Dissertation

Scripts I have written in the process my dissertation: Characterising indel diversity in Lepidoptera to infer the evolutionary effects of genetic drift and selection

Cloning and Requirements

To download the repository + install reqirements use:

github clone https://github.com/swift-213/Dissertation.git

cd Dissertation

python3 -m pip install -r Dissertation_requirements.txt

Assembly_information.py

A script that pulls out number of lines, SNPs, homologous site and Indels for all or a specified list of contigs. Indel positions are recorded in a [Chromosome, Start, End]. Indels of lengths 1-100 are binned for every length. All Indels are also binned by length in ranges 1-100, 101-200 etc. All specific Indel lengths are also recorded.

Usage:

python3 Assembly_info.py -inputs -outputs

The only required input is the VCF file. If you wish to specify specific contigs or chromosomes to be run use -i2 and use a textfile with each contig name on a new row.

Inputs

Flags	Input	Required
-i	VCF file	Yes
-i2	Textfile specifying which contigs to use	No
--Use_specific_Contigs	If using -i2 also include this flag	No

Outputs

Flag	Output	Printed to terminal	Output type	Required
-o	Number of lines, number of homozygous sites, number of SNPs, number of Indels	Yes	Textfile	No
-o2	Chromosome, start, end position of all Indels	No	Bed file	No
-o3	Indels of lengths 1-100 binned by length	Yes	Textfile	No
-o4	All Indels binned by length in ranges	Yes	Textfile	No
-o5	Every specific Indel length binned	No	Textfile	No

If no output file is specified with a flag the outputs with Yes in printed to terminal will print outputs to terminal but no outputs will be saved

Indel_sorter.py

This script takes Indels start and end positions to discern Indel length and then bins Indels between 1-100 and then all Indel lengths are binned in ranges e.g. 1-100, 101-200 etc.

Usage:

python3 exon_R_indel_sorter.py -inputs -outputs 

Inputs

Flag	Input	Required
-i	Indel positions textfile with Chromosome, Start, End format	Yes

Outputs

Flag	Output	Printed to terminal	Output type	Required
-o	Indels of lengths 1-100 binned by length	Yes	Textfile	No
-o2	All Indels binned by length in ranges	Yes	Textfile	No

If no output file is specified with a flag the outputs with Yes in printed to terminal will print outputs to terminal but no outputs will be saved

Repeat_finder.py

A script that finds masked repetitive regions in fasta files

Usage:

python3 Repeat_finder.py -inputs -outputs 

Inputs

Flag	Input	Required
-i	reference fasta file	Yes
-i2	Textfile specifying which contigs to use	No

Outputs

Flag	Output	Printed to terminal	Output type	Required
-o	Chromosome, start and end position of masked repeat	No	Textfile	No

If no output file is specified with a flag the outputs with Yes in printed to terminal will print outputs to terminal but no outputs will be saved

SNP_finder.py

A script that finds polymorphic bases between two haplotypes on specified contigs

Usage:

python3 SNP_finder.py -inputs -outputs 

Inputs

Flag	Input	Required
-i	VCF file	Yes
-i2	Textfile specifying which contigs to use	No
--Use_specific_Contigs	If using -i2 also include this flag	No

Outputs

Flag	Output	Printed to terminal	Output type	Required
-o	Number of lines, number of homozygous sites, number of SNPs	Yes	Textfile	No

If no output file is specified with a flag the outputs with Yes in printed to terminal will print outputs to terminal but no outputs will be saved