def main():
path = "../tests/test_data/"
fn_peaklist = os.path.join(path, "variableMetadata.txt")
fn_matrix = os.path.join(path, "dataMatrix.txt")
df = in_out.combine_peaklist_matrix(fn_peaklist, fn_matrix)
ion_mode = "pos"
db_out = "results_{}.sqlite".format(ion_mode)
graphs = group_features(df,
db_out,
max_rt_diff=5.0,
coeff_thres=0.7,
pvalue_thres=0.01,
method="pearson")
nx.write_gml(graphs, "graphs.gml")
# graphs = nx.read_gml("graphs.gml")
path = "../beamspy/data"
lib_isotopes = in_out.read_isotopes(os.path.join(path, "isotopes.txt"),
ion_mode)
lib_adducts = in_out.read_adducts(os.path.join(path, "adducts.txt"),
ion_mode)
lib_multiple_charged_ions = in_out.read_multiple_charged_ions(
os.path.join(path, "multiple_charged_ions.txt"), ion_mode)
lib_mass_differences = in_out.read_mass_differences(
os.path.join(path, "multiple_charged_differences.txt"), ion_mode)
print(lib_isotopes)
print(lib_adducts)
ppm = 5.0
annotate_adducts(graphs, db_out, ppm, lib_adducts)
annotate_isotopes(graphs, db_out, ppm, lib_isotopes)
annotate_oligomers(graphs, db_out, ppm, lib_adducts)
annotate_multiple_charged_ions(graphs, db_out, ppm,
lib_multiple_charged_ions)
# annotate_molecular_formulae(df, lib_adducts, ppm, db_out)
annotate_compounds(df, lib_adducts, ppm, db_out,
"lipidmaps_full_20181217_v1")
df_out = summary(df, db_out)
fn_out = "summary_{}.txt".format(ion_mode)
df_out.to_csv(fn_out, sep="\t", index=False, encoding="utf-8")
pdf_out = "report_{}.pdf".format(ion_mode)
plots.report(db=db_out,
pdf_out=pdf_out,
column_corr="r_value",
column_pvalue="p_value",
column_ppm_error="ppm_error",
column_adducts="adduct")
def main():
path = "../tests/test_data/"
fn_peaklist = os.path.join(path, "peaklist_lcms_pos_theoretical.txt")
fn_matrix = os.path.join(path, "dataMatrix_lcms_theoretical.txt")
df = in_out.combine_peaklist_matrix(fn_peaklist, fn_matrix)
ion_mode = "pos"
db_out = "results.sqlite".format(ion_mode)
graphs = group_features(df,
db_out,
max_rt_diff=5.0,
coeff_thres=0.7,
pvalue_thres=0.01,
method="pearson")
nx.write_gml(graphs, "graphs.gml")
# graphs = nx.read_gml("graphs.gml")
path = "../beamspy/data"
lib_isotopes = in_out.read_isotopes(os.path.join(path, "isotopes.txt"),
ion_mode)
lib_adducts = in_out.read_adducts(os.path.join(path, "adducts.txt"),
ion_mode)
print(lib_isotopes)
print(lib_adducts)
ppm = 5.0
annotate_adducts(graphs, db_out, ppm, lib_adducts)
annotate_isotopes(graphs, db_out, ppm, lib_isotopes)
# annotate_molecular_formulae(df, lib_adducts, ppm, db_out)
annotate_compounds(df, lib_adducts, ppm, db_out,
"hmdb_full_v4_0_20200909_v1")
df_out = summary(df, db_out)
fn_out = "summary.txt"
df_out.to_csv(fn_out, sep="\t", index=False, encoding="utf-8")
pdf_out = "report.pdf"
plots.report(db=db_out,
pdf_out=pdf_out,
column_corr="r_value",
column_pvalue="p_value",
column_ppm_error="ppm_error",
column_adducts="adduct")
def main():
print("Executing BEAMSpy version {}.".format(__version__))
parser = argparse.ArgumentParser(
description='Annotation package of LC-MS and DIMS data',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
# formatter_class=RawTextHelpFormatter)
subparsers = parser.add_subparsers(dest='step')
parser_gf = subparsers.add_parser('group-features', help='Group features.')
parser_app = subparsers.add_parser(
'annotate-peak-patterns',
help='Annotate peak patterns, molecular formulae and metabolites.')
parser_amf = subparsers.add_parser('annotate-mf',
help='Annotate molecular formulae.')
parser_am = subparsers.add_parser('annotate-compounds',
help='Annotate metabolites.')
parser_sr = subparsers.add_parser('summary-results',
help='Summarise results.')
parser_gui = subparsers.add_parser('start-gui', help='Start GUI.')
