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Update CLI for adducts
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@RJMW
RJMW committed May 10, 2020
1 parent 3f8ae6d commit d126247
Showing 1 changed file with 41 additions and 23 deletions.
64 changes: 41 additions & 23 deletions msnpy/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,7 @@ def main(): # pragma: no cover
help="")

parser_ast.add_argument('-m', '--mf-db',
type=str, required=False, default="http://multiomics-int.cs.bham.ac.uk",
type=str, required=False, default="http://mfdb.bham.ac.uk",
help="Molecular formulae database")

parser_ast.add_argument('-d', '--output-db',
Expand All @@ -206,18 +206,20 @@ def main(): # pragma: no cover
type=str, required=True,
help="Json file containing the annotated spectral trees.")

parser_ast.add_argument('-a', '--adducts', nargs='+', required=True,
help="Adducts and the mass difference separated by an underscore"
"e.g. [M+H]+_1.0072764 [M+NH4]+_18.0338254 [M+Na]+_22.9892214",
default=['[M+H]+_1.0072764',
'[M+Na]+_18.0338254',
'[M+NH4]+_22.9892214'])
parser_ast.add_argument('-a', '--adducts',
action='append', nargs=2, required=False,
metavar=('name', 'mass'), default=[["[M+H]+", 1.007276]],
help="Adduct and the mass difference separated by a space. "
"Use quotes when the adduct name includes a space. "
"Default: [M+H]+ 1.007276")

parser_ast.add_argument('-u', '--adducts-file',
type=str, required=False,
help="Tab-separated list that includes two columns - 'name' and 'exact_mass'")

parser_ast.add_argument('-f', '--filter',
action='store_true', required=False,
help="Filter the spectral tree annotations")


help="Filter the spectral tree annotations.")

#################################
# RANK SPECTRAL TREES
Expand All @@ -242,19 +244,19 @@ def main(): # pragma: no cover
# CONVERT SPECTRA TREES - TO DIMSPY.PEAKLISTS AND MSP FILES
##################################################################
parser_cvst.add_argument('-i', '--input',
type=str, required=True,
help="Json file containing annotated spectral trees or dimspy peaklist hdf5 file")
type=str, required=True,
help="Json file containing annotated spectral trees or dimspy peaklist hdf5 file")

parser_cvst.add_argument('-o', '--output',
type=str, required=True,
help="Out folder containing spectra")
type=str, required=True,
help="Out folder containing spectra")

parser_cvst.add_argument('-x', '--input_type',
default="json", type=str, required=False,
help="If input is either a dimspy peaklist or a msnpy json")

parser_cvst.add_argument('-n', '--name', type=str, required=False,
help="Name to use for suffixing files")
help="Name to use for suffixing files")

parser_cvst.add_argument('-a', '--adjust_mz',
action='store_true', required=False,
Expand All @@ -265,8 +267,8 @@ def main(): # pragma: no cover
help="Filter the spectral tree annotations")

parser_cvst.add_argument('-p', '--ppm',
default=5.0, type=float, required=False,
help="Mass tolerance in Parts per million.")
default=5.0, type=float, required=False,
help="Mass tolerance in Parts per million.")

parser_cvst.add_argument('-s', '--msp',
action='store_true', required=False,
Expand All @@ -277,8 +279,8 @@ def main(): # pragma: no cover
help="If MSP file is to be created what type (massbank, msp)")

parser_cvst.add_argument('-z', '--polarity',
type=str, required=False, default='NA',
help="Polarity to add to the MSP file (positive or negative)")
type=str, required=False, default='NA',
help="Polarity to add to the MSP file (positive or negative)")

parser_cvst.add_argument('-y', '--ms1',
action='store_true', required=False,
Expand Down Expand Up @@ -327,10 +329,27 @@ def main(): # pragma: no cover

if args.step == "annotate-spectral-trees":
spectral_trees = load_trees(args.input, format="json")

if args.adducts_file and args.adducts != [['[M+H]+', 1.007276]]:
raise argparse.ArgumentTypeError(
"-a/adducts and -u/--adducts-file can not be used together.")

elif not args.adducts_file and not args.adducts:
raise argparse.ArgumentTypeError(
"Provide a list of adducts. Use -a/adducts or -u/--adducts-file")

adducts = {}
for a in args.adducts:
al = a.replace('__ob__', '[').replace('__cb__', ']').split("_")
adducts[al[0]] = al[1]
if args.adducts_file:
with open(args.adducts_file) as inp:
line = inp.readline()
if "name\texact_mass" in line:
for line in inp.readlines():
line = line.split("\t")
adducts[line[0]] = float(line[1])
else:
for a in args.adducts:
name = a[0].replace('__ob__', '[').replace('__cb__', ']')
adducts[name] = float(a[1])

st = annotate_mf(spectral_trees=spectral_trees,
db_out=args.output_db,
Expand Down Expand Up @@ -390,6 +409,5 @@ def main(): # pragma: no cover
polarity=args.polarity)



if __name__ == "__main__":
main()

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