Dependencies

biogl

This script needs the biogl module to function properly. If you use (or can get) pip, you can simply do

python3 -m pip install biogl

to add the package to a location reachable by your Python installation.

Otherwise, you can clone the biogl repo and source it locally (to run from anywhere, you'll need to add it to your PYTHONPATH environment variable, a process that varies by OS):

git clone https://github.com/glarue/biogl.git

palign

This script also requires palign to run the alignment steps (using DIAMOND or BLAST), which you can clone and then add to your PATH:

git clone https://github.com/glarue/palign.git

Recommended: networkx

In use-cases with more than two files, reciprologs builds a graph representation of all of the reciprocal best hits (RBH), which allows construction of maximal cliques where every member is a RBH of every other member (e.g. A-B, A-C, B-C, A-D --> A-B-C, A-D). In order to do this efficiently, the Python package networkx is needed (via pip or otherwise). If you want less-strict requirements for clustering (e.g. A-B, A-C, A-D --> A-B-C-D), see the --chain argument.

Usage info

usage: reciprologs [-h] [-p PARALLEL_PROCESSES] [-q PERCENTAGE] [--chain]
                   [--subset subset_1 [subset_2 ...]] [--ignore_same_id]
                   [--ignore_same_prefix <prefix_delimiter>] [-o [OUTPUT]]
                   [-d path [path ...]] [-b BLAST_FILE] [--overwrite]
                   [--one_to_one] [--logging] [--no_hash_tag]
                   file_1 file_2 ... [file_1 file_2 ... ...]
                   {diamondp,diamondx,blastn,blastp,blastx,tblastn,tblastx}

Find reciprocal best hits between two or more files. Any unrecognized
arguments will be passed along to the chosen alignment program.

positional arguments:
  file_1 file_2 ...     files to use to build reciprolog sets (space
                        separated)
  {diamondp,diamondx,blastn,blastp,blastx,tblastn,tblastx}
                        type of alignment program to run

optional arguments:
  -h, --help            show this help message and exit
  -p PARALLEL_PROCESSES, --parallel_processes PARALLEL_PROCESSES
                        run the alignment step using multiple parallel
                        processes (default: 1)
  -q PERCENTAGE, --query_percentage_threshold PERCENTAGE
                        require a specified fraction of the query length to
                        match in order for a hit to qualify (lowest
                        allowable percentage (default: None)
  --chain               cluster reciprologs without requiring all-by-all
                        pairwise relationships, e.g. A-B, A-C, A-D --> A-B-
                        C-D (default: False)
  --subset subset_1 [subset_2 ...]
                        Files containing subsets of headers to be used as
                        queries for each input file. Supplied in the same
                        order as the input files; one header per line. To
                        omit a subset file for a given input file, provide
                        "." as the argument, e.g. for three input files
                        with only 1 & 3 with subsets: --subsets subset_1 .
                        subset_2 (default: None)
  --ignore_same_id      ignore hits where both query and subject have
                        identical IDs (default: False)
  --ignore_same_prefix <prefix_delimiter>
                        ignore hits where both query and subject have
                        identical prefixes, where the prefix for each ID is
                        delimited by the specified <prefix_delimiter>
                        (default: None)
  -o [OUTPUT], --output [OUTPUT]
                        output filename (use flag without argument for
                        stdout; omit flag to use auto-naming) (default:
                        stdout)
  -d path [path ...], --alignment_source_directory path [path ...]
                        check for existing alignment files to use in this
                        directory first (default: None)
  -b BLAST_FILE, --blast_file BLAST_FILE
                        aggregated BLAST output to use (both directions)
                        (default: None)
  --overwrite           overwrite existing output files (instead of using
                        them to bypass alignment step) (default: False)
  --one_to_one          remove any many-to-one reciprolog relationships in
                        each pairwise set, such that each member of each
                        pairwise comparison is only present exactly one
                        time in output (default: False)
  --logging             output a log of best-hit choice criteria (default:
                        False)
  --no_hash_tag         do not auto-tag output files with MD5 hashes of
                        source files (default: False)