3.4. 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
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