Merge pull request #49 from Mesnage-Org/dataframe_error_ftrs_reader

Added ppm and time delta widgets

pgfinder/validation.py

@@ -16,6 +16,10 @@ def validate_raw_data_df(raw_data_df):
 
     if not isinstance(raw_data_df, pd.DataFrame):
         raise ValueError('raw_data_df must be a DataFrame.')
+
+    if isinstance(raw_data_df, pd.DataFrame):
+        print("File is okay")
+
 
     colnames = ['ID',
                 'rt',
@@ -24,6 +28,7 @@ def validate_raw_data_df(raw_data_df):
                 'inferredStructure',
                 'maxIntensity']
 
+
     if not set(colnames).issubset(set(raw_data_df.columns.to_list())):
         raise('raw_data_df column names are incorrect')
 

pgfinder_interactive.ipynb

@@ -88,7 +88,13 @@
     "    else:\n",
     "        csv_filepath = os.path.join(mass_lists_path, rb_masses.value)\n",
     "        theo_masses = matching.theo_masses_reader(csv_filepath)\n",
-    "    \n",
+    "\n",
+    "    # Load ppm value\n",
+    "    user_ppm = ppm_tol.value\n",
+    "\n",
+    "    # Load time delta value\n",
+    "    user_time_delta = time_delta.value\n",
+    "\n",
     "    # Make sure mod list is a list\n",
     "    mod_list = list(selector_mods.value)\n",
     "    \n",
@@ -97,7 +103,7 @@
     "    validation.validate_theo_masses_df(theo_masses)\n",
     "    validation.validate_enabled_mod_list(mod_list)\n",
     "\n",
-    "    results = matching.data_analysis(uploaded_df, theo_masses, 0.5, mod_list, 10)\n",
+    "    results = matching.data_analysis(uploaded_df, theo_masses, user_time_delta, mod_list, user_ppm)\n",
     "    \n",
     "    # Make the download button\n",
     "    results_csv_str = results.to_csv()\n",
@@ -125,6 +131,9 @@
     "# Layout for a bigger button\n",
     "big_button = widgets.Layout(width='auto')\n",
     "\n",
+    "# Style for wider description\n",
+    "wide_style = {'description_width': 'initial'}\n",
+    "\n",
     "# Deconvoluted Data file upload\n",
     "data_uploader = widgets.FileUpload(\n",
     "    accept = '.txt,.ftrs', \n",
@@ -153,7 +162,29 @@
     "    description = 'Upload Mass Library',\n",
     "    multiple = False,\n",
     "    layout = big_button\n",
-    ") \n",
+    ")\n",
+    "\n",
+    "# Set PPM tolerance\n",
+    "ppm_tol = widgets.BoundedFloatText(\n",
+    "    value = 10.0,\n",
+    "    min = 1,\n",
+    "    max = 100,\n",
+    "    step = 0.1,\n",
+    "    description = 'Set ppm tolerance',\n",
+    "    disabled = False,\n",
+    "    style = wide_style\n",
+    "    )\n",
+    "\n",
+    "# Set time delta for in source clean up\n",
+    "time_delta = widgets.BoundedFloatText(\n",
+    "    value = 0.5,\n",
+    "    min = 0,\n",
+    "    max = 100,\n",
+    "    step = 0.01,\n",
+    "    description = 'Set time delta value',\n",
+    "    disabled = False,\n",
+    "    style = wide_style\n",
+    ")\n",
     "\n",
     "# Analysis button\n",
     "button = widgets.Button(description=\"Run Analysis\")\n",
@@ -268,7 +299,51 @@
     "hidePrompt": true
    },
    "source": [
-    "## Step 4: Run Analysis\n",
+    "## Step 4: Set PPM tolerance"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "hideCode": true,
+    "hidePrompt": true
+   },
+   "outputs": [],
+   "source": [
+    "display(ppm_tol)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "hideCode": true,
+    "hidePrompt": true
+   },
+   "source": [
+    "## Step 5: Set time window for in-source decay and salt adduct clean up"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "hideCode": true,
+    "hidePrompt": true
+   },
+   "outputs": [],
+   "source": [
+    "display(time_delta)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "hideCode": true,
+    "hidePrompt": true
+   },
+   "source": [
+    "## Step 6: Run Analysis\n",
     "Click run analysis.\n",
     "After the analysis is complete, a download button will appear."
    ]