python_tools

Various Python scripts I've written for analysis

merge_htseq.py

This tool is a script to pull together the results from multiple samples put through htseq into one text file which can be used in R for analysis

laneCounter.py

Biopython script to count reads per lane from illumina paired-end read files

nucleotideFilter.py

Biopython script to calculate the percentage of nucleotides per read in a pair and discard both reads in pair if nucleotide % threshold is exceeded

gtfCDSextender.py

Script utilising GTFparse (https://github.com/openvax/gtfparse) to read in a GTF file and extend the CDS regions by user specified amount. Useful for mapping of RiboSeq data to transcripts.

aaPercent.py

Calculate the amino acid % for CDS regions in transcript fasta file

codonContext.py

Calculate the codon context (frequency of codon pairs/ frequency of amino acid pairs encoded by that codon pair) for CDS regions in transcript fasta file