Python get_test_data 예제들

예제 #1

파일: test_fasta_glycopeptide.py 프로젝트: mobiusklein/glycan_profiling

    def test_throughput(self):
        fasta_file = fixtures.get_test_data("phil-82-proteins.fasta")
        glycan_file = fixtures.get_test_data("IAV_matched_glycans.txt")
        db_file = self.setup_tempfile("")
        print(db_file)

        glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, db_file)
        glycan_builder.start()

        glycopeptide_builder = naive_glycopeptide.MultipleProcessFastaGlycopeptideHypothesisSerializer(
            fasta_file, db_file, glycan_builder.hypothesis_id, constant_modifications=constant_modifications,
            variable_modifications=variable_modifications, max_missed_cleavages=2)
        glycopeptide_builder.start()
        self.clear_file(db_file)

예제 #2

파일: test_fasta_glycopeptide.py 프로젝트: mstim/glycresoft

    def test_throughput(self):
        fasta_file = fixtures.get_test_data("phil-82-proteins.fasta")
        glycan_file = fixtures.get_test_data("IAV_matched_glycans.txt")
        db_file = self.setup_tempfile("")
        print(db_file)

        glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, db_file)
        glycan_builder.start()

        glycopeptide_builder = naive_glycopeptide.MultipleProcessFastaGlycopeptideHypothesisSerializer(
            fasta_file, db_file, glycan_builder.hypothesis_id, constant_modifications=constant_modifications,
            variable_modifications=variable_modifications, max_missed_cleavages=2)
        glycopeptide_builder.start()
        self.clear_file(db_file)

예제 #3

파일: test_fasta_glycopeptide.py 프로젝트: mobiusklein/glycan_profiling

    def test_extract_forward_backward(self):
        fasta_file = fixtures.get_test_data("yeast_glycoproteins.fa")
        glycan_file = self.setup_tempfile(simple_n_glycans)
        forward_db = self.setup_tempfile("")
        reverse_db = self.setup_tempfile("")

        glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, forward_db)
        glycan_builder.start()

        builder = naive_glycopeptide.MultipleProcessFastaGlycopeptideHypothesisSerializer(
            fasta_file, forward_db, 1)
        cnt = builder.extract_proteins()
        assert cnt == 251

        glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, reverse_db)
        glycan_builder.start()

        rev_builder = naive_glycopeptide.ReversingMultipleProcessFastaGlycopeptideHypothesisSerializer(
            fasta_file, reverse_db, 1)
        cnt = rev_builder.extract_proteins()
        assert cnt == 251
        fwd_prots = builder.query(serialize.Protein).all()
        rev_prots = rev_builder.query(serialize.Protein).all()

        for fx, rx in zip(fwd_prots, rev_prots):
            assert fx.name == rx.name
            assert len(fx.glycosylation_sites) == len(rx.glycosylation_sites)

예제 #4

파일: test_fasta_glycopeptide.py 프로젝트: mstim/glycresoft

    def test_extract_forward_backward(self):
        fasta_file = fixtures.get_test_data("yeast_glycoproteins.fa")
        glycan_file = self.setup_tempfile(simple_n_glycans)
        forward_db = self.setup_tempfile("")
        reverse_db = self.setup_tempfile("")

        glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, forward_db)
        glycan_builder.start()

        builder = naive_glycopeptide.MultipleProcessFastaGlycopeptideHypothesisSerializer(
            fasta_file, forward_db, 1)
        cnt = builder.extract_proteins()
        assert cnt == 251

        glycan_builder = TextFileGlycanHypothesisSerializer(glycan_file, reverse_db)
        glycan_builder.start()

        rev_builder = naive_glycopeptide.ReversingMultipleProcessFastaGlycopeptideHypothesisSerializer(
            fasta_file, reverse_db, 1)
        cnt = rev_builder.extract_proteins()
        assert cnt == 251
        fwd_prots = builder.query(serialize.Protein).all()
        rev_prots = rev_builder.query(serialize.Protein).all()

        for fx, rx in zip(fwd_prots, rev_prots):
            assert fx.name == rx.name
            assert len(fx.glycosylation_sites) == len(rx.glycosylation_sites)

