fixed bug in reading sciex files

pattilab · Sep 21, 2021 · 83546e0 · 83546e0
1 parent da6a23e
commit 83546e0
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Showing 4 changed files with 5 additions and 3 deletions.
diff --git a/exampleData/Asp-Mal_1uM_5Da.DecoID b/exampleData/Asp-Mal_1uM_5Da.DecoID
diff --git a/examples/exampleUsage.py b/examples/exampleUsage.py
@@ -16,6 +16,7 @@
 #filename of peak list
 peakFile = "../exampleData/peak_table.csv"
 
+
 #set parameters
 usePeaks = True
 DDA = True #data is DDA

diff --git a/src/DecoID/DecoID.py b/src/DecoID/DecoID.py
@@ -738,7 +738,8 @@ def readRawDataFile(filename, maxMass, resolution, useMS1, ppmWidth = 50,offset=
                         #settings = filter.split("@")[1].split()[0]
                         #fragmentMode = settings[:3]
                         #NCE = float(settings[3:])
-                        CE = temp["precursorList"]["precursor"][0]["activation"]['collision energy']
+                        try: CE = temp["precursorList"]["precursor"][0]["activation"]['collision energy']
+                        except: CE = -1
                         rt = temp["scanList"]["scan"][0]["scan start time"]
                         mzs = list(zip(temp["m/z array"],temp["intensity array"]))
                         tempSpecs = []

diff --git a/src/setup.py b/src/setup.py
@@ -3,13 +3,13 @@
 setup(
   name = 'DecoID',         # How you named your package folder (MyLib)
   packages = ["DecoID"],   # Chose the same as "name"
-  version = '0.3.1',      # Start with a small number and increase it with every change you make
+  version = '0.3.2',      # Start with a small number and increase it with every change you make
   license='MIT',        # Chose a license from here: https://help.github.com/articles/licensing-a-repository
   description = 'Metabolomics software for database assisted deconvolution of MS/MS spectra',   # Give a short description about your library
   author = 'Ethan Stancliffe',                   # Type in your name
   author_email = 'estancl1234@gmail.com',      # Type in your E-Mail
   url = 'https://github.com/e-stan/DecoID',   # Provide either the link to your github or to your website
-  download_url = 'https://github.com/e-stan/DecoID/archive/v0.3.1.tar.gz',    # I explain this later on
+  download_url = 'https://github.com/e-stan/DecoID/archive/v0.3.2.tar.gz',    # I explain this later on
   keywords = ['Metabolomics', 'Deconvolution', 'MS/MS',"Metabolite ID"],   # Keywords that define your package best
   install_requires=[            # I get to this in a second
           'numpy',