def main():
'''
define input and output files and, write final output to a file handle
:return:
'''
argvs = get_cli_args()
in_file = argvs.INFILE
out_file = argvs.OUTFILE
fh_in = get_fh(in_file, "r")
list_headers, list_sequences = get_header_and_sequence_lists(fh_in)
fh_out = get_fh(out_file, "w")
print_sequence_stats(list_headers, list_sequences, fh_out)
fh_out.close()
def test_get_fh():
fh_in = open("test.txt", "r")
assert get_fh("test.txt", "r") == fh_in
fh_out = open("out.txt", "w")
assert get_fh("out.txt", "w") == fh_out
def test_get_fh_4_IOError():
# does it raise IOError
# this should exit
with pytest.raises(SystemExit):
get_fh("does_not_exist.txt", "r")
def test_get_fh_4_ValueError():
# does it raise IOError
# this should exit
with pytest.raises(SystemExit):
get_fh("ss.txt", "rrr")
"""
Test Suite for PDB_FASTA_SPLITTER
"""
import pytest
# pylint: disable=C0116
# pylint: disable=C0103
from pdb_fasta_splitter import write_in_file, _check_size_of_lists, \
get_header_and_sequence_lists, get_fh
LIST_HEADER = ['>1sequence', '>1secstr', ">2sequence", ">2secstr"]
LIST_SEQS = ['ACGTAC', 'ACGTCC', 'ACCGGT', 'AAAACT']
LIST_SEQS_NOT_EQUAL = ['ACGTAC', 'ACGTCC', 'ACCGGT']
FILE_HANDLE = get_fh("ss.txt", "r")
AMINO_ACID = get_fh("test_pdb_protein.fasta", "w")
SEC_STR = get_fh("test_pdb_ss.fasta", "w")
def test_write_in_file():
count_amino, count_sec_str = write_in_file(AMINO_ACID, SEC_STR, LIST_HEADER, LIST_SEQS)
assert count_amino == 2
assert count_sec_str == 2
def test__check_size_of_lists():
assert _check_size_of_lists(LIST_HEADER, LIST_SEQS)
with pytest.raises(SystemExit):
_check_size_of_lists(LIST_HEADER, LIST_SEQS_NOT_EQUAL)