Add `pyfastani._fastani` Cython code wrapping the FastANI C++ code

pyfastani/__init__.py

+__author__ = "Martin Larralde <martin.larralde@embl.de>"
+__license__ = "MIT"
+__version__ = "0.1.0"

pyfastani/_fastani.pyx

+# coding: utf-8
+# cython: language_level=3, linetrace=True, language=cpp
+
+cimport libcpp11.chrono
+from libc.stdint cimport uint64_t
+from libc.stdlib cimport malloc, realloc, free
+from libcpp.functional cimport function
+from libcpp.string cimport string
+from libcpp.unordered_map cimport unordered_map
+from libcpp.vector cimport vector
+
+cimport fastani.map.map_stats
+from fastani.cgi.compute_core_identity cimport (
+    computeCGI,
+    correctRefGenomeIds,
+    computeGenomeLengths,
+    outputCGI
+)
+from fastani.cgi.cgid_types cimport CGI_Results
+from fastani.map cimport base_types
+from fastani.map.compute_map cimport Map
+from fastani.map.map_parameters cimport Parameters
+from fastani.map.map_stats cimport recommendedWindowSize
+from fastani.map.win_sketch cimport Sketch
+from fastani.map.base_types cimport (
+    MappingResult,
+    MappingResultsVector_t,
+)
+
+from _utils cimport new_map_with_result_vector
+
+import os
+
+
+
+cdef extern from "<chrono>" namespace "std" nogil:
+    pass
+
+
+# cdef class MinimizerInfo:
+#     cdef base_types.MinimizerInfo* _mi
+#
+#     def __cinit__(self):
+#         self._mi = new base_types.MinimizerInfo()
+#
+#     def __dealloc__(self):
+#         free(self._mi)
+
+
+def main(query_file, ref_file, output_file):
+
+    cdef Parameters parameters
+    parameters.kmerSize = 16;
+    parameters.minReadLength = 3000;
+    parameters.alphabetSize = 4;
+    parameters.minFraction = 0.2;
+    parameters.threads = 1;
+    parameters.p_value = 1e-03;
+    parameters.percentageIdentity = 80;
+    parameters.visualize = False;
+    parameters.matrixOutput = False;
+    parameters.referenceSize = 5000000;
+    parameters.reportAll = True;
+
+    # Add each query as an individual genome
+    parameters.querySequences.push_back(os.fsencode(query_file))
+    parameters.refSequences.push_back(os.fsencode(ref_file))
+
+    # Add output file
+    parameters.outFileName = os.fsencode(output_file)
+
+    # Compute optimal window size
+    parameters.windowSize = fastani.map.map_stats.recommendedWindowSize(
+        parameters.p_value,
+        parameters.kmerSize,
+        parameters.alphabetSize,
+        parameters.percentageIdentity,
+        parameters.minReadLength,
+        parameters.referenceSize
+    )
+
+    # Build the sketch for the reference
+    cdef Sketch* reference_sketch = new Sketch(parameters)
+
+    # Final output vector
+    cdef vector[CGI_Results] finalResults
+    cdef vector[CGI_Results] finalResults_local
+
+
+    # query/ref output vector
+    cdef MappingResultsVector_t mapResults
+    cdef uint64_t totalQueryFragments = 0
+
+    # mapper
+    cdef Map* mapper = new_map_with_result_vector(parameters, reference_sketch[0], totalQueryFragments, 0, mapResults)
+
+    #
+    computeCGI(parameters, mapResults, mapper[0], reference_sketch[0], totalQueryFragments, 0, parameters.outFileName, finalResults_local);
+    # correctRefGenomeIds(finalResults_local) <-- only useful for OpenMP multithreaded
+
+    finalResults.insert(finalResults.end(), finalResults_local.begin(), finalResults_local.end());
+
+    # report
+    cdef unordered_map[string, uint64_t] genomeLengths
+    computeGenomeLengths(parameters, genomeLengths)
+    outputCGI(parameters, genomeLengths, finalResults, parameters.outFileName);