Commit 4166d8c1 authored by mirandaa's avatar mirandaa
Browse files

working reformat

parent bd7082c8
......@@ -2,29 +2,39 @@ import os
from chem_parser import txt2dict
from gooey import Gooey, GooeyParser
@Gooey(program_name="MFQL Dessert")
@Gooey( program_name="MFQL Dessert")
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('compound', metavar='Compound', help='Compound name')
parser.add_argument('mfql_dir', metavar='Directory where to store the results' , help='output dir for MFQL files'
,default='.' , widget='DirChooser')
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='')
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='')
ms1_group.add_argument('formula_ms1', metavar='Chemical Formula for MS1', help='Specify formula (eg h2o or C[1..20]H[4..80]O[0..1])')
ms1_group.add_argument('ms_mode', metavar='Select the Mode to use'
, choices=['+', '-'])
ms1_optgroup = parser.add_argument_group(
"MS1 Adduct (optional)",
"Specify adduct type, this is optional for ranged formulas")
ms1_optgroup.add_argument('adduct_ms1', metavar='Chemical Formula for MS1 Adduct' , help = 'for example H'
, nargs = '?', default='')
ms2_optgroup = parser.add_argument_group(
"Fragments (optional)",
"Specify the chemical formulas of fragments, if applicable.")
ms2_optgroup.add_argument('formula_ms2', metavar='Chemical Formulas fragments' , help = 'seperated by comma if there are multiple'
, 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()
return args
def addDicts(cc, af, ms):
#adjust for the adduct
# only H, NH4 and HCOO are defined
......@@ -103,8 +113,6 @@ def res2dbe(res):
def main():
args = getArgs()
ms = args.ms_mode
cc = txt2dict(args.formula_ms1)
af = txt2dict(args.adduct_ms1) #get chemical composition of adduct
......@@ -133,4 +141,6 @@ def main():
f.write(line6 + '\n')
if __name__ == "__main__":
# main()
args = getArgs()
\ No newline at end of file
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