Commit bd7082c8 authored by mirandaa's avatar mirandaa
Browse files

updatef format

parent 242e1322
......@@ -6,13 +6,20 @@ from gooey import Gooey, GooeyParser
def getArgs():
parser = GooeyParser(description='MFQL generator v0.0.1')
parser.add_argument('compound', metavar='Compound', help='Human reabable name for reference')
parser.add_argument('formula_ms1', metavar='Chemical Formula for MS1' , help='Specify formula (eg h2o or C[1..20]H[4..80]O[0..1])')
parser.add_argument('adduct_ms1', metavar='Chemical Formula for MS1 Adduct', help='Specify adduct type (optional for ranges)'
ms1_group = parser.add_argument_group(
"Chemical Formula",
"in normal (eg H2O) or ranged format (eg C[1..20]H[4..80]O[0..1])")
ms1_group.add_argument('formula_ms1', metavar='Chemical Formula for MS1' , help='Specify formula')
ms1_group.add_argument('adduct_ms1', metavar='Chemical Formula for MS1 Adduct', help='Specify adduct type (optional for ranged format)'
, nargs = '?', default='')
parser.add_argument('formula_ms2', metavar='Chemical Formula for fragments,', help='Specify fragment formula\none per line (if applicable)'
, nargs = '?')
parser.add_argument('ms_mode', metavar='Select the Mode to use', help='MS mode'
ms1_group.add_argument('ms_mode', metavar='Select the Mode to use', help='MS mode'
, choices=['+', '-'])
ms2_group = parser.add_argument_group(
"Fragment Formula",
"Add fragments if applicable")
ms2_group.add_argument('formula_ms2', metavar='Chemical Formula for fragments,', help='Specify fragment formula seperated by comma'
, nargs = '?', default='')
parser.add_argument('mfql_dir', metavar='Directory where to store the results', help='output dir for MFQL files'
,default='./mfql_dir/' , widget='DirChooser')
args = parser.parse_args()
......@@ -96,6 +103,8 @@ def res2dbe(res):
def main():
args = getArgs()
print(args.formula_ms2)
return
ms = args.ms_mode
cc = txt2dict(args.formula_ms1)
af = txt2dict(args.adduct_ms1) #get chemical composition of adduct
......
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