#################################
# GROUP FEATURES
#################################
parser_gf.add_argument('-l',
'--peaklist',
type=str,
required=True,
help="Tab-delimited peaklist.")
parser_gf.add_argument('-i',
'--intensity-matrix',
type=str,
required=True,
help="Tab-delimited intensity matrix.")
#parser_gf.add_argument('-x', '--xset-matrix',
# type=str, required=False, help="Tab-delimited intensity matrix")
parser_gf.add_argument('-d',
'--db',
type=str,
required=True,
help="Sqlite database to write results.")
parser_gf.add_argument(
'-r',
'--max-rt-diff',
default=5.0,
type=float,
required=True,
help="Maximum difference in retention time between two peaks.")
parser_gf.add_argument('-m',
'--method',
default="pearson",
choices=["pearson", "spearman"],
required=True,
help="Method to apply for grouping features.")
parser_gf.add_argument('-c',
'--coeff-threshold',
default=0.7,
type=float,
required=True,
help="Threshold for correlation coefficient.")
parser_gf.add_argument('-p',
'--pvalue-threshold',
default=0.01,
type=float,
required=True,
help="Threshold for p-value.")
parser_gf.add_argument('-g',
'--gml-file',
type=str,
required=True,
help="Write graph to GraphML format.")
parser_gf.add_argument('-n',
'--ncpus',
type=int,
required=False,
help="Number of central processing units (CPUs).")
#################################
# ANNOTATE PEAK PATTERS
#################################
parser_app.add_argument('-l',
'--peaklist',
type=str,
required=True,
help="Tab-delimited peaklist.")
parser_app.add_argument('-i',
'--intensity-matrix',
type=str,
required=False,
help="Tab-delimited intensity matrix.")
parser_app.add_argument('-g',
'--gml-file',
type=str,
required=False,
help="Correlation graph in GraphML format.")
parser_app.add_argument('-d',
'--db',
type=str,
required=True,
help="Sqlite database to write results.")
parser_app.add_argument('-a',
'--adducts',
action='store_true',
required=False,
help="Annotate adducts.")
parser_app.add_argument('-b',
'--adducts-library',
action='append',
required=False,
default=[],
help="List of adducts.")
parser_app.add_argument('-e',
'--isotopes',
action='store_true',
required=False,
help="Annotate isotopes.")
parser_app.add_argument('-f',
'--isotopes-library',
required=False,
help="List of isotopes.")
parser_app.add_argument('-r',
'--multiple-charged-ions',
action='store_true',
required=False,
help="Annotate multiple-charged ions.")
parser_app.add_argument('-s',
'--multiple-charged-ions-library',
required=False,
help="List of multiple charged ions.")
parser_app.add_argument('-o',
'--oligomers',
action='store_true',
required=False,
help="Annotate oligomers.")
parser_app.add_argument('-m',
'--ion-mode',
choices=["pos", "neg"],
required=True,
help="Ion mode of the libraries.")
parser_app.add_argument('-p',
'--ppm',
default=3.0,
type=float,
required=True,
help="Mass tolerance in parts per million.")
parser_app.add_argument('-u',
'--max-monomer-units',
default=2,
type=int,
required=False,
help="Maximum number of monomer units.")
