diff --git a/python/README.rst b/python/README.rst index 7eab1fe..5b6e5a2 100644 --- a/python/README.rst +++ b/python/README.rst @@ -9,7 +9,7 @@ minimap2 and provides a convenient interface to calling minimap2 in Python. Installation ------------ -The minimap2 model can be installed directly with: +The minimap2 module can be installed directly with: .. code:: shell @@ -31,13 +31,13 @@ The following Python program shows the key functionality of this module: .. code:: python import minimap2 as mm - a = mm.Aligner("test/MT-human.fa") + a = mm.Aligner("test/MT-human.fa") # load or build index if not a: raise Exception("ERROR: failed to load/build index") for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"): print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str)) It builds an index from the specified sequence file (or loads an index if a -pre-built index is supplied), aligns a sequence against it, traverses each hit +pre-built index is specified), aligns a sequence against it, traverses each hit and prints them out. APIs @@ -81,9 +81,9 @@ Arguments: .. code:: python - map(query_seq) + map(seq) -This methods maps :code:`query_seq` against the index. It *yields* a generator, +This method maps :code:`seq` against the index. It *yields* a generator, generating a series of :code:`Alignment` objects. Class minimap2.Alignment