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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Part of pymzml test cases
"""
import os
import re
import pymzml.run as run
import unittest
from pymzml.spec import Spectrum, Chromatogram
import test_file_paths
class runTest(unittest.TestCase):
"""
"""
def setUp(self):
"""
"""
self.paths = test_file_paths.paths
file_compressed_indexed = self.paths[2]
file_compressed_unindexed = self.paths[1]
file_uncompressed_indexed = self.paths[0]
file_uncompressed_unindexed = self.paths[0]
file_bad_obo_version = self.paths[10]
file_no_obo_version = self.paths[11]
self.reader_compressed_indexed = run.Reader(file_compressed_indexed)
self.reader_compressed_unindexed = run.Reader(file_compressed_unindexed)
self.reader_uncompressed_indexed = run.Reader(file_uncompressed_indexed)
self.reader_uncompressed_unindexed = run.Reader(file_uncompressed_unindexed)
self.reader_bad_obo_version = run.Reader(file_bad_obo_version)
self.reader_set_obo_version = run.Reader(
file_bad_obo_version, obo_version="3.25.0"
)
self.reader_set_year_obo_version = run.Reader(
file_uncompressed_indexed, obo_version="23:06:2017"
)
self.reader_set_bad_obo_version = run.Reader(
file_uncompressed_indexed, obo_version="bad_obo_version"
)
self.reader_set_no_obo_version = run.Reader(file_no_obo_version)
def test_with_context(self):
with run.Reader(self.paths[0]) as reader:
reader[2]
def test_setting_measured_precision(self):
reader = run.Reader(self.paths[2], MS_precisions={1: 61})
spec = reader[1]
self.assertEqual(spec.measured_precision, 61)
def test_determine_file_encoding(self):
"""
"""
encoding = self.reader_compressed_indexed._determine_file_encoding(
self.paths[2]
)
self.assertEqual(encoding, "ISO-8859-1")
encoding = self.reader_compressed_unindexed._determine_file_encoding(
self.paths[1]
)
self.assertEqual(encoding, "ISO-8859-1")
encoding = self.reader_uncompressed_indexed._determine_file_encoding(
self.paths[3]
)
self.assertEqual(encoding, "ISO-8859-1")
encoding = self.reader_uncompressed_unindexed._determine_file_encoding(
self.paths[0]
)
self.assertEqual(encoding, "ISO-8859-1")
def test_init_iter(self):
"""
"""
mzml_version = self.reader_compressed_indexed.info["mzml_version"]
obo_version = self.reader_compressed_indexed.info["obo_version"]
spec_count = self.reader_compressed_indexed.info["spectrum_count"]
run_id = self.reader_uncompressed_unindexed.info["run_id"]
start_time = self.reader_uncompressed_unindexed.info["start_time"]
self.assertEqual(mzml_version, "1.1.0")
self.assertEqual(obo_version, "3.25.0")
self.assertIsInstance(spec_count, int)
self.assertEqual(run_id, "exp105-01-ds5562-Pos")
self.assertEqual(start_time, "2013-09-10T10:31:08Z")
mzml_version = self.reader_compressed_unindexed.info["mzml_version"]
obo_version = self.reader_compressed_unindexed.info["obo_version"]
spec_count = self.reader_compressed_unindexed.info["spectrum_count"]
run_id = self.reader_uncompressed_unindexed.info["run_id"]
start_time = self.reader_uncompressed_unindexed.info["start_time"]
self.assertEqual(mzml_version, "1.1.0")
self.assertEqual(obo_version, "3.25.0")
self.assertIsInstance(spec_count, int)
self.assertEqual(run_id, "exp105-01-ds5562-Pos")
self.assertEqual(start_time, "2013-09-10T10:31:08Z")
mzml_version = self.reader_uncompressed_indexed.info["mzml_version"]
obo_version = self.reader_uncompressed_indexed.info["obo_version"]
spec_count = self.reader_uncompressed_indexed.info["spectrum_count"]
run_id = self.reader_uncompressed_unindexed.info["run_id"]
start_time = self.reader_uncompressed_unindexed.info["start_time"]
self.assertEqual(mzml_version, "1.1.0")
self.assertEqual(obo_version, "3.25.0")
self.assertIsInstance(spec_count, int)
self.assertEqual(run_id, "exp105-01-ds5562-Pos")
self.assertEqual(start_time, "2013-09-10T10:31:08Z")
mzml_version = self.reader_uncompressed_unindexed.info["mzml_version"]
obo_version = self.reader_uncompressed_unindexed.info["obo_version"]
spec_count = self.reader_uncompressed_unindexed.info["spectrum_count"]
run_id = self.reader_uncompressed_unindexed.info["run_id"]
start_time = self.reader_uncompressed_unindexed.info["start_time"]
self.assertEqual(mzml_version, "1.1.0")
self.assertEqual(obo_version, "3.25.0")
self.assertIsInstance(spec_count, int)
self.assertEqual(run_id, "exp105-01-ds5562-Pos")
self.assertEqual(start_time, "2013-09-10T10:31:08Z")
mzml_version = self.reader_bad_obo_version.info["mzml_version"]
