From b7250862ede5e95f721c4a61e68d46a6f18abbc2 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Wed, 16 Jun 2021 01:24:35 +0200
Subject: [PATCH] Update examples in `README.md` to use the new type interface
---
README.md | 10 ++++++----
pyfastani/_fastani.pyx | 25 +++++++++++++++++--------
2 files changed, 23 insertions(+), 12 deletions(-)
diff --git a/README.md b/README.md
index f6ec1b4..ee0e60b 100644
--- a/README.md
+++ b/README.md
@@ -77,19 +77,21 @@ instead of `bytes(record.seq)`.
import pyfastani
import Bio.SeqIO
-m = pyfastani.Mapper()
+sketch = pyfastani.Sketch()
# add a single draft genome to the mapper, and index it
ref = list(Bio.SeqIO.parse("vendor/FastANI/data/Shigella_flexneri_2a_01.fna", "fasta"))
-m.add_draft("Shigella_flexneri_2a_01", (bytes(record.seq) for record in ref))
-m.index()
+sketch.add_draft("S. flexneri", (bytes(record.seq) for record in ref))
+
+# index the sketch and get a mapper
+mapper = sketch.index()
# read the query and query the mapper
query = Bio.SeqIO.read("vendor/FastANI/data/Escherichia_coli_str_K12_MG1655.fna", "fasta")
hits = m.query_sequence(bytes(query.seq))
for hit in hits:
- print("Escherichia_coli_str_K12_MG1655", hit.name, hit.identity, hit.matches, hit.fragments)
+ print("E. coli", hit.name, hit.identity, hit.matches, hit.fragments)
```
### 🧪 [Scikit-bio](https://github.com/biocore/scikit-bio)
diff --git a/pyfastani/_fastani.pyx b/pyfastani/_fastani.pyx
index 27575b1..94c173d 100644
--- a/pyfastani/_fastani.pyx
+++ b/pyfastani/_fastani.pyx
@@ -363,11 +363,10 @@ cdef class Sketch:
cdef Mapper mapper = Mapper.__new__(Mapper)
mapper._param = self._param # copy params
mapper._sk = self._sk
- mapper._names = self._names
+ mapper._names = self._names.copy()
mapper._lengths.swap(self._lengths)
# reset the current sketch
self._sk = new Sketch_t(self._param)
- self._names = []
self.clear()
# return the new mapper
return mapper
@@ -517,13 +516,18 @@ cdef class Mapper:
contigs (iterable or `str` or `bytes`): The genome to query the mapper
with.
- Note:
+ Returns:
+ `list` of `~pyfastani.Hit`: The hits found for the query.
+
+ Hint:
Sequence must be larger than the window size, the k-mer size,
and the fragment length to be mapped, otherwise an empty list
of hits will be returned.
- Returns:
- `list` of `~pyfastani.Hit`: The hits found for the query.
+ Note:
+ This method is reentrant and releases the GIL when hashing
+ the blocks allowing to query the mapper in parallel for
+ several individual genomes.
"""
# delegate to C code
@@ -538,13 +542,18 @@ cdef class Mapper:
sequence (`str` or `bytes`): The genome to query the mapper
with.
- Note:
+ Returns:
+ `list` of `~pyfastani.Hit`: The hits found for the query.
+
+ Hint:
Sequence must be larger than the window size, the k-mer size,
and the fragment length to be mapped, otherwise an empty list
of hits will be returned.
- Returns:
- `list` of `~pyfastani.Hit`: The hits found for the query.
+ Note:
+ This method is reentrant and releases the GIL when hashing
+ the blocks allowing to query the mapper in parallel for
+ several individual genomes.
"""
# delegate to C code
--
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