Bioinformatics scripts

Mostly for transcriptomics.

How to use

Add the following to your /.bashrc file (/.zshrc file for Bio-Linux)

export PATH=~/path/to/scripts:$PATH

Documentation

blast_parser.py

Returns a fasta file that contains the sequences that (0) have Blast hits (1) have no Blast hits.

blast_parser.py -i <input fasta> -x <blast xml> -c <0 (query hits), 1 (query nonhits)> -o <output>

fasta_parser.py

Outputs a fasta file from that contains the sequences specified in the tag file.

fasta_parser.py -i <input fasta> -t <tags> -s <separator> -o <output>

fasta_summarizer.py

Gets the longest, shortest, mean length and N50 for Trinity assembly.

fasta_summarizer.py -f <input fasta> -o <output>

oases_unigene_parser.py

Gets unigenes by getting the locus with (1) Greatest confidence score and in case of a tie (2) longest of the tie.

oases_unigene_parser.py -f <input fasta> -o <output>

trinity_longest_parser.py

Gets unigenes by getting the longest gene in the cluster.

trinity_longest_parser.py -f <input fasta> -o <output>

WEGO_formatter.py

Formats a GO file to WEGO's native format.

WEGO_formatter.py -i <GO file> -o <output>