obo_version = self.reader_bad_obo_version.info["obo_version"]
spec_count = self.reader_bad_obo_version.info["spectrum_count"]
run_id = self.reader_bad_obo_version.info["run_id"]
start_time = self.reader_bad_obo_version.info["start_time"]
self.assertEqual(mzml_version, "1.1.0")
# run._obo_version_validator 2017 default obo = 4.1.0
self.assertEqual(obo_version, "4.1.0")
self.assertIsInstance(spec_count, int)
self.assertEqual(run_id, "exp105-01-ds5562-Pos")
self.assertEqual(start_time, "2013-09-10T10:31:08Z")
mzml_version = self.reader_set_obo_version.info["mzml_version"]
obo_version = self.reader_set_obo_version.info["obo_version"]
spec_count = self.reader_set_obo_version.info["spectrum_count"]
run_id = self.reader_set_obo_version.info["run_id"]
start_time = self.reader_set_obo_version.info["start_time"]
self.assertEqual(mzml_version, "1.1.0")
self.assertEqual(obo_version, "3.25.0")
self.assertIsInstance(spec_count, int)
self.assertEqual(run_id, "exp105-01-ds5562-Pos")
self.assertEqual(start_time, "2013-09-10T10:31:08Z")
mzml_version = self.reader_set_year_obo_version.info["mzml_version"]
obo_version = self.reader_set_year_obo_version.info["obo_version"]
spec_count = self.reader_set_year_obo_version.info["spectrum_count"]
run_id = self.reader_set_year_obo_version.info["run_id"]
start_time = self.reader_set_year_obo_version.info["start_time"]
self.assertEqual(mzml_version, "1.1.0")
# run._obo_version_validator 2017 default obo = 4.1.0
self.assertEqual(obo_version, "4.1.0")
self.assertIsInstance(spec_count, int)
self.assertEqual(run_id, "exp105-01-ds5562-Pos")
self.assertEqual(start_time, "2013-09-10T10:31:08Z")
mzml_version = self.reader_set_bad_obo_version.info["mzml_version"]
obo_version = self.reader_set_bad_obo_version.info["obo_version"]
spec_count = self.reader_set_bad_obo_version.info["spectrum_count"]
run_id = self.reader_set_bad_obo_version.info["run_id"]
start_time = self.reader_set_bad_obo_version.info["start_time"]
self.assertEqual(mzml_version, "1.1.0")
# run._obo_version_validator set invalid obo = 1.1.0
self.assertEqual(obo_version, "1.1.0")
self.assertIsInstance(spec_count, int)
self.assertEqual(run_id, "exp105-01-ds5562-Pos")
self.assertEqual(start_time, "2013-09-10T10:31:08Z")
mzml_version = self.reader_set_no_obo_version.info["mzml_version"]
obo_version = self.reader_set_no_obo_version.info["obo_version"]
spec_count = self.reader_set_no_obo_version.info["spectrum_count"]
run_id = self.reader_set_no_obo_version.info["run_id"]
start_time = self.reader_set_no_obo_version.info["start_time"]
self.assertEqual(mzml_version, "1.1.0")
# run._obo_version_validator set invalid obo = 1.1.0
self.assertEqual(obo_version, "1.1.0")
self.assertIsInstance(spec_count, int)
self.assertEqual(run_id, "exp105-01-ds5562-Pos")
self.assertEqual(start_time, "2013-09-10T10:31:08Z")
def test_next(self):
"""
"""
ret = self.reader_compressed_indexed.next()
self.assertIsInstance(ret, Spectrum)
ret = self.reader_compressed_unindexed.next()
self.assertIsInstance(ret, Spectrum)
ret = self.reader_uncompressed_indexed.next()
self.assertIsInstance(ret, Spectrum)
ret = self.reader_uncompressed_unindexed.next()
self.assertIsInstance(ret, Spectrum)
def test_get_spec_count(self):
self.assertEqual(self.reader_compressed_indexed.get_spectrum_count(), 2918)
self.assertEqual(self.reader_compressed_unindexed.get_spectrum_count(), 2918)
self.assertEqual(self.reader_uncompressed_unindexed.get_spectrum_count(), 2918)
self.assertEqual(self.reader_uncompressed_unindexed.get_spectrum_count(), 2918)
def test_chrom_count_chrom_file(self):
reader = run.Reader(self.paths[3])
self.assertEqual(reader.get_chromatogram_count(), 3)
def test_chrom_count_spec_file(self):
reader = run.Reader(self.paths[0])
self.assertEqual(reader.get_chromatogram_count(), None)
def test_readers_remeber_spawned_spectra(self):
"""
Make multiple Readers, spawn 10 spectra each, mix them
and map them back to the reader who spawned them.
"""
pass
def test_read_custom_regex(self):
custom_regex_file = os.path.join(
os.path.dirname(__file__),
"data",
"Manuels_custom_ids.mzML"
)
reader = run.Reader(
custom_regex_file,
index_regex=re.compile(
b'.*idRef="ManuelsCustomID=(?P<ID>.*) diesdas">(?P<offset>[0-9]*)</offset>'
)
)
ids = sorted([k for k in reader.info['offset_dict'].keys() if k != 'TIC'])
assert ids == list(range(1, 11))
if __name__ == "__main__":
unittest.main(verbosity=3)
|
