2.7. interhost.py - SNP calling, multi-alignment, and phylogenetics

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

usage: interhost.py subcommand

2.7.1. subcommands

[F: Possible choices: snpEff, align_mafft, multichr_mafft

2.7.2. Sub-commands

2.7.2.1. snpEff

Annotate variants in VCF file with translation consequences using snpEff.

interhost.py snpEff [-h] [--emailAddress EMAILADDRESS] [--tmp_dir TMP_DIR]
                    [--tmp_dirKeep]
                    [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                    [--version]
                    inVcf genomes [genomes ...] outVcf

2.7.2.1.1. Positional Arguments

inVcf: Input VCF file
genomes: genome name (snpEff db name, or NCBI accessions)
outVcf: Output VCF file

2.7.2.1.2. Named Arguments

--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

Base directory for temp files. [default: ‘/tmp’]

Default: '/tmp'

--tmp_dirKeep

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.

Default: False

--loglevel

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

Verboseness of output. [default: ‘INFO’]

Default: 'INFO'

--version, -V

show program’s version number and exit

2.7.2.2. align_mafft

Run the mafft alignment on the input FASTA file.

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

2.7.2.2.1. Positional Arguments

inFastas: Input FASTA files.
outFile: Output file containing alignment result (default format: FASTA)

2.7.2.2.2. Named Arguments

--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: None).

--gapOpeningPenalty

Gap opening penalty (default: 1.53).

Default: 1.53

--ep

Offset (works like gap extension penalty).

--verbose

Full output (default: False).

Default: False

--outputAsClustal

Write output file in Clustal format rather than FASTA

--maxiters

Maximum number of refinement iterations (default: 0).: Note: if “–localpair” or “–globalpair” is specified this defaults to 1000.

Default: 0

--threads

Number of threads; by default all cores are used

Default: 2

--loglevel

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

Verboseness of output. [default: ‘INFO’]

Default: 'INFO'

--version, -V

show program’s version number and exit

--tmp_dir

Base directory for temp files. [default: ‘/tmp’]

Default: '/tmp'

--tmp_dirKeep

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.

Default: False

2.7.2.3. 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)

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

2.7.2.3.1. Positional Arguments

inFastas: Input FASTA files.
outDirectory: Location for the output files (default is cwd: None)

2.7.2.3.2. Named Arguments

--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: None).

--gapOpeningPenalty

Gap opening penalty (default: 1.53).

Default: 1.53

--ep

Offset (works like gap extension penalty).

--verbose

Full output (default: False).

Default: False

--outputAsClustal

Write output file in Clustal format rather than FASTA

--maxiters

Maximum number of refinement iterations (default: 0).: Note: if “–localpair” or “–globalpair” is specified this defaults to 1000.

Default: 0

--outFilePrefix

Prefix for the output file name (default: ‘aligned’)

Default: 'aligned'

--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; by default all cores are used

Default: 2

--loglevel

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

Verboseness of output. [default: ‘INFO’]

Default: 'INFO'

--version, -V

show program’s version number and exit

--tmp_dir

Base directory for temp files. [default: ‘/tmp’]

Default: '/tmp'

--tmp_dirKeep

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.

Default: False