_help p...2318 days ago
2262 days ago
Perl script to merge LastZ overlaps
#!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '2135 days ago
2085 days ago
904 days ago
Bash script to calculate difference between column !
Space Separated awk '{ $5 = $2 - $4 } 1' inputput.txt > outdiff.txt Or with tab separation: awk 'BEGIN { OFS = "\t" } { $5 = $2 - $4 } 1' inputput.txt > outdiff.txt104 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 c...13 days ago