From 507020f9f2fe2c0c2a9f46afe2040b833ed3a1b7 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 18 Jul 2022 15:00:35 +0200
Subject: [PATCH] Improve some parts of the `pyfastani` class documentation
---
pyfastani/_fastani.pyx | 23 +++++++++++++++++++----
1 file changed, 19 insertions(+), 4 deletions(-)
diff --git a/pyfastani/_fastani.pyx b/pyfastani/_fastani.pyx
index 24d14af..79889d4 100644
--- a/pyfastani/_fastani.pyx
+++ b/pyfastani/_fastani.pyx
@@ -363,6 +363,10 @@ cdef class _Parameterized:
cdef class Sketch(_Parameterized):
"""An index computing minimizers over the reference genomes.
+ Use this class to add reference genomes with the `add_genome` or
+ `add_draft` methods, then call the `index` method to obtain a `Mapper`
+ that can be used to map query genomes.
+
Attributes:
minimizers (`~pyfastani.Minimizers`): A view over the minimizers
currently recorded in the sketch.
@@ -400,7 +404,7 @@ cdef class Sketch(_Parameterized):
uint64_t reference_size=5_000_000,
bint protein=False,
):
- f"""__init__(self, *, k=16, fragment_length=3000, minimum_fraction=0.2, p_value=1e-03, percentage_identity=80, reference_size=5000000, protein=False)\n--
+ """__init__(self, *, k=16, fragment_length=3000, minimum_fraction=0.2, p_value=1e-03, percentage_identity=80, reference_size=5e9, protein=False)\n--
Create a new FastANI sequence sketch.
@@ -1072,8 +1076,8 @@ cdef class Mapper(_Parameterized):
Query the mapper for a complete genome.
Arguments:
- sequence (`str` or `bytes`): The genome to query the mapper
- with.
+ sequence (`str` or `bytes`): The closed genome to query the
+ mapper with.
Returns:
`list` of `~pyfastani.Hit`: The hits found for the query.
@@ -1162,7 +1166,18 @@ cdef class Minimizers:
cdef class Hit:
- """A single hit found when querying the mapper with a genome.
+ """A single hit found when querying a `Mapper` with a genome.
+
+ Attributes:
+ name (`object`): The name of the genome that produced a hit, as
+ given to `Sketch.add_genome` or `Sketch.add_draft`.
+ matches (`int`): The number of fragments that matched the target
+ genome.
+ fragments (`int`): The total number of fragments used to compare
+ the query and target genomes.
+ identity (`float`): The average nucleotide identity between the
+ two genomes, given as a percentage.
+
"""
# --- Attributes ---------------------------------------------------------
--
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