예제 #5

파일: test_glycan_chromatogram_analyzer.py 프로젝트: mstim/glycresoft

import unittest
import tempfile
import os

from glycan_profiling.test import fixtures
from glycan_profiling.test.test_constrained_combinatorics import (FILE_SOURCE)
from glycan_profiling.profiler import MzMLGlycanChromatogramAnalyzer, GeneralScorer
from glycan_profiling.database.builder.glycan import CombinatorialGlycanHypothesisSerializer
from glycan_profiling.serialize import AnalysisDeserializer

agp_glycomics_mzml = fixtures.get_test_data(
    "AGP_Glycomics_20150930_06.deconvoluted.mzML")


class GlycanProfilerConsumerTest(unittest.TestCase):
    def setup_tempfile(self, content):
        file_name = tempfile.mktemp() + '.tmp'
        open(file_name, 'w').write(content)
        return file_name

    def clear_file(self, path):
        open(path, 'wb').close()

    def _make_hypothesis(self):
        file_name = self.setup_tempfile(FILE_SOURCE)
        builder = CombinatorialGlycanHypothesisSerializer(
            file_name, file_name + '.db')
        builder.run()
        self.clear_file(file_name)
        return file_name + '.db'

예제 #6

 def load_spectra(self):
     return list(
         ProcessedMzMLDeserializer(
             get_test_data("example_glycopeptide_spectra.mzML")))

예제 #7

import unittest
import tempfile
import os
import glob

import ms_peak_picker
import ms_deisotope
from ms_deisotope.output.mzml import ProcessedMzMLDeserializer

from glycan_profiling.test import fixtures
from glycan_profiling.profiler import SampleConsumer

agp_glycomics_mzml = fixtures.get_test_data(
    "AGP_Glycomics_20150930_06.centroid.mzML")


class SampleConsumerTest(unittest.TestCase):
    def build_args(self):
        ms1_peak_picking_args = {"transforms": []}

        msn_peak_picking_args = {"transforms": []}

        ms1_deconvolution_args = {
            "scorer": ms_deisotope.scoring.PenalizedMSDeconVFitter(35.0, 2.0),
            "max_missed_peaks": 1,
            "averagine": ms_deisotope.glycan,
            "truncate_after": SampleConsumer.MS1_ISOTOPIC_PATTERN_WIDTH,
            "ignore_below": SampleConsumer.MS1_IGNORE_BELOW
        }

        msn_deconvolution_args = {

예제 #8

파일: test_mzid_glycopeptide.py 프로젝트: mobiusklein/glycan_profiling

import unittest
import tempfile

from glycan_profiling.serialize.hypothesis.peptide import Peptide, Protein, Glycopeptide
from glycan_profiling.database.builder.glycopeptide import informed_glycopeptide
from glycan_profiling.database.builder.glycan import (
    CombinatorialGlycanHypothesisSerializer)
from glycan_profiling import serialize

from glycan_profiling.test import fixtures
from glycan_profiling.test.test_constrained_combinatorics import FILE_SOURCE as GLYCAN_RULE_FILE_SOURCE


MZID_PATH = fixtures.get_test_data("AGP_Proteomics2.mzid")


class MzIdGlycopeptideTests(unittest.TestCase):

    def setup_tempfile(self, source):
        file_name = tempfile.mktemp()
        open(file_name, 'w').write(source)
        return file_name

    def clear_file(self, path):
        open(path, 'wb')

    def test_build_hypothesis(self):
        glycan_file = self.setup_tempfile(GLYCAN_RULE_FILE_SOURCE)
        mzid_path = MZID_PATH
        db_file = glycan_file + '.db'

예제 #9

파일: test_target_decoy.py 프로젝트: mobiusklein/glycan_profiling

 def _get_instance(self):
     pairs = np.loadtxt(fixtures.get_test_data('numpairs.txt'))
     return target_decoy.NearestValueLookUp(map(list, pairs))

