Commit 404a772c authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.8.6

parent f4801501

.travis.yml

+15 −1
Original line number Diff line number Diff line
@@ -6,6 +6,12 @@ python: 
  - '2.7'

  - '3.5'



stages:

  - lint

  - test

  - name: deploy

    if: tag IS present



env:

  global:

    - PYTHON=python
@@ -13,12 +19,19 @@ env: 
    - secure: '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'



_deploy_common: &deploy_common

  if: tag IS present

  install:

    - $PYTHON -m pip install cibuildwheel twine



matrix:

  include:

    - stage: lint

      python: '3.5'

      addons: {}

      install:

        - $PYTHON -m pip install flake8 flake8-import-order

      script:

        - flake8 .



    - stage: deploy

      python: '3.5'

      services:
@@ -32,6 +45,7 @@ matrix: 
        - $PYTHON setup.py sdist

        - twine check dist/*

        - twine upload --skip-existing dist/*



    - stage: deploy

      os: osx

      language: generic

doc/source/conf.py

+4 −11
Original line number Diff line number Diff line
@@ -14,15 +14,9 @@ 
# All configuration values have a default; values that are commented out

# serve to show the default.



import sys, os



# If your extensions are in another directory, add it here. If the directory

# is relative to the documentation root, use os.path.abspath to make it

# absolute, like shown here.

#sys.path.append(os.path.abspath('.'))

## curr_dir = os.path.dirname( __file__ )

## bx_dir = os.path.join( curr_dir, '..', '..', 'lib')

## sys.path.insert( 0, bx_dir )

import bx



# General configuration
@@ -175,10 +169,9 @@ htmlhelp_basename = 'bx-doc' 


# Grouping the document tree into LaTeX files. List of tuples

# (source start file, target name, title, author, document class [howto/manual]).

latex_documents = [

  ('index', 'bx-python.tex', ur'bx-python Documentation',

   ur'James Taylor', 'manual'),

]

latex_documents = [(

    'index', 'bx-python.tex', u'bx-python Documentation',

    u'James Taylor', 'manual'), ]



# The name of an image file (relative to this directory) to place at the top of

# the title page.

ez_setup.py

+24 −17
Original line number Diff line number Diff line
@@ -6,18 +6,16 @@ Setuptools bootstrapping installer. 
Run this script to install or upgrade setuptools.

"""



import contextlib

import optparse

import os

import platform

import shutil

import subprocess

import sys

import tempfile

import zipfile

import optparse

import subprocess

import platform

import textwrap

import contextlib

import warnings



import zipfile

from distutils import log



try:
@@ -244,6 +242,8 @@ def has_powershell(): 
        except Exception:

            return False

    return True





download_file_powershell.viable = has_powershell
@@ -260,6 +260,8 @@ def has_curl(): 
        except Exception:

            return False

    return True





download_file_curl.viable = has_curl
@@ -276,6 +278,8 @@ def has_wget(): 
        except Exception:

            return False

    return True





download_file_wget.viable = has_wget
@@ -291,6 +295,8 @@ def download_file_insecure(url, target): 
    # Write all the data in one block to avoid creating a partial file.

    with open(target, "wb") as dst:

        dst.write(data)





download_file_insecure.viable = lambda: True
@@ -387,5 +393,6 @@ def main(): 
    archive = download_setuptools(**_download_args(options))

    return _install(archive, _build_install_args(options))





if __name__ == '__main__':

    sys.exit(main())

lib/bx/align/__init__.py

+1 −1
Original line number Diff line number Diff line
@@ -4,4 +4,4 @@ the abstract alignment classes and `maf`, `axt`, and `lav` for readers and 
writers in various formats.

"""



from bx.align.core import *
 
from bx.align.core import *  # noqa

lib/bx/align/axt.py

+113 −86
Original line number Diff line number Diff line
@@ -4,22 +4,29 @@ alignments. 


.. _AXT: http://genome.ucsc.edu/goldenPath/help/axt.html

"""

import itertools



from six import Iterator



from bx import interval_index_file

from bx.align import *

from bx.align import (

    Alignment,

    Component,

    src_split

)



# Tools for dealing with pairwise alignments in AXT format





class MultiIndexed(object):

    """Similar to 'indexed' but wraps more than one axt_file"""



    def __init__(self, axt_filenames, keep_open=False):

        self.indexes = [Indexed(axt_file, axt_file + ".index") for axt_file in axt_filenames]



    def get(self, src, start, end):

        blocks = []

        for index in self.indexes: blocks += index.get( src, start, end )

        for index in self.indexes:

            blocks += index.get(src, start, end)

        return blocks
@@ -27,14 +34,17 @@ class Indexed( object ): 
    """Indexed access to a axt using overlap queries, requires an index file"""



    def __init__(self, axt_filename, index_filename=None, keep_open=False, species1=None, species2=None, species_to_lengths=None, support_ids=False):

        if index_filename is None: index_filename = axt_filename + ".index"

        if index_filename is None:

            index_filename = axt_filename + ".index"

        self.indexes = interval_index_file.Indexes(filename=index_filename)

        self.axt_filename = axt_filename

        # nota bene: (self.species1 = species1 or "species1") is incorrect if species1=""

        self.species1 = species1

        if (self.species1 == None): self.species1 = "species1"

        if self.species1 is None:

            self.species1 = "species1"

        self.species2 = species2

        if (self.species2 == None): self.species2 = "species2"

        if self.species2 is None:

            self.species2 = "species2"

        self.species_to_lengths = species_to_lengths

        self.support_ids = support_ids            # for extra text at end of axt header lines

        if keep_open:
@@ -58,6 +68,7 @@ class Indexed( object ): 
            finally:

                f.close()





class Reader(Iterator):