#################################
# ANNOTATE MOLECULAR FORMULAE
#################################
parser_amf.add_argument('-l',
'--peaklist',
type=str,
required=True,
help="Tab-delimited peaklist.")
parser_amf.add_argument('-i',
'--intensity-matrix',
type=str,
required=False,
help="Tab-delimited intensity matrix.")
parser_amf.add_argument('-d',
'--db',
type=str,
required=True,
help="Sqlite database to write results.")
parser_amf.add_argument('-c',
'--db-mf',
type=str,
default="http://mfdb.bham.ac.uk",
help="Molecular formulae database (reference).")
parser_amf.add_argument('-a',
'--adducts-library',
type=str,
default=None,
required=False,
help="List of adducts to search for.")
parser_amf.add_argument('-m',
'--ion-mode',
choices=["pos", "neg"],
required=True,
help="Ion mode of the libraries.")
parser_amf.add_argument('-p',
'--ppm',
default=3.0,
type=float,
required=True,
help="Mass tolerance in parts per million.")
parser_amf.add_argument(
'-z',
'--max-mz',
type=float,
required=False,
default=500.0,
help="Maximum m/z value to assign molecular formula(e).")
#################################
# ANNOTATE METABOLITES
#################################
parser_am.add_argument('-l',
'--peaklist',
type=str,
required=True,
help="Tab-delimited peaklist.")
parser_am.add_argument('-i',
'--intensity-matrix',
type=str,
required=False,
help="Tab-delimited intensity matrix.")
parser_am.add_argument('-d',
'--db',
type=str,
required=True,
help="Sqlite database to write results.")
parser_am.add_argument('-c',
'--db-compounds',
type=str,
required=False,
help="Metabolite database (reference).")
parser_am.add_argument(
'-n',
'--db-name',
type=str,
default="",
required=True,
help="Name compound / metabolite database (within --db-compounds).")
parser_am.add_argument('-a',
'--adducts-library',
type=str,
default=None,
required=False,
help="List of adducts to search for.")
parser_am.add_argument('-m',
'--ion-mode',
choices=["pos", "neg"],
required=True,
help="Ion mode of the libraries.")
parser_am.add_argument('-p',
'--ppm',
default=3.0,
type=float,
required=True,
help="Mass tolerance in parts per million.")
#################################
# SUMMARY RESULTS
#################################
parser_sr.add_argument('-l',
'--peaklist',
type=str,
required=True,
help="Tab-delimited peaklist")
parser_sr.add_argument('-i',
'--intensity-matrix',
type=str,
required=False,
help="Tab-delimited intensity matrix.")
parser_sr.add_argument('-o',
'--output',
type=str,
required=True,
help="Output file for the summary")
parser_sr.add_argument('-p',
'--pdf',
type=str,
required=False,
help="Output pdf file for the summary plots")
parser_sr.add_argument(
'-d',
'--db',
type=str,
required=True,
help=
"Sqlite database that contains the results from the previous steps.")
parser_sr.add_argument(
'-s',
'--sep',
default="tab",
choices=["tab", "comma"],
required=True,
help=
"Values on each line of the output are separated by this character.")
parser_sr.add_argument(
'-r',
'--single-row',
action="store_true",
help=
"Concatenate the annotations for each spectral feature and represent in a single row."
)
parser_sr.add_argument(
'-c',
'--single-column',
action="store_true",
help=
"Concatenate the annotations for each spectral feature and keep seperate columns for molecular formula, adduct, name, etc."
)
parser_sr.add_argument(
'-n',
'--ndigits-mz',
default=None,
type=int,
required=False,
help="Digits after the decimal point for m/z values.")
parser_sr.add_argument(
'-t',
'--convert-rt',
default=None,
choices=["sec", "min", None],
required=False,
help=
"Covert the retention time to seconds or minutes. An additional column will be added."
