HIVClustering

A Python 3 library that makes inferences on HIV-1 transmission networks. To install

sudo python3 setup.py install

Dependencies

1). The low level HyPhy Python library.

Clone the HyPhy repo git://github.com/veg/hyphy.git

cd [hyphy]/src/lib
sudo python3 setup.py install

2). The higher level Python-HyPhy interface (hppy)

Clone the hppy repo git://github.com/nlhepler/hppy.git

cd [hppy]
sudo python3 setup.py install

USAGE

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] [-a ATTRIBUTES]
                     [-j] [-k FILTER] [-s SEQUENCES] [-n {remove,report}]

Read filenames.

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). 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
  -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)
  -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. 1983) 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
                        The reg.exp pattern to split up sequence ids; only
                        used if format is regexp
  -a ATTRIBUTES, --attributes ATTRIBUTES
                        Load a CSV file with optional node attributes
  -j, --json            Output the network report as a JSON object
  -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.
  -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