HIV molecular clustering tools


License
MIT
Install
pip install hivclustering==1.6.2

Documentation

HIVClustering

A Python 3 library that makes infers molecular transmission networks from sequence data. A part of HIV-TRACE, available at http://hivtrace.org

Related projects

  1. BioExt Provides the bealign utility for codon-aware mapping to a reference sequence.
  2. TN93 Provides the tn93 tool for rapid computation of pairwise genetic distances between aligned sequence.

Dependencies

HIVClustering can be installed in one easy step. Prior to installation, please ensure that you python 3 installed.

pip3 install hivclustering

To install a version that has not yet been published, i.e. the dev branch, use

git clone https://github.com/veg/hivclustering.git
git checkout develop
python3 setup.py install

Components

  1. hivnetworkcsv: the workhorse of the package which consumes pairwise distance files (and, optionally, other sources of data) and infers the molecular transmission network subject to a variety of user-selectable parameters.

  2. hivnetworkannotate : imports network node attributes (read from a .csv, .tsv, or .json) to a JSON file output by hivnetworkcsv

optional arguments:
usage: hivnetworkcsv [-h] [-i INPUT] [-u UDS] [-d DOT] [-c CLUSTER]
                     [-t THRESHOLD] [-e EDI] [-z OLD_EDI] [-f FORMAT]
                     [-x EXCLUDE] [-r RESISTANCE] [-p PARSER PARSER]
                     [-a ATTRIBUTES] [-J | -j] [-o] [-k FILTER] [-s SEQUENCES]
                     [-n {remove,report}] [-y CENTRALITIES] [-l]
                     [--cycle-report-file CYCLE_REPORT_FILENAME]
                     [-g TRIANGLES] [-C {report,remove}] [-F CONTAMINANT_FILE]
                     [-M] [-B] [--no-degree-fit] [-X EXTRACT] [-O OUTPUT]
                     [-P PRIOR] [-A AUTO_PROF] [--after AFTER]
                     [--before BEFORE] [--import-attributes IMPORT_ATTR]
                     [--subcluster-annotation SUBCLUSTER_ANNOTATION SUBCLUSTER_ANNOTATION]

Construct a molecular transmission network.

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input CSV file with inferred genetic links (or stdin
                        if omitted). Can be specified multiple times for
                        multiple input files (e.g. to include a reference
                        database). Must be a CSV file with three columns:
                        ID1,ID2,distance.
  -u UDS, --uds UDS     Input CSV file with UDS data. Must be a CSV file with
                        three columns: ID1,ID2,distance.
  -d DOT, --dot DOT     Output DOT file for GraphViz (or stdout if omitted)
  -c CLUSTER, --cluster CLUSTER
                        Output a CSV file with cluster assignments for each
                        sequence
  -t THRESHOLD, --threshold THRESHOLD
                        Only count edges where the distance is less than this
                        threshold. Provide comma-separated values to compute
                        subclusters if the output mode is JSON. If -t auto is
                        specified, a heuristic is used to determine an ad hoc
                        optimal threshold.
  -e EDI, --edi EDI     A .json file with clinical information
  -z OLD_EDI, --old_edi OLD_EDI
                        A .csv file with legacy EDI dates
  -f FORMAT, --format FORMAT
                        Sequence ID format. One of AEH (ID | sample_date |
                        otherfiels default), LANL (e.g. B_HXB2_K03455_1983 :
                        subtype_country_id_year -- could have more fields),
                        regexp (match a regular expression, use the first
                        group as the ID), or plain (treat as sequence ID only,
                        no meta); one per input argument if specified
  -x EXCLUDE, --exclude EXCLUDE
                        Exclude any sequence which belongs to a cluster
                        containing a "reference" strain, defined by the year
                        of isolation. The value of this argument is an integer
                        year (e.g. 1984) so that any sequence isolated in or
                        before that year (e.g. <=1983) is considered to be a
                        lab strain. This option makes sense for LANL or AEH
                        data.
  -r RESISTANCE, --resistance RESISTANCE
                        Load a JSON file with resistance annotation by
                        sequence
  -p PARSER PARSER, --parser PARSER PARSER
                        The reg.exp pattern to split up sequence ids; only
                        used if format is regexp; format is INDEX EXPRESSION
                        (consumes two arguments)
  -a ATTRIBUTES, --attributes ATTRIBUTES
                        Load a CSV file with optional node attributes
  -J, --compact-json    Output the network report as a compact JSON object
  -j, --json            Output the network report as a JSON object
  -o, --singletons      Include singletons in JSON output
  -k FILTER, --filter FILTER
                        Only return clusters with ids listed by a newline
                        separated supplied file.
  -s SEQUENCES, --sequences SEQUENCES
                        Provide the MSA with sequences which were used to make
                        the distance file. Can be specified multiple times to
                        include mutliple MSA files
  -n {remove,report}, --edge-filtering {remove,report}
                        Compute edge support and mark edges for removal using
                        sequence-based triangle tests (requires the -s
                        argument) and either only report them or remove the
                        edges before doing other analyses
  -y CENTRALITIES, --centralities CENTRALITIES
                        Output a CSV file with node centralities
  -l, --edge-filter-cycles
                        Filter edges that are in cycles other than triangles
  --cycle-report-file CYCLE_REPORT_FILENAME
                        Prints cycle report to specified file
  -g TRIANGLES, --triangles TRIANGLES
                        Maximum number of triangles to consider in each
                        filtering pass
  -C {report,remove}, --contaminants {report,remove}
                        Screen for contaminants by marking or removing
                        sequences that cluster with any of the contaminant IDs
                        (-F option) [default is not to screen]
  -F CONTAMINANT_FILE, --contaminant-file CONTAMINANT_FILE
                        IDs of contaminant sequences
  -M, --multiple-edges  Permit multiple edges (e.g. different dates) to link
                        the same pair of nodes in the network [default is to
                        choose the one with the shortest distance]
  -B, --bridges         Report all bridges (edges whose removal would cause
                        the graph to disconnect)
  --no-degree-fit       Do not perform degree distribution fitting
  -X EXTRACT, --extract EXTRACT
                        If provided, extract all the sequences
  -O OUTPUT, --output OUTPUT
                        Write the output file to
  -P PRIOR, --prior PRIOR
                        When running in JSON output mode, provide a JSON file
                        storing a previous (subset) version of the network for
                        consistent cluster naming
  -A AUTO_PROF, --auto-profile AUTO_PROF
                        If provided supercedes most other output and inference
                        settings; will add edges from shortest to longest and
                        report network statistics as a function of distance
                        cutoff
  --after AFTER         [assumes DATES are available] If provided (as
                        YYYYMMDD) then only allow EDGES that connect nodes
                        with dates at or AFTER this date
  --before BEFORE       [assumes DATES are available] If provided (as
                        YYYYMMDD) then only allow EDGES that connect nodes
                        with dates at or BEFORE this date
  --import-attributes IMPORT_ATTR
                        Import node attributes from this JSON
  --subcluster-annotation SUBCLUSTER_ANNOTATION SUBCLUSTER_ANNOTATION
                        As "dist" "field"". Use subcluster annotation for
                        distance "dist" from node attribute "field"