)
args = parser.parse_args()
print(args)
separators = {"tab": "\t", "comma": ","}
if args.step == "group-features":
df = in_out.combine_peaklist_matrix(args.peaklist,
args.intensity_matrix)
graph = grouping.group_features(df,
db_out=args.db,
max_rt_diff=args.max_rt_diff,
coeff_thres=args.coeff_threshold,
pvalue_thres=args.pvalue_threshold,
method=args.method,
ncpus=args.ncpus)
nx.write_gml(graph, str(args.gml_file))
if args.step == "annotate-peak-patterns":
if args.gml_file:
inp = nx.read_gml(args.gml_file)
elif args.intensity_matrix:
inp = in_out.combine_peaklist_matrix(args.peaklist,
args.intensity_matrix)
else:
inp = in_out.read_peaklist(args.peaklist)
if args.adducts:
if len(args.adducts_library
) > 0 and args.adducts_library is not None:
for i, a in enumerate(args.adducts_library):
try:
lib = in_out.read_adducts(a, args.ion_mode)
except:
lib = in_out.read_mass_differences(a, args.ion_mode)
if i > 0:
add = True
else:
add = False
annotation.annotate_adducts(inp,
db_out=args.db,
ppm=args.ppm,
lib=lib,
add=add)
else:
path = 'data/adducts.txt'
p = os.path.join(os.path.dirname(os.path.abspath(__file__)),
path)
lib = in_out.read_adducts(p, args.ion_mode)
annotation.annotate_adducts(inp,
db_out=args.db,
ppm=args.ppm,
lib=lib,
add=False)
if args.isotopes:
if args.isotopes_library is not None:
lib = in_out.read_isotopes(args.isotopes_library,
args.ion_mode)
annotation.annotate_isotopes(inp,
db_out=args.db,
ppm=args.ppm,
lib=lib)
else:
path = 'data/isotopes.txt'
p = os.path.join(os.path.dirname(os.path.abspath(__file__)),
path)
lib = in_out.read_isotopes(p, args.ion_mode)
annotation.annotate_isotopes(inp,
db_out=args.db,
ppm=args.ppm,
lib=lib)
if args.multiple_charged_ions:
if len(args.multiple_charged_ions_library
) > 0 and args.multiple_charged_ions_library is not None:
for i, m in enumerate(args.multiple_charged_ions_library):
try:
lib = in_out.read_multiple_charged_ions(
m, args.ion_mode)
except:
lib = in_out.read_mass_differences(m, args.ion_mode)
if i > 0:
add = True
else:
add = False
annotation.annotate_multiple_charged_ions(inp,
db_out=args.db,
ppm=args.ppm,
lib=lib,
add=add)
else:
path = 'data/multiple_charged_ions.txt'
p = os.path.join(os.path.dirname(os.path.abspath(__file__)),
path)
lib = in_out.read_multiple_charged_ions(p, args.ion_mode)
if args.oligomers:
annotation.annotate_oligomers(inp,
db_out=args.db,
ppm=args.ppm,
lib=lib)
if args.step == "annotate-mf":
if args.intensity_matrix:
df = in_out.combine_peaklist_matrix(args.peaklist,
args.intensity_matrix)
else:
df = in_out.read_peaklist(args.peaklist)
if args.adducts_library:
lib = in_out.read_adducts(args.adducts_library, args.ion_mode)
else:
path = 'data/adducts.txt'
p = os.path.join(os.path.dirname(os.path.abspath(__file__)), path)
lib = in_out.read_adducts(p, args.ion_mode)
annotation.annotate_molecular_formulae(df,
ppm=args.ppm,
lib_adducts=lib,
db_out=args.db,
db_in=args.db_mf,
max_mz=args.max_mz)
if args.step == "annotate-compounds":
if args.intensity_matrix:
df = in_out.combine_peaklist_matrix(args.peaklist,
args.intensity_matrix)
else:
df = in_out.read_peaklist(args.peaklist)
if args.adducts_library:
lib = in_out.read_adducts(args.adducts_library, args.ion_mode)
else:
path = 'data/adducts.txt'
p = os.path.join(os.path.dirname(os.path.abspath(__file__)), path)
lib = in_out.read_adducts(p, args.ion_mode)
annotation.annotate_compounds(df,
lib_adducts=lib,
ppm=args.ppm,
db_out=args.db,
db_name=args.db_name,
db_in="")
if args.step == "summary-results":
if args.intensity_matrix:
df = in_out.combine_peaklist_matrix(args.peaklist,
args.intensity_matrix)
else:
df = in_out.read_peaklist(args.peaklist)
df_out = annotation.summary(df,
db=args.db,
single_row=args.single_row,
single_column=args.single_column,
convert_rt=args.convert_rt,
ndigits_mz=args.ndigits_mz)
df_out.to_csv(args.output,
sep=separators[args.sep],
index=False,
encoding="utf-8")
if args.pdf:
plots.report(db=args.db,
pdf_out=args.pdf,
column_corr="r_value",
column_pvalue="p_value",
column_ppm_error="ppm_error",
column_adducts="adduct")
if args.step == "start-gui":
from PySide2 import QtWidgets
from beamspy.gui import BeamsApp
app = QtWidgets.QApplication(sys.argv)
app.setStyle("Fusion")
form = BeamsApp()
form.show()
sys.exit(app.exec_())
def setUp(self):
self.df = combine_peaklist_matrix(
to_test_data("peaklist_lcms_pos_theoretical.txt"),
to_test_data("dataMatrix_lcms_theoretical.txt"))
def run(self):
if not os.path.isfile(
self.lineEdit_peaklist.text()) or not os.path.isfile(
self.lineEdit_intensity_matrix.text()):
QtWidgets.QMessageBox.critical(
None, "Select file",
"Select file(s) for Peaklist and/or Intensity Matrix",
QtWidgets.QMessageBox.Ok)
return
elif self.lineEdit_sql_database.text() == "":
QtWidgets.QMessageBox.critical(
None, "Select File",
"Select file for SQLite database to save output",
QtWidgets.QMessageBox.Ok)
return
if self.checkBox_annotate_compounds.isChecked():
if len(self.listWidget_databases.selectedItems()
) == 0 and not self.checkBox_filename_reference.isChecked():
QtWidgets.QMessageBox.critical(
None, "Select File",
"Select database or file for 'Annotate Compounds / Metabolites'",
QtWidgets.QMessageBox.Ok)
return
if self.checkBox_create_summary.isChecked(
) and self.lineEdit_summary_filename.text() == "":
QtWidgets.QMessageBox.critical(None, "Save File As",
"Select file to save summary",
QtWidgets.QMessageBox.Ok)
return
self.hide()
lib_ion_mode = {"Positive": "pos", "Negative": "neg"}
if self.checkBox_group_features.isChecked():
print("Grouping features....")
if self.comboBox_grouping_method.currentText(
) == "Pearson correlation":
method = "pearson"
else:
method = "spearman"
df = in_out.combine_peaklist_matrix(
self.lineEdit_peaklist.text(),
self.lineEdit_intensity_matrix.text())
graph = grouping.group_features(
df,
db_out=self.lineEdit_sql_database.text(),
max_rt_diff=self.doubleSpinBox_max_rt.value(),
coeff_thres=self.doubleSpinBox_coefficent.value(),
pvalue_thres=self.doubleSpinBox_p_value.value(),
method=method,
block=int(self.doubleSpinBox_block.value()),
ncpus=int(self.doubleSpinBox_ncpus.value()))
nx.write_gml(graph, str(self.lineEdit_graph.text()))
print("Done")
print("")
if self.checkBox_annotate_peak_patterns.isChecked():
print("Annotating peak patterns....")
if str(self.lineEdit_graph.text()) != "":
inp = nx.read_gml(str(self.lineEdit_graph.text()))
else:
inp = in_out.combine_peaklist_matrix(
self.lineEdit_peaklist.text(),
self.lineEdit_intensity_matrix.text())
if self.checkBox_adduct_library.isChecked():
print("Adducts...."),
if self.lineEdit_adduct_library.text() == "Use default":
path = 'data/adducts.txt'
p = os.path.join(
os.path.dirname(os.path.abspath(__file__)), path)
lib = in_out.read_adducts(
p, lib_ion_mode[self.comboBox_ion_mode.currentText()])
elif os.path.isfile(self.lineEdit_adduct_library.text()):
try:
lib = in_out.read_adducts(
self.lineEdit_adduct_library.text(),
lib_ion_mode[self.comboBox_ion_mode.currentText()])
except:
lib = in_out.read_mass_differences(
self.lineEdit_adduct_library.text(),
lib_ion_mode[self.comboBox_ion_mode.currentText()])
