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] [--emailAddress EMAILADDRESS] [--tmp_dir TMP_DIR] [--tmp_dirKeep] [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}] [--version] inVcf genomes [genomes ...] outVcf
- Positional arguments:
inVcf Input VCF file genomes genome name (snpEff db name, or NCBI accessions) outVcf Output VCF file - Options:
--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. --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.