2.4. intrahost.py - within-host genetic variation (iSNVs)ΒΆ

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

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

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

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

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

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