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# Copyright 1999 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from __future__ import print_function
import string
from Bio._py3k import StringIO
from Bio import File
import warnings
from Bio import BiopythonDeprecationWarning
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonDeprecationWarning)
from Bio import ParserSupport
# pyUnit
def pb(b):
if b:
return 1
return 0
# TaggingConsumer
print("Running tests on TaggingConsumer")
class TestHandle(object):
def write(self, s):
print(s)
h = TestHandle()
tc = ParserSupport.TaggingConsumer(handle=h, colwidth=5)
tc.start_section() # '***** start_section\n'
tc.test1('myline') # 'test1: myline\n'
tc.end_section() # '***** end_section\n'
# is_blank_line
print("Running tests on is_blank_line")
is_blank_line = lambda *args, **keywds: \
pb(ParserSupport.is_blank_line(*args, **keywds))
print(is_blank_line('\n')) # 1
print(is_blank_line('\r\n')) # 1
print(is_blank_line('\r')) # 1
print(is_blank_line('')) # 1
print(is_blank_line('', allow_spaces=1)) # 1
print(is_blank_line('', allow_spaces=0)) # 1
print(is_blank_line(string.whitespace, allow_spaces=1)) # 1
print(is_blank_line('hello')) # 0
print(is_blank_line('hello', allow_spaces=1)) # 0
print(is_blank_line('hello', allow_spaces=0)) # 0
print(is_blank_line(string.whitespace, allow_spaces=0)) # 0
# safe_readline
print("Running tests on safe_readline")
data = """This
file"""
h = File.UndoHandle(StringIO(data))
safe_readline = ParserSupport.safe_readline
print(safe_readline(h)) # "This"
print(safe_readline(h)) # "file"
try:
safe_readline(h)
except ValueError:
print("correctly failed")
else:
print("ERROR, should have failed")
# safe_peekline
print("Running tests on safe_peekline")
safe_peekline = ParserSupport.safe_peekline
data = """This
file"""
h = File.UndoHandle(StringIO(data))
print(safe_peekline(h)) # "This"
h.readline()
print(safe_peekline(h)) # "file"
h.readline()
try:
safe_peekline(h)
except ValueError:
print("correctly failed")
else:
print("ERROR, should have failed")
h.saveline('hello')
print(safe_peekline(h)) # 'hello'
# read_and_call
print("Running tests on read_and_call")
data = """>gi|132871|sp|P19947|RL30_BACSU 50S RIBOSOMAL PROTEIN L30 (BL27)
MAKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVSHLVSVKEQ
>gi|132679|sp|P19946|RL15_BACSU 50S RIBOSOMAL PROTEIN L15
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQRLPKRGFTNIN
RKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKKLTVKANKFSASAKEAVEAAG
GTAEVI
"""
h = File.UndoHandle(StringIO(data))
rac = ParserSupport.read_and_call
lines = []
def m(line):
lines.append(line)
rac(h, m)
print(lines[-1][:10]) # '>gi|132871'
rac(h, m, start='MAKLE', end='KEQ', contains='SVIG')
rac(h, m, blank=0)
# These should be errors. If they're not, then complain.
try:
rac(h, m, blank=1)
except ValueError:
print("correctly failed")
else:
print("ERROR, should have failed")
try:
rac(h, m, start='foobar')
except ValueError:
print("correctly failed")
else:
print("ERROR, should have failed")
try:
rac(h, m, end='foobar')
except ValueError:
print("correctly failed")
else:
print("ERROR, should have failed")
try:
rac(h, m, contains='foobar')
except ValueError:
print("correctly failed")
else:
print("ERROR, should have failed")
try:
rac(h, m, blank=0)
except ValueError:
print("correctly failed")
else:
print("ERROR, should have failed")
# attempt_read_and_call
print("Running tests on attempt_read_and_call")
data = """>gi|132871|sp|P19947|RL30_BACSU 50S RIBOSOMAL PROTEIN L30 (BL27)
MAKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVSHLVSVKEQ
>gi|132679|sp|P19946|RL15_BACSU 50S RIBOSOMAL PROTEIN L15
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQRLPKRGFTNIN
RKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKKLTVKANKFSASAKEAVEAAG
GTAEVI"""
h = File.UndoHandle(StringIO(data))
arac = lambda *args, **keywds: \
pb(ParserSupport.attempt_read_and_call(*args, **keywds))
lines = []
def m(line):
lines.append(line)
print(arac(h, m, contains="RIBOSOMAL PROTEIN")) # 1
print(arac(h, m, start="foobar")) # 0
print(arac(h, m, blank=1)) # 0
print(arac(h, m, end="LVSVKEQ")) # 1