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Merge pull request #6429 from johnbradley/python3-fixes
Python 3 fixes from GCC-BOSC-2018
This commit is contained in:
Nicola Soranzo
@@ -1002,8 +1002,7 @@ def get_file_peek(file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipc
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:type is_multi_byte: bool
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>>> fname = get_test_fname('4.bed')
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>>> get_file_peek(fname, LINE_COUNT=1)
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u'chr22\\t30128507\\t31828507\\tuc003bnx.1_cds_2_0_chr22_29227_f\\t0\\t+\\n'
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>>> assert get_file_peek(fname, LINE_COUNT=1) == u'chr22\\t30128507\\t31828507\\tuc003bnx.1_cds_2_0_chr22_29227_f\\t0\\t+\\n'
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"""
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# Set size for file.readline() to a negative number to force it to
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# read until either a newline or EOF. Needed for datasets with very
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@@ -105,7 +105,8 @@ def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload"):
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to Posix line endings.
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>>> fname = get_test_fname('temp.txt')
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>>> open(fname, 'wt').write("1 2\\r3 4")
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>>> with open(fname, 'wt') as fh:
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... fh.write("1 2\\r3 4")
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>>> convert_newlines(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir())
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(2, None)
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>>> open(fname).read()
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@@ -133,7 +134,8 @@ def sep2tabs(fname, in_place=True, patt="\\s+", tmp_dir=None, tmp_prefix="gxuplo
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Transforms in place a 'sep' separated file to a tab separated one
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>>> fname = get_test_fname('temp.txt')
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>>> open(fname, 'wt').write("1 2\\n3 4\\n")
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>>> with open(fname, 'wt') as fh:
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... fh.write("1 2\\n3 4\\n")
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>>> sep2tabs(fname)
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(2, None)
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>>> open(fname).read()
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@@ -170,7 +172,8 @@ def convert_newlines_sep2tabs(fname, in_place=True, patt="\\s+", tmp_dir=None, t
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so that files do not need to be read twice
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>>> fname = get_test_fname('temp.txt')
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>>> open(fname, 'wt').write("1 2\\r3 4")
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>>> with open(fname, 'wt') as fh:
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... fh.write("1 2\\r3 4")
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>>> convert_newlines_sep2tabs(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir())
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(2, None)
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>>> open(fname).read()
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@@ -596,10 +599,11 @@ class FilePrefix(object):
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def line_iterator(self):
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s = self.string_io()
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s_len = len(s.getvalue())
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for line in s:
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if line.endswith("\n") or line.endswith("\r"):
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yield line
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elif s.pos == s.len and not self.truncated:
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elif s.tell() == s_len and not self.truncated:
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# At the end, return the last line if it wasn't truncated when reading it in.
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yield line
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@@ -265,8 +265,7 @@ class TextToolParameter(ToolParameter):
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>>> p = TextToolParameter(None, XML('<param name="_name" type="text" value="default" />'))
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>>> print(p.name)
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_name
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>>> sorted(p.to_dict(trans).items())
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[('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'TextToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', u'default')]
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>>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'TextToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', u'default')]
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"""
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def __init__(self, tool, input_source):
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@@ -310,10 +309,8 @@ class IntegerToolParameter(TextToolParameter):
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>>> p = IntegerToolParameter(None, XML('<param name="_name" type="integer" value="10" />'))
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>>> print(p.name)
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_name
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>>> sorted(p.to_dict(trans).items())
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[('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'IntegerToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'integer'), ('value', u'10')]
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>>> type(p.from_json("10", trans))
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<type 'int'>
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>>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'IntegerToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'integer'), ('value', u'10')]
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>>> assert type(p.from_json("10", trans)) == int
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>>> type(p.from_json("_string", trans))
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Traceback (most recent call last):
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...
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@@ -386,10 +383,8 @@ class FloatToolParameter(TextToolParameter):
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>>> p = FloatToolParameter(None, XML('<param name="_name" type="float" value="3.141592" />'))
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>>> print(p.name)
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_name
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>>> sorted(p.to_dict(trans).items())
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[('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'FloatToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'float'), ('value', u'3.141592')]
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>>> type(p.from_json("36.1", trans))
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<type 'float'>
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>>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', None), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('max', None), ('min', None), ('model_class', 'FloatToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'float'), ('value', u'3.141592')]
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>>> assert type(p.from_json("36.1", trans)) == float
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>>> type(p.from_json("_string", trans))
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Traceback (most recent call last):
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...
