Results for "Tab"
Bio-Scripts
Blast result parser with Perl and Bioperl
...ry end, hit start, hit end, positives, and identical # The results are tab-deliminated and ready for imp...file") or die "Cannot open $outfile: $!"; # print the header info for tab-deliminated columns print OU...2918 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 $row; # To see the structure }2528 days ago
Create genome scaffolding with Perl
...$projOpts->{"query"}), -verbose => 0}); } print(STDERR "Loading query sequences into memory..."); open(my $queryFile, "=21 tab-separated values, got %d)",...2312 days ago
- # generate dotplot lastdb test/ref.fa lastal -f TAB test/ref.fa test/contigs.reduced.pacbio.fa | last-dotplot - test/contigs.reduced.pacbio.fa.ref.png lastal -f TAB test/ref.fa test/contigs.reduced.nanopore.fa | last-dotplot - test/contigs.reduced.nanopore.fa.ref.png
2255 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, '2129 days ago
- ...Counter Generates table of filtered base counts at...Summaries (BETA Tool) Tabulates pileup metrics for infe...Generates recalibration table for Base Quality Score Reca...
2079 days ago
- ...FS command contains the field separator character which is used to divide fields on the input line. The default is “white space”, meaning space and tab characters. FS can be reassig...
898 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.txt98 days ago
Python script to finds extact similar sequence between two multi fasta files !
...ommandline import os import sys def perform_local_blast(query_file, subject_file, output_file): # Set up the BLAST command with format 6 (tab-delimited) blastn_cline...7 days ago
