New upstream version 0.5.8

    - '3.7'

    - '3.6'

    - '3.5'

    - '3.4'

    - '2.7'

    - 'pypy'

    - 'pypy3'

install:

    - pip wheel -f wheelhouse cython pysam numpy || true

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

    - pip install -f wheelhouse -e git+https://github.com/biopython/biopython.git#egg=biopython || true

    - pip install -f wheelhouse cython pysam biopython requests coverage pyfasta 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

    - export PATH=$PATH:$PWD

    - cd ..

before_script:

    - if [ $(python --version) -gt 2.6 ]; then env pip install biopython; fi

    - env python tests/data/download_gene_fasta.py

    - python tests/data/download_gene_fasta.py

script: nosetests --with-coverage --cover-package=pyfaidx

deploy:

  provider: pypi

    secure: MbSaeuitkVTZqxa0PJ3RcR1aMf+B/sMbcx2sWOo9xfLlRFDFpYWJZ0EfXWEhrVu2YWXpBsasgunTDWSi0jNcZMH92MzOC+UTVYr45LO5sy6hm4iSiAgm/DPgYWdjP0SFKr7eL/HWPS+gHvgkXL1upleX21O358bxaezoasuKFvs=

  on:

    all_branches: true

    python: 3.6

    python: 3.7

    tags: true

    repo: mdshw5/pyfaidx

matrix:

  include:

    - os: windows

      language: sh

      python: "3.7"

      before_install:

        - choco install python3

        - export PATH="/c/Python37:/c/Python37/Scripts:$PATH"

        - python -m virtualenv $HOME/venv

        - source $HOME/venv/Scripts/activate

  allow_failures:

    - python: 'nightly'

    - python: 'pypy3'

    - python: 'pypy'

    - python: nightly

    - python: pypy3

    - python: pypy

    - os: windows

  fast_finish: true

cache:

    directories:

        - wheelhouse

after_success:

    - bash <(curl -s https://codecov.io/bash)

    - if [ $TRAVIS_PYTHON_VERSION == '3.4' ] && [ $TRAVIS_TAG ]; then python scripts/benchmark.py 1000; fi

environment:

  matrix:

    # For Python versions available on Appveyor, see

    # http://www.appveyor.com/docs/installed-software#python

    - PYTHON: "C:\\Python27"

    - PYTHON: "C:\\Python33"

    - PYTHON: "C:\\Python34"

    - PYTHON: "C:\\Python35"

    - PYTHON: "C:\\Python27-x64"

    - PYTHON: "C:\\Python33-x64"

      DISTUTILS_USE_SDK: "1"

    - PYTHON: "C:\\Python34-x64"

      DISTUTILS_USE_SDK: "1"

    - PYTHON: "C:\\Python35-x64"

install:

  # Fix for problem building extensions for x64 under Python 3.3 and 3.4

  # See: http://help.appveyor.com/discussions/problems/4278-cant-build-some-c-extensions-with-python-34-x64

  # Used same solution as Matplotlib: https://github.com/matplotlib/matplotlib/blob/master/appveyor.yml

  - cmd: copy ci\appveyor\vcvars64.bat "C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\bin\amd64"

  # We need wheel installed to build wheels

  - "%PYTHON%\\python.exe -m pip install -r dev-requirements.txt"

build: off

test_script:

  - "%PYTHON%\\python.exe setup.py nosetests"

CALL "C:\Program Files\Microsoft SDKs\Windows\v7.1\Bin\SetEnv.cmd" /x64

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

__version__ = '0.5.7'

__version__ = '0.5.8'

class KeyFunctionError(ValueError):

        """

        return len(self.seq)

    def __eq__(self, other):

        """

        >>> Sequence('chr1', 'ACT') == 'ACT'

        True

        """

        return str(self) == str(other)

    @property

    def fancy_name(self):

        """ Return the fancy name for the sequence, including start, end, and complementation.

        for rname in self.keys():

            yield self[rname]

    def __len__(self):

        """Return the cumulative length of all FastaRecords in self.records."""

        return sum(len(record) for record in self)

    def get_seq(self, name, start, end, rc=False):

        """Return a sequence by record name and interval [start, end).

                lower.write(line)

def fetch_chr22(filename):

    from subprocess import Popen, PIPE

    import requests

    import gzip

    grch36 = 'ftp://ftp-trace.ncbi.nih.gov//1000genomes/ftp/pilot_data/technical/reference/human_b36_male.fa.gz'

    curl = Popen(['curl', '-s', grch36], stdout=PIPE)

    gz = Popen(['gzip', '-dcq'], stdin=curl.stdout, stdout=PIPE)

    with gz.stdout as remote:

        with open(filename, 'w') as fasta:

    with requests.get('https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/technical/reference/human_b36_male.fa.gz') as compressed:

        with open(filename, 'w') as fasta, gzip.GzipFile(fileobj=compressed.raw) as gz:

            chr22 = False

            for line in remote:

            for line in gz:

                if line[0:3] == '>22':

                    fasta.write(line)

                    chr22 = True

        fake_file.write('N' * mod_70 + '\n')

def bgzip_compress_fasta(filename):

    from subprocess import call

    call(' '.join(['bgzip', '-c', filename, '>', filename + '.gz']), shell=True)

    from Bio.bgzf import BgzfWriter

    with BgzfWriter(filename=filename + '.gz') as compressed, open(filename, 'r') as fasta:

        for line in fasta:

            compressed.write(line)

def fetch_chr22_vcf(filename):

    from subprocess import call

    call(['curl', '-s', 'ftp://ftp-trace.ncbi.nih.gov//1000genomes/ftp/pilot_data/release/2010_07/exon/snps/CEU.exon.2010_03.genotypes.vcf.gz',

          '-o', filename])

    call(['curl', '-s', 'ftp://ftp-trace.ncbi.nih.gov//1000genomes/ftp/pilot_data/release/2010_07/exon/snps/CEU.exon.2010_03.genotypes.vcf.gz.tbi',

          '-o', filename + '.tbi'])

    import requests

    with requests.get('https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/exon/snps/CEU.exon.2010_03.genotypes.vcf.gz') as vcf:

        with open(filename, 'wb') as out:

            out.write(vcf.content)

    with requests.get('https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/exon/snps/CEU.exon.2010_03.genotypes.vcf.gz.tbi') as tbi:

        with open(filename + '.tbi', 'wb') as out:

            out.write(tbi.content)

if __name__ == "__main__":