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@@ -462,8 +457,7 @@ class BooleanToolParameter(ToolParameter):
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>>> p = BooleanToolParameter(None, XML('<param name="_name" type="boolean" checked="yes" truevalue="_truevalue" falsevalue="_falsevalue" />'))
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>>> print(p.name)
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_name
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>>> sorted(p.to_dict(trans).items())
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[('argument', None), ('falsevalue', '_falsevalue'), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'BooleanToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('truevalue', '_truevalue'), ('type', 'boolean'), ('value', 'true')]
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>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('falsevalue', '_falsevalue'), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'BooleanToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('truevalue', '_truevalue'), ('type', 'boolean'), ('value', 'true')]
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>>> print(p.from_json('true'))
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True
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>>> print(p.to_param_dict_string(True))
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@@ -676,8 +670,7 @@ class HiddenToolParameter(ToolParameter):
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>>> p = HiddenToolParameter(None, XML('<param name="_name" type="hidden" value="_value"/>'))
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>>> print(p.name)
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_name
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>>> sorted(p.to_dict(trans).items())
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[('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'HiddenToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'hidden'), ('value', u'_value')]
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>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'HiddenToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'hidden'), ('value', u'_value')]
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"""
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def __init__(self, tool, input_source):
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@@ -704,8 +697,7 @@ class ColorToolParameter(ToolParameter):
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_name
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>>> print(p.to_param_dict_string("#fdeada"))
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#fdeada
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>>> sorted(p.to_dict(trans).items())
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[('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ColorToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'color'), ('value', u'#ffffff')]
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>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'ColorToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'color'), ('value', u'#ffffff')]
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>>> p = ColorToolParameter(None, XML('<param name="_name" type="color" value="#ffffff" rgb="True"/>'))
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>>> print(p.to_param_dict_string("#fdeada"))
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(253, 234, 218)
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@@ -743,8 +735,7 @@ class BaseURLToolParameter(HiddenToolParameter):
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>>> p = BaseURLToolParameter(None, XML('<param name="_name" type="base_url" value="_value"/>'))
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>>> print(p.name)
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_name
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>>> sorted(p.to_dict(trans).items())
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[('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'BaseURLToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'base_url'), ('value', u'_value')]
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>>> assert sorted(p.to_dict(trans).items()) == [('argument', None), ('help', ''), ('hidden', True), ('is_dynamic', False), ('label', ''), ('model_class', 'BaseURLToolParameter'), ('name', '_name'), ('optional', False), ('refresh_on_change', False), ('type', 'base_url'), ('value', u'_value')]
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"""
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def __init__(self, tool, input_source):
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@@ -8,7 +8,6 @@ from __future__ import print_function
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import logging
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import os
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import resource
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import string
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import sys
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import tempfile
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from copy import deepcopy
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@@ -19,11 +18,15 @@ import bx.interval_index_file
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import bx.intervals
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from six.moves import xrange
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try:
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from string import maketrans
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except ImportError:
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maketrans = str.maketrans
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assert sys.version_info[:2] >= (2, 6)
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log = logging.getLogger(__name__)
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GAP_CHARS = ['-']
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SRC_SPLIT_CHAR = '.'
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@@ -138,7 +141,7 @@ class TempFileHandler(object):
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# an object corresponding to a reference layered alignment
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class RegionAlignment(object):
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DNA_COMPLEMENT = string.maketrans("ACGTacgt", "TGCAtgca")
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DNA_COMPLEMENT = maketrans("ACGTacgt", "TGCAtgca")
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MAX_SEQUENCE_SIZE = sys.maxsize # Maximum length of sequence allowed
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def __init__(self, size, species=[], temp_file_handler=None):
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@@ -222,7 +225,7 @@ class GenomicRegionAlignment(RegionAlignment):
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class SplicedAlignment(object):
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DNA_COMPLEMENT = string.maketrans("ACGTacgt", "TGCAtgca")
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DNA_COMPLEMENT = maketrans("ACGTacgt", "TGCAtgca")
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def __init__(self, exon_starts, exon_ends, species=[], temp_file_handler=None):
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if not isinstance(exon_starts, list):
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