3.3. interhost.py - species and population-level genetic variationΒΆ

This script contains a number of utilities for SNP calling, multi-alignment,
phylogenetics, etc.

usage: interhost.py subcommand
Sub-commands:
snpEff

Undocumented

Annotate variants in VCF file with translation consequences using snpEff. 

usage: interhost.py snpEff [-h] [--tmpDir TMPDIR] [--tmpDirKeep]
                           [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                           [--version]
                           inVcf genome outVcf
Positional arguments:
inVcf Input VCF file
genome genome name
outVcf Output VCF file
Options:
--tmpDir=/tmp Base directory for temp files. [default: %(default)s]
--tmpDirKeep=False
 Keep the tmpDir if an exception occurs while running. Default is to delete all temp files at the end, even if there’s a failure.
--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
align_mafft

Undocumented

Run the mafft alignment on the input FASTA file.

usage: interhost.py align_mafft [-h] [--localpair | --globalpair]
                                [--preservecase] [--reorder]
                                [--gapOpeningPenalty GAPOPENINGPENALTY]
                                [--ep EP] [--verbose] [--outputAsClustal]
                                [--maxiters MAXITERS] [--threads THREADS]
                                [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                                [--version] [--tmpDir TMPDIR] [--tmpDirKeep]
                                inFastas [inFastas ...] outFile
Positional arguments:
inFastas Input FASTA files.
outFile Output file containing alignment result (default format: FASTA)
Options:
--localpair All pairwise alignments are computed with the Smith-Waterman algorithm.
--globalpair All pairwise alignments are computed with the Needleman-Wunsch algorithm.
--preservecase Preserve base or aa case, as well as symbols.
--reorder Output is ordered aligned rather than in the order of the input (default: %(default)s).
--gapOpeningPenalty=1.53
 Gap opening penalty (default: %(default)s).
--ep Offset (works like gap extension penalty).
--verbose=False
 Full output (default: %(default)s).
--outputAsClustal
 Write output file in Clustal format rather than FASTA
--maxiters=0 Maximum number of refinement iterations (default: %(default)s). Note: if “–localpair” or “–globalpair” is specified this defaults to 1000.
--threads=-1 Number of processing threads (default: %(default)s, where -1 indicates use of all available cores).
--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
--tmpDir=/tmp Base directory for temp files. [default: %(default)s]
--tmpDirKeep=False
 Keep the tmpDir if an exception occurs while running. Default is to delete all temp files at the end, even if there’s a failure.
multichr_mafft

Undocumented

Run the mafft alignment on a series of chromosomes provided in sample-partitioned FASTA files. Output as FASTA. (i.e. file1.fasta would contain chr1, chr2, chr3; file2.fasta would also contain chr1, chr2, chr3)

usage: interhost.py multichr_mafft [-h] [--localpair | --globalpair]
                                   [--preservecase] [--reorder]
                                   [--gapOpeningPenalty GAPOPENINGPENALTY]
                                   [--ep EP] [--verbose] [--outputAsClustal]
                                   [--maxiters MAXITERS] [--threads THREADS]
                                   [--outFilePrefix OUTFILEPREFIX]
                                   [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                                   [--version] [--tmpDir TMPDIR]
                                   [--tmpDirKeep]
                                   inFastas [inFastas ...] outDirectory
Positional arguments:
inFastas Input FASTA files.
outDirectory Location for the output files (default is cwd: %(default)s)
Options:
--localpair All pairwise alignments are computed with the Smith-Waterman algorithm.
--globalpair All pairwise alignments are computed with the Needleman-Wunsch algorithm.
--preservecase Preserve base or aa case, as well as symbols.
--reorder Output is ordered aligned rather than in the order of the input (default: %(default)s).
--gapOpeningPenalty=1.53
 Gap opening penalty (default: %(default)s).
--ep Offset (works like gap extension penalty).
--verbose=False
 Full output (default: %(default)s).
--outputAsClustal
 Write output file in Clustal format rather than FASTA
--maxiters=0 Maximum number of refinement iterations (default: %(default)s). Note: if “–localpair” or “–globalpair” is specified this defaults to 1000.
--threads=-1 Number of processing threads (default: %(default)s, where -1 indicates use of all available cores).
--outFilePrefix=singlechr
 Prefix for the output file name (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
--tmpDir=/tmp Base directory for temp files. [default: %(default)s]
--tmpDirKeep=False
 Keep the tmpDir if an exception occurs while running. Default is to delete all temp files at the end, even if there’s a failure.