Some useful scripts we use all the time for quick manipulation of files. Most of these scripts are written by us, but we do use others scripts as well, as mentioned below.
sequence length in a one line fasta file
cat fasta.fa | ./RunSeqLength | less
Convert a multifasta file to 2line fasta
file | fasta2oneline.ba > Singleline.file.fasta
Add columns to a blast output
addcolumns.py input_file blast_file output_file
This is code written by Author: John Nash so please do look at the code for the LICENSE information or below\
Function: Takes a multiple fasta file and removes a set of sequences to makes a second fasta file. Useful for pulling subsets of sequences from entire genomes.
Author: John Nash
Copyright (c) National Research Council of Canada, 2000-2003, all rights reserved.
Licence: This script may be used freely as long as no fee is charged for use, and as long as the author/copyright attributions are not removed.
Syntax:
subset_fasta -i list_file < fasta_file > subset_file
For more options, run the command
subset_fasta -h
Format a corrupt fasta file to the right fasta format using biopython.
Check_fasta_format.py -c CONTIGS -o OUTPUT
Extract all the sequences of interest from a fasta file using this script
Extract_Interested_Seq.py -in CONTIGS -i INDEX -o OUTPUT
This code is writted by Author: Kirill Kryukov, so please do look at the code for the LICENSE information. FASTQ Splitter - a script for partitioning a FASTQ file into n pieces
Syntax:
fastq-splitter.pl [options] <file>
For more options, run the command
perl fastq-splitter.pl -h
This file can be used instead of or in addition to your .bashrc file found in your home directory. It includes aliases to common mispellings and fat-fingers on the command line, changes your prompt to always display the time and your current path, and adds ~'s when you are inside a Singularity container.
Right now it is set to work with Carbonate. If you want to try it out, you can source it like so:
source bashrc
# or
. bashrcIf you like it you can save your old bashrc file like this:
cp ~/.bashrc ~/.bashrc_save
If that succeeded, do:
rm ~/.bashrc
Then copy this bashrc to ~/.bashrc. You can also add that source command into your own .bashrc file. Note the . in front!
Contact [email protected] if you have any questions.