diff matchms_filtering_wrapper.py @ 0:3d275fbdf741 draft

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/matchms_filtering_wrapper.py	Tue Mar 22 16:08:03 2022 +0000
@@ -0,0 +1,77 @@
+import argparse
+import sys
+
+from matchms.exporting import save_as_mgf, save_as_msp
+from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz,\
+    add_retention_index, add_retention_time, clean_compound_name
+from matchms.filtering import default_filters, normalize_intensities, select_by_mz, select_by_relative_intensity
+from matchms.importing import load_from_mgf, load_from_msp
+
+
+def main(argv):
+    parser = argparse.ArgumentParser(description="Compute MSP similarity scores")
+    parser.add_argument("--spectra", type=str, required=True, help="Mass spectra file to be filtered.")
+    parser.add_argument("--spectra_format", type=str, required=True, help="Format of spectra file.")
+    parser.add_argument("--output", type=str, required=True, help="Filtered mass spectra file.")
+    parser.add_argument("-normalise_intensities", action='store_true',
+                        help="Normalize intensities of peaks (and losses) to unit height.")
+    parser.add_argument("-default_filters", action='store_true',
+                        help="Collection of filters that are considered default and that do no require any (factory) arguments.")
+    parser.add_argument("-clean_metadata", action='store_true',
+                        help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata.")
+    parser.add_argument("-relative_intensity", action='store_true',
+                        help="Keep only peaks within set relative intensity range (keep if to_intensity >= intensity >= from_intensity).")
+    parser.add_argument("--from_intensity", type=float, help="Lower bound for intensity filter")
+    parser.add_argument("--to_intensity", type=float, help="Upper bound for intensity filter")
+    parser.add_argument("-mz_range", action='store_true',
+                        help="Keep only peaks between set m/z range (keep if to_mz >= m/z >= from_mz).")
+    parser.add_argument("--from_mz", type=float, help="Lower bound for m/z  filter")
+    parser.add_argument("--to_mz", type=float, help="Upper bound for m/z  filter")
+    args = parser.parse_args()
+
+    if not (args.normalise_intensities
+            or args.default_filters
+            or args.clean_metadata
+            or args.relative_intensity
+            or args.mz_range):
+        raise ValueError('No filter selected.')
+
+    if args.spectra_format == 'msp':
+        spectra = list(load_from_msp(args.spectra))
+    elif args.queries_format == 'mgf':
+        spectra = list(load_from_mgf(args.spectra))
+    else:
+        raise ValueError(f'File format {args.spectra_format} not supported for mass spectra file.')
+
+    filtered_spectra = []
+    for spectrum in spectra:
+        if args.normalise_intensities:
+            spectrum = normalize_intensities(spectrum)
+
+        if args.default_filters:
+            spectrum = default_filters(spectrum)
+
+        if args.clean_metadata:
+            filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_losses, add_parent_mass,
+                       add_retention_index, add_retention_time, clean_compound_name]
+            for metadata_filter in filters:
+                spectrum = metadata_filter(spectrum)
+
+        if args.relative_intensity:
+            spectrum = select_by_relative_intensity(spectrum, args.from_intensity, args.to_intensity)
+
+        if args.mz_range:
+            spectrum = select_by_mz(spectrum, args.from_mz, args.to_mz)
+
+        filtered_spectra.append(spectrum)
+
+    if args.spectra_format == 'msp':
+        save_as_msp(filtered_spectra, args.output)
+    else:
+        save_as_mgf(filtered_spectra, args.output)
+
+    return 0
+
+
+if __name__ == "__main__":
+    main(argv=sys.argv[1:])