    """Iterate over all axt blocks in a file in order"""
@@ -65,9 +76,11 @@ class Reader( Iterator ): 
        self.file = file

        # nota bene: (self.species1 = species1 or "species1") is incorrect if species1=""

        self.species1 = species1

        if (self.species1 == None): self.species1 = "species1"

        if self.species1 is None:

            self.species1 = "species1"

        self.species2 = species2

        if (self.species2 == None): self.species2 = "species2"

        if self.species2 is None:

            self.species2 = "species2"

        self.species_to_lengths = species_to_lengths

        self.support_ids = support_ids            # for extra text at end of axt header lines

        self.attributes = {}
@@ -81,28 +94,34 @@ class Reader( Iterator ): 
    def close(self):

        self.file.close()





class ReaderIter(Iterator):

    def __init__(self, reader):

        self.reader = reader



    def __iter__(self):

        return self



    def __next__(self):

        v = next(self.reader)

        if not v: raise StopIteration

        if not v:

            raise StopIteration

        return v





class Writer(object):



    def __init__(self, file, attributes={}):

        self.file = file

        self.block = 0

        self.src_split = True

        if ("src_split" in attributes):

        if "src_split" in attributes:

            self.src_split = attributes["src_split"]



    def write(self, alignment):

        if (len(alignment.components) != 2):

            raise ValueError("%d-component alignment is not compatible with axt" % \

        if len(alignment.components) != 2:

            raise ValueError(

                "%d-component alignment is not compatible with axt" %

                len(alignment.components))

        c1 = alignment.components[0]

        c2 = alignment.components[1]
@@ -111,13 +130,14 @@ class Writer( object ): 
            c1 = c1.reverse_complement()

            c2 = c2.reverse_complement()



        if (self.src_split):

        if self.src_split:

            spec1, chr1 = src_split(c1.src)

            spec2, chr2 = src_split(c2.src)

        else:

            chr1, chr2 = c1.src, c2.src



        self.file.write( "%d %s %d %d %s %d %d %s %s\n" % \

        self.file.write(

            "%d %s %d %d %s %d %d %s %s\n" %

            (self.block, chr1, c1.start+1, c1.start+c1.size,

             chr2, c2.start+1, c2.start+c2.size, c2.strand,

             alignment.score))
@@ -139,25 +159,30 @@ class Writer( object ): 
# first species is always on plus strand

# when second species is on minus strand, start and stop are counted from sequence end





def read_next_axt(file, species1, species2, species_to_lengths=None, support_ids=False):

    line = readline(file, skip_blank=True)

    if not line: return

    if not line:

        return

    fields = line.split()

    if (len(fields) < 9) or ((not support_ids) and (len(fields) > 9)):

    if len(fields) < 9 or (not support_ids and len(fields) > 9):

        raise ValueError("bad axt-block header: %s" % line)

    attributes = {}

    if (len(fields) > 9):

    if len(fields) > 9:

        attributes["id"] = "_".join(fields[9:])

    seq1 = readline(file)

    if not line or line.isspace(): raise ValueError("incomplete axt-block; header: %s" % line)

    if not line or line.isspace():

        raise ValueError("incomplete axt-block; header: %s" % line)

    seq2 = readline(file)

    if not line or line.isspace(): raise ValueError("incomplete axt-block; header: %s" % line)

    if not line or line.isspace():

        raise ValueError("incomplete axt-block; header: %s" % line)

    # Build 2 component alignment

    alignment = Alignment(attributes=attributes, species_to_lengths=species_to_lengths)

    # Build component for species 1

    component = Component()

    component.src = fields[1]

    if (species1 != ""): component.src = species1 + "." + component.src

    if species1 != "":

        component.src = species1 + "." + component.src

    component.start = int(fields[2]) - 1  # (axt intervals are origin-1

    end = int(fields[3])                  # and inclusive on both ends)

    component.size = end - component.start
@@ -167,7 +192,8 @@ def read_next_axt( file, species1, species2, species_to_lengths=None, support_id 
    # Build component for species 2

    component = Component()

    component.src = fields[4]

    if (species2 != ""): component.src = species2 + "." + component.src

    if species2 != "":

        component.src = species2 + "." + component.src

    component.start = int(fields[5]) - 1

    end = int(fields[6])

    component.size = end - component.start
@@ -177,18 +203,19 @@ def read_next_axt( file, species1, species2, species_to_lengths=None, support_id 
    # add score

    try:

        alignment.score = int(fields[8])

    except:

    except ValueError:

        try:

            alignment.score = float(fields[8])

        except:

        except ValueError:

            alignment.score = fields[8]

    return alignment





def readline(file, skip_blank=False):

    """Read a line from provided file, skipping any blank or comment lines"""

    while 1:

    while True:

        line = file.readline()

        if not line: return None

        if not line:

            return None

        if line[0] != '#' and not (skip_blank and line.isspace()):

            return line