Commit d64af6ce authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.5.4

parent e3d8d1b3

.travis.yml

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+2 −2
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@@ -11,8 +11,8 @@ python: 
    - 'pypy'

    - 'pypy3'

install:

    - pip wheel -f wheelhouse coverage biopython cython pysam pyvcf || true

    - pip install -f wheelhouse biopython cython pysam pyfasta coverage pyvcf || true

    - pip wheel -f wheelhouse coverage biopython cython pysam pyvcf numpy || true

    - pip install -f wheelhouse biopython cython pysam pyfasta coverage pyvcf numpy || true

    - python setup.py install

    - if [ ! -f samtools-1.2 ]; then curl -sL https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2 | tar -xjv; fi

    - cd samtools-1.2

README.rst

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+16 −5
Original line number Diff line number Diff line
@@ -261,6 +261,17 @@ Sequence names are truncated on any whitespace. This is a limitation of the inde 
    gi|557361099|gb|KF435150.1| Homo sapiens MDM4 protein variant Y (MDM4) mRNA, complete cds, alternatively spliced

    gi|557361097|gb|KF435149.1| Homo sapiens MDM4 protein variant G (MDM4) mRNA, complete cds



Records can be accessed efficiently as numpy arrays:



.. code:: python



    # new in v0.5.4

    >>> from pyfaidx import Fasta

    >>> import numpy as np

    >>> genes = Fasta('tests/data/genes.fasta')

    >>> np.asarray(genes['NM_001282543.1'])

    array(['C', 'C', 'C', ..., 'A', 'A', 'A'], dtype='|S1')



Sequence can be buffered in memory using a read-ahead buffer

for fast sequential access:

pyfaidx/__init__.py

+16 −1
Original line number Diff line number Diff line
@@ -5,6 +5,7 @@ Fasta file -> Faidx -> Fasta -> FastaRecord -> Sequence 


from __future__ import division

import os

import sys

from os.path import getmtime

from six import PY2, PY3, string_types, integer_types

from six.moves import zip_longest
@@ -19,9 +20,12 @@ import warnings 
from math import ceil

from threading import Lock



if sys.version_info > (3, ):

    buffer = memoryview



dna_bases = re.compile(r'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)')



__version__ = '0.5.3.1'

__version__ = '0.5.4'





class KeyFunctionError(ValueError):
@@ -762,6 +766,7 @@ class Faidx(object): 


class FastaRecord(object):

    __slots__ = ['name', '_fa']



    def __init__(self, name, fa):

        self.name = name

        self._fa = fa
@@ -887,6 +892,16 @@ class FastaRecord(object): 
        """ Read the actual defline from self._fa.faidx mdshw5/pyfaidx#54 """

        return self._fa.faidx.get_long_name(self.name)



    @property

    def __array_interface__(self):

        """ Implement numpy array interface for issue #139"""

        return {

            'shape': (len(self), ),

            'typestr': '|S1',

            'version': 3,

            'data': buffer(str(self).encode('ascii'))

        }





class MutableFastaRecord(FastaRecord):

    def __init__(self, name, fa):

tests/test_FastaRecord.py

+17 −5
Original line number Diff line number Diff line
@@ -9,6 +9,7 @@ from difflib import Differ 
path = os.path.dirname(__file__)

os.chdir(path)





class TestFastaRecord(TestCase):

    def setUp(self):

        pass
@@ -28,8 +29,9 @@ class TestFastaRecord(TestCase): 
        reference_upper = Fasta(filename, sequence_always_upper=True)

        reference_normal = Fasta(filename)

        os.remove('data/genes.fasta.lower.fai')

        assert reference_upper['gi|557361099|gb|KF435150.1|'][1:100].seq == reference_normal['gi|557361099|gb|KF435150.1|'][1:100].seq.upper()



        assert reference_upper['gi|557361099|gb|KF435150.1|'][

            1:100].seq == reference_normal['gi|557361099|gb|KF435150.1|'][

                1:100].seq.upper()



    def test_long_names(self):

        """ Test that deflines extracted using FastaRecord.long_name are
@@ -60,7 +62,8 @@ class TestFastaRecord(TestCase): 
                        line_len = len(line)

                        fasta_uniform_len.write(line)

                    elif line_len > len(line):

                        fasta_uniform_len.write(line.rstrip() + b'N' * (line_len - len(line)) + b'\n')

                        fasta_uniform_len.write(line.rstrip() + b'N' *

                                                (line_len - len(line)) + b'\n')

                    else:

                        fasta_uniform_len.write(line)

        fasta = Fasta('data/issue_62.fa', as_raw=True)
@@ -98,6 +101,14 @@ class TestFastaRecord(TestCase): 
        os.remove('data/padded.fasta')

        os.remove('data/padded.fasta.fai')



    def test_numpy_array(self):

        """ Test the __array_interface__ """

        import numpy

        filename = "data/genes.fasta.lower"

        reference = Fasta(filename)

        np_array = numpy.asarray(reference[0])

        assert isinstance(np_array, numpy.ndarray)





class TestMutableFastaRecord(TestCase):

    def setUp(self):
@@ -124,7 +135,8 @@ class TestMutableFastaRecord(TestCase): 
        fasta = Fasta('data/genes.fasta', mutable=False)

        chunk = fasta['gi|557361099|gb|KF435150.1|'][0:100]

        mutable['gi|557361099|gb|KF435150.1|'][0:100] = chunk.seq

        assert str(fasta['gi|557361099|gb|KF435150.1|']) == str(mutable['gi|557361099|gb|KF435150.1|'])

        assert str(fasta['gi|557361099|gb|KF435150.1|']) == str(

            mutable['gi|557361099|gb|KF435150.1|'])



    def test_mutate_fasta_to_N(self):

        mutable = Fasta('data/genes_mutable.fasta', mutable=True)