3.4. intrahost.py - within-host genetic variation (iSNVs)

This script contains a number of utilities for intrahost variant calling and annotation for viral genomes.

usage: intrahost.py subcommand

Sub-commands:

tabfile_rename

Undocumented

Take input tab file and copy to an output file while changing the values in a specific column based on a mapping file. The first line will pass through untouched (it is assumed to be a header).

usage: intrahost.py tabfile_rename [-h] [--col_idx COL]
                                   [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                                   [--version]
                                   inFile mapFile outFile

Positional arguments:

inFile	Input flat file
mapFile	Map file. Two-column headerless file that maps input values to output values. This script will error if there are values in inFile that do not exist in mapFile.
outFile	Output flat file

Options:

--col_idx=0	Which column number to replace (0-based index). [default: %(default)s]
--loglevel=DEBUG
	Verboseness of output. [default: %(default)s] Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION
--version, -V	show program’s version number and exit

vphaser_to_vcf

Undocumented

Convert vPhaser2 parsed filtered output text file into VCF format. We require the consensus assemblies for all these samples in a multi-alignment FASTA format as well, in order to resolve the ambiguity in vPhaser’s output. All sample names and coordinates must be identical between inFile, inRef, and multiAlign. We also require the reference genome FASTA (inRef) to determine reference alleles. Requires a single-chromosome genome.

usage: intrahost.py vphaser_to_vcf [-h]
                                   [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                                   [--version]
                                   inFile refFasta multiAlignment outVcf

Positional arguments:

inFile	Input vPhaser2 text file
refFasta	Reference genome FASTA
multiAlignment	Consensus genomes multi-alignment FASTA
outVcf	Output VCF file

Options:

--loglevel=DEBUG
	Verboseness of output. [default: %(default)s] Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION
--version, -V	show program’s version number and exit

Fws

Undocumented

Compute the Fws statistic on iSNV data. See Manske, 2012 (Nature)

usage: intrahost.py Fws [-h]
                        [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                        [--version]
                        inVcf outVcf

Positional arguments:

inVcf	Input VCF file
outVcf	Output VCF file

Options:

--loglevel=DEBUG
	Verboseness of output. [default: %(default)s] Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION
--version, -V	show program’s version number and exit

iSNV_table

Undocumented

Convert VCF iSNV data to tabular text

usage: intrahost.py iSNV_table [-h]
                               [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                               [--version]
                               inVcf outFile

Positional arguments:

inVcf	Input VCF file
outFile	Output text file

Options:

--loglevel=DEBUG
	Verboseness of output. [default: %(default)s] Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION
--version, -V	show program’s version number and exit

iSNP_per_patient

Undocumented

Aggregate tabular iSNP data per patient x position (all time points averaged)

usage: intrahost.py iSNP_per_patient [-h]
                                     [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                                     [--version]
                                     inFile outFile

Positional arguments:

inFile	Input text file
outFile	Output text file

Options:

--loglevel=DEBUG
	Verboseness of output. [default: %(default)s] Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION
--version, -V	show program’s version number and exit