def test_each():
upper = lambda x: x.upper()
eq_(run(Fun(linecmd('echo "a\nb\nc"')) |
each(upper) |
strip('\n') |
join),
'ABC')
def multiple_alignment_use_files(file_input, alignment_type=SeqTypeData().TYPE_DEFAULT):
muscle_cmd = SeqTypeData().type2cmd_f[alignment_type]
result = iterpipes.run(iterpipes.linecmd(str(muscle_cmd) + " -in \"" + file_input + "\""))
result_list = []
for i in result:
result_list.append(i.strip())
# iores = StringIO()
# for i in result_list:
# print(i[0])
# iores.write(i)
name = file_input[:file_input.rfind('.')] + "-aligned.fa"
with open(name, "wt") as tmpfd:
tmpfd.write("\n".join(result_list))
return fasta_tools.read_fasta(name, False)
def multiple_alignment_use_files(file_input,
alignment_type=SeqTypeData().TYPE_DEFAULT):
muscle_cmd = SeqTypeData().type2cmd_f[alignment_type]
result = iterpipes.run(
iterpipes.linecmd(str(muscle_cmd) + " -in \"" + file_input + "\""))
result_list = []
for i in result:
result_list.append(i.strip())
# iores = StringIO()
# for i in result_list:
# print(i[0])
# iores.write(i)
name = file_input[:file_input.rfind('.')] + "-aligned.fa"
with open(name, "wt") as tmpfd:
tmpfd.write("\n".join(result_list))
return fasta_tools.read_fasta(name, False)
def test_linecmd():
text = six.u('абв\nabc\n')
tr = linecmd('tr a-z A-Z')
eq_(list(tr(text)), [six.u('абв\n'), six.u('ABC\n')])