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fixed a few typos

This commit is contained in:
Heng Li 2017-09-16 22:52:26 -04:00
parent 1d90742b35
commit f8cb865ec5
1 changed files with 5 additions and 5 deletions
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10
python/README.rst
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@ -9,7 +9,7 @@ minimap2 and provides a convenient interface to calling minimap2 in Python.
Installation Installation
------------ ------------
The minimap2 model can be installed directly with: The minimap2 module can be installed directly with:
.. code:: shell .. code:: shell
@ -31,13 +31,13 @@ The following Python program shows the key functionality of this module:
.. code:: python .. code:: python
import minimap2 as mm 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") if not a: raise Exception("ERROR: failed to load/build index")
for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"): for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"):
print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str)) 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 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. and prints them out.
APIs APIs
@ -81,9 +81,9 @@ Arguments:
.. code:: python .. 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. generating a series of :code:`Alignment` objects.
Class minimap2.Alignment Class minimap2.Alignment