else:
raise IOError(
"Provide a valid filename for adducts or 'Use default'"
)
print("")
print(lib)
annotation.annotate_adducts(
inp,
db_out=self.lineEdit_sql_database.text(),
ppm=self.doubleSpinBox_pp_ppm_error.value(),
lib=lib)
print("Done")
if self.checkBox_isotopes.isChecked():
print("Isotopes...."),
if self.lineEdit_isotopes.text() == "Use default":
path = 'data/isotopes.txt'
p = os.path.join(
os.path.dirname(os.path.abspath(__file__)), path)
lib = in_out.read_isotopes(
p, lib_ion_mode[self.comboBox_ion_mode.currentText()])
elif os.path.isfile(self.lineEdit_isotopes.text()):
lib = in_out.read_isotopes(
self.lineEdit_isotopes.text(),
lib_ion_mode[self.comboBox_ion_mode.currentText()])
else:
raise IOError(
"Provide a valid filename for isotopes or 'Use default'"
)
print("")
print(lib)
annotation.annotate_isotopes(
inp,
db_out=self.lineEdit_sql_database.text(),
ppm=self.doubleSpinBox_pp_ppm_error.value(),
lib=lib)
print("Done")
if self.checkBox_multiple_charged.isChecked():
print("Multiple charged ions...."),
if self.lineEdit_multiple_charged.text() == "Use default":
path = 'data/multiple_charged_ions.txt'
p = os.path.join(
os.path.dirname(os.path.abspath(__file__)), path)
lib = in_out.read_multiple_charged_ions(
p, lib_ion_mode[self.comboBox_ion_mode.currentText()])
elif os.path.isfile(self.lineEdit_multiple_charged.text()):
lib = in_out.read_multiple_charged_ions(
self.lineEdit_multiple_charged.text(),
lib_ion_mode[self.comboBox_ion_mode.currentText()])
else:
raise IOError(
"Provide a valid filename for multiple charged ions or 'Use default'"
)
annotation.annotate_multiple_charged_ions(
inp,
db_out=self.lineEdit_sql_database.text(),
ppm=self.doubleSpinBox_pp_ppm_error.value(),
lib=lib)
print("Done")
if self.checkBox_oligomers.isChecked():
print("Oligomers...."),
if self.lineEdit_default_adduct_library.text(
) == "Use default":
path = 'data/adducts.txt'
p = os.path.join(
os.path.dirname(os.path.abspath(__file__)), path)
lib = in_out.read_adducts(
p, lib_ion_mode[self.comboBox_ion_mode.currentText()])
elif os.path.isfile(
self.lineEdit_default_adduct_library.text()):
try:
lib = in_out.read_adducts(
self.lineEdit_default_adduct_library.text(),
lib_ion_mode[self.comboBox_ion_mode.currentText()])
except:
lib = in_out.read_mass_differences(
self.lineEdit_default_adduct_library.text(),
lib_ion_mode[self.comboBox_ion_mode.currentText()])
else:
raise IOError("Provide a valid filename for adducts")
inp = in_out.combine_peaklist_matrix(
self.lineEdit_peaklist.text(),
self.lineEdit_intensity_matrix.text())
annotation.annotate_oligomers(
inp,
db_out=self.lineEdit_sql_database.text(),
ppm=self.doubleSpinBox_pp_ppm_error.value(),
lib=lib,
maximum=self.spinBox_max_monomer_units.value())
print("Done")
print
if self.checkBox_annotate_molecular_formulae.isChecked():
print("Annotating molecular formulae...."),
df = in_out.combine_peaklist_matrix(
self.lineEdit_peaklist.text(),
self.lineEdit_intensity_matrix.text())
if self.lineEdit_default_adduct_library.text() == "Use default":
path = 'data/adducts.txt'
p = os.path.join(os.path.dirname(os.path.abspath(__file__)),
path)
lib = in_out.read_adducts(
p, lib_ion_mode[self.comboBox_ion_mode.currentText()])
elif os.path.isfile(self.lineEdit_default_adduct_library.text()):
try:
lib = in_out.read_adducts(
self.lineEdit_default_adduct_library.text(),
lib_ion_mode[self.comboBox_ion_mode.currentText()])
except:
lib = in_out.read_mass_differences(
self.lineEdit_default_adduct_library.text(),
lib_ion_mode[self.comboBox_ion_mode.currentText()])
