3.4. 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

Annotate variants in VCF file with translation consequences using snpEff.

usage: interhost.py snpEff [-h] [--tmp_dir TMP_DIR] [--tmp_dirKeep]
                           [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                           [--version]
                           inVcf genomes [genomes ...] outVcf emailAddress
Positional arguments:
inVcf Input VCF file
genomes genome name (snpEff db name, or NCBI accessions)
outVcf Output VCF file
emailAddress Your email address. To access the Genbank CoreNucleotide database, NCBI requires you to specify your email address with each request. In case of excessive usage of the E-utilities, NCBI will attempt to contact a user at the email address provided before blocking access.
Options:
--tmp_dir=/tmp Base directory for temp files. [default: %(default)s]
--tmp_dirKeep=False
 Keep the tmp_dir if an exception occurs while running. Default is to delete all temp files at the end, even if there’s a failure.
--loglevel=INFO
 

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

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] [--tmp_dir TMP_DIR]
                                [--tmp_dirKeep]
                                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 Number of threads (default: all available cores)
--loglevel=INFO
 

Verboseness of output. [default: %(default)s]

Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION

--version, -V show program’s version number and exit
--tmp_dir=/tmp Base directory for temp files. [default: %(default)s]
--tmp_dirKeep=False
 Keep the tmp_dir if an exception occurs while running. Default is to delete all temp files at the end, even if there’s a failure.
multichr_mafft

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]
                                   [--outFilePrefix OUTFILEPREFIX]
                                   [--sampleRelationFile SAMPLERELATIONFILE]
                                   [--sampleNameListFile SAMPLENAMELISTFILE]
                                   [--threads THREADS]
                                   [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                                   [--version] [--tmp_dir TMP_DIR]
                                   [--tmp_dirKeep]
                                   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.
--outFilePrefix=aligned
 Prefix for the output file name (default: %(default)s)
--sampleRelationFile
 If the parameter sampleRelationFile is specified (as a file path), a JSON file will be written mapping sample name to sequence position in the output.
--sampleNameListFile
 If the parameter sampleRelationFile is specified (as a file path), a file will be written mapping sample names in the order of their sequence positions in the output.
--threads Number of threads (default: all available cores)
--loglevel=INFO
 

Verboseness of output. [default: %(default)s]

Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION

--version, -V show program’s version number and exit
--tmp_dir=/tmp Base directory for temp files. [default: %(default)s]
--tmp_dirKeep=False
 Keep the tmp_dir if an exception occurs while running. Default is to delete all temp files at the end, even if there’s a failure.