ervin 0.0.6

ERVin is a collection of tools developed to assist in discovering ERV sequences within genomic data

ERVin

This is a tool to allow for the detection of ERVs in genome segments

This has been designed primarily with a view to be used on OSX, cross-compatibility with other UNIX-based architectures may exist, but it almost certainly will not run on Microsoft Windows systems

Installation

pip install ervin

Requirements

• Python 3.6+ (Download)
• NCBI BLAST suite must be installed locally (Download)
• Local genome db to be queried
  • This can be located in a directory of your choosing, but must be named in a config.json file
    • There is a config.json.templ file which will be used to create a config.json file from with the contained defaults at first run if you do not provide your own

Current functionality

ERViN Currently:

• When provided with a .fasta file of probe sequences
  • Runs local tblastn against the specified genome database, filtering the results based on alignment length and e-value (optional arguments which result in default values of >400 and <0.009 respectively when omitted)
  • Parses and merges filtered results where appropriate
  • Runs resultant fasta records against a local Viruses refseq database (a copy will be downloaded if not user provided, and will be kept up-to-date) using tblastn, grouping the records in a final set of output files based on their top hit

Usage

Arguments

Argument	Verbose	Description	Type	Required	Default
-f	--file	Source fasta file containing the sample probe records to run through tblastn	Filepath	True
-gdb	--genome_database	Name of the genome database against which the probe records are to be BLASTed (located in the genome db store specified in the config file	str	True
-o	--output_dir	Location to which to write the result files	str	False	<current_working_directory>/OUTPUT
-a	--alignment_len_threshold	Minimum length threshold that BLAST result alignment sequence lengths should exceed	int	False	400
-e	--e_value	Maximum e-value threshold that BLAST result e-values should exceed	float	False	0.009

Examples

ervin -f data/fasta_file.fasta -gdb genome_db

ervin -f data/fasta_file.fasta -gdb genome_db -o results/probe_blaster_output

ervin -f data/fasta_file.fasta -gdb genome_db -o results/probe_blaster_output -a 500

ervin -f data/fasta_file.fasta -gdb genome_db -o results/probe_blaster_output -e 0.0008

ervin -f data/fasta_file.fasta -gdb genome_db -o results/probe_blaster_output -a 800 -e 0.01