else:
raise IOError("Provide a valid filename for adducts")
if self.comboBox_source_mf.currentText(
) == "Tab-delimited text file":
db_in = self.lineEdit_filename_mf.text()
rules = None
max_mz = None
else:
db_in = "http://mfdb.bham.ac.uk"
rules = self.checkBox_heuristic_rules.isChecked()
max_mz = self.spinBox_max_mz.value()
print("")
print(lib)
annotation.annotate_molecular_formulae(
df,
lib_adducts=lib,
ppm=self.doubleSpinBox_mf_ppm_error.value(),
db_out=self.lineEdit_sql_database.text(),
db_in=db_in,
rules=rules,
max_mz=max_mz)
print("Done")
print("")
if self.checkBox_annotate_compounds.isChecked():
print("Annotating compounds...."),
df = in_out.combine_peaklist_matrix(
self.lineEdit_peaklist.text(),
self.lineEdit_intensity_matrix.text())
if self.lineEdit_default_adduct_library.text() == "Use default":
path = 'data/adducts.txt'
p = os.path.join(os.path.dirname(os.path.abspath(__file__)),
path)
lib = in_out.read_adducts(
p, lib_ion_mode[self.comboBox_ion_mode.currentText()])
elif os.path.isfile(self.lineEdit_default_adduct_library.text()):
try:
lib = in_out.read_adducts(
self.lineEdit_default_adduct_library.text(),
lib_ion_mode[self.comboBox_ion_mode.currentText()])
except:
lib = in_out.read_mass_differences(
self.lineEdit_default_adduct_library.text(),
lib_ion_mode[self.comboBox_ion_mode.currentText()])
else:
raise IOError("Provide a valid filename for adducts")
if self.checkBox_filename_reference.isChecked():
print("")
print(lib)
annotation.annotate_compounds(
df,
lib_adducts=lib,
ppm=self.doubleSpinBox_cpds_ppm_error.value(),
db_out=self.lineEdit_sql_database.text(),
db_name=None,
db_in=self.lineEdit_filename_reference.text())
else:
for db_name in self.listWidget_databases.selectedItems():
annotation.annotate_compounds(
df,
lib_adducts=lib,
ppm=self.doubleSpinBox_cpds_ppm_error.value(),
db_out=self.lineEdit_sql_database.text(),
db_name=self.db_names[db_name.text()])
print("Done")
print
if self.checkBox_create_summary.isChecked():
print("Creating summary...."),
if self.checkBox_convert_rt.isChecked():
lib = {"Seconds": "sec", "Minutes": "min"}
convert_rt = lib[self.comboBox_convert_rt.currentText()]
else:
convert_rt = None
if self.checkBox_mz_digits.isChecked():
ndigits_mz = self.spinBox_mz_digits.value()
else:
ndigits_mz = None
df = in_out.combine_peaklist_matrix(
self.lineEdit_peaklist.text(),
self.lineEdit_intensity_matrix.text())
if self.comboBox_annotations_format.currentText(
) == "Single row for each feature and separate columns":
single_row = True
single_column = False
elif self.comboBox_annotations_format.currentText(
) == "Single row for each feature and merged columns":
single_row = True
single_column = True
else:
single_row = False
single_column = False
df_out = annotation.summary(df,
db=self.lineEdit_sql_database.text(),
single_row=single_row,
single_column=single_column,
convert_rt=convert_rt,
ndigits_mz=ndigits_mz)
separators = {"tab": "\t", "comma": ","}
df_out.to_csv(
self.lineEdit_summary_filename.text(),
sep=separators[self.comboBox_separator.currentText()],
index=False,
encoding="utf-8")
ext = os.path.splitext(self.lineEdit_summary_filename.text())[1]
if ext == "":
pdf_out = str(self.lineEdit_summary_filename.text()) + ".pdf"
else:
pdf_out = str(self.lineEdit_summary_filename.text()).replace(
ext, ".pdf")
plots.report(db=str(self.lineEdit_sql_database.text()),
pdf_out=pdf_out,
column_corr="r_value",
column_pvalue="p_value",
column_ppm_error="ppm_error",
column_adducts="adduct")
print("Done")
print("")
self.close()