예제 #10

파일: test_glycan_chromatogram_analyzer.py 프로젝트: mobiusklein/glycan_profiling

import unittest
import tempfile
import os


from glycan_profiling.test import fixtures
from glycan_profiling.test.test_constrained_combinatorics import (
    FILE_SOURCE)
from glycan_profiling.profiler import MzMLGlycanChromatogramAnalyzer, GeneralScorer
from glycan_profiling.database.builder.glycan import CombinatorialGlycanHypothesisSerializer
from glycan_profiling.serialize import AnalysisDeserializer


agp_glycomics_mzml = fixtures.get_test_data(
    "AGP_Glycomics_20150930_06.deconvoluted.mzML")


class GlycanProfilerConsumerTest(unittest.TestCase):

    def setup_tempfile(self, content):
        file_name = tempfile.mktemp()
        open(file_name, 'w').write(content)
        return file_name

    def clear_file(self, path):
        open(path, 'wb').close()

    def _make_hypothesis(self):
        file_name = self.setup_tempfile(FILE_SOURCE)
        builder = CombinatorialGlycanHypothesisSerializer(
            file_name, file_name + '.db')

예제 #11

import unittest
import tempfile
import os
import glob

import ms_peak_picker
import ms_deisotope
from ms_deisotope.output.mzml import ProcessedMzMLDeserializer

import numpy as np

from glycan_profiling.test import fixtures
from glycan_profiling.profiler import SampleConsumer

agp_glycomics_mzml = fixtures.get_test_data(
    "AGP_Glycomics_20150930_06.centroid.mzML")
agp_glycproteomics_mzml = fixtures.get_test_data(
    "20150710_3um_AGP_001_29_30.mzML")
agp_glycproteomics_mzml_reference = fixtures.get_test_data(
    "20150710_3um_AGP_001_29_30.preprocessed.mzML")


class SampleConsumerBase(object):
    def make_output_directory(self):
        path = tempfile.mkdtemp()
        return path

    def cleanup(self, directory):
        files = glob.glob(os.path.join(directory, "*"))
        for f in files:
            try:

예제 #12

import unittest
import tempfile

from glycan_profiling.serialize.hypothesis.peptide import Peptide, Protein, Glycopeptide
from glycan_profiling.database.builder.glycopeptide import informed_glycopeptide
from glycan_profiling.database.builder.glycan import (
    CombinatorialGlycanHypothesisSerializer)
from glycan_profiling import serialize

from glycan_profiling.test import fixtures
from glycan_profiling.test.test_constrained_combinatorics import FILE_SOURCE as GLYCAN_RULE_FILE_SOURCE

MZID_PATH = fixtures.get_test_data("AGP_Proteomics2.mzid")


class MzIdGlycopeptideTests(unittest.TestCase):
    def setup_tempfile(self, source):
        file_name = tempfile.mktemp() + '.tmp'
        open(file_name, 'w').write(source)
        return file_name

    def clear_file(self, path):
        open(path, 'wb')

    def test_build_hypothesis(self):
        glycan_file = self.setup_tempfile(GLYCAN_RULE_FILE_SOURCE)
        mzid_path = MZID_PATH
        db_file = glycan_file + '.db'

        glycan_builder = CombinatorialGlycanHypothesisSerializer(
            glycan_file, db_file)

예제 #13

파일: test_glycopeptide_scorers.py 프로젝트: mobiusklein/glycan_profiling

 def load_spectra(self):
     return list(ProcessedMzMLDeserializer(get_test_data("example_glycopeptide_spectra.mzML")))

예제 #14

파일: test_sample_consumer.py 프로젝트: mobiusklein/glycan_profiling

import unittest
import tempfile
import os
import glob

import ms_peak_picker
import ms_deisotope
from ms_deisotope.output.mzml import ProcessedMzMLDeserializer

import numpy as np

from glycan_profiling.test import fixtures
from glycan_profiling.profiler import SampleConsumer


agp_glycomics_mzml = fixtures.get_test_data("AGP_Glycomics_20150930_06.centroid.mzML")
agp_glycproteomics_mzml = fixtures.get_test_data("20150710_3um_AGP_001_29_30.mzML")
agp_glycproteomics_mzml_reference = fixtures.get_test_data("20150710_3um_AGP_001_29_30.preprocessed.mzML")


class SampleConsumerBase(object):
    def make_output_directory(self):
        path = tempfile.mkdtemp()
        return path

    def cleanup(self, directory):
        files = glob.glob(os.path.join(directory, "*"))
        for f in files:
            try:
                os.remove(f)
            except OSError:

예제 #15

 def _get_instance(self):
     pairs = np.loadtxt(fixtures.get_test_data('numpairs.txt'))
     return target_decoy.NearestValueLookUp(map(list, pairs))