chromaquant 0.3.1__py3-none-any.whl → 0.4.0__py3-none-any.whl

chromaquant/Handle/__init__.py

@@ -9,4 +9,5 @@ Created 10-19-2024
 
 """
 
-from .handleDirectories import *
+from .handleDirectories import *
+from .fileChecks import *

chromaquant/Handle/fileChecks.py

@@ -0,0 +1,172 @@
+"""
+
+COPYRIGHT STATEMENT:
+
+ChromaQuant – A quantification software for complex gas chromatographic data
+
+Copyright (c) 2024, by Julia Hancock
+              Affiliation: Dr. Julie Elaine Rorrer
+	      URL: https://www.rorrerlab.com/
+
+License: BSD 3-Clause License
+
+---
+
+SUBPACKAGE FOR FILE NAMING AND HANDLING PROTOCOLS
+
+Julia Hancock
+Started 12/10/2024
+
+"""
+
+""" PACKAGES """
+import os
+import numpy as np
+import pandas as pd
+
+""" FUNCTIONS """
+
+#Function for checking if file exists and adding number if so, used for new breakdowns
+def fileCheck(path):
+    #Inspired by https://stackoverflow.com/questions/13852700/create-file-but-if-name-exists-add-number
+    filename, extension = os.path.splitext(path)
+    i = 1
+    
+    while os.path.exists(path):
+        path = filename + " ("+str(i)+")" + extension
+        i += 1
+    
+    return path
+
+#Function for selecting FID peak, MS peak, and FIDpMS pathnames according to sample name and phase
+def fileNamer(sname,sphase,sub_Dict,pathData):
+    """
+    Parameters
+    ----------
+    sname : STR
+        The name of the sample.
+    sphase : STR
+        A string that describes whether sample is gas ("G") or liquid ("L").
+    sub_Dict : Dict
+        A dictionary of substrings to add to sample name to create file names
+    pathData : STR
+        A string containing the pathname to the datafiles directory
+        
+    Returns
+    -------
+    paths : List
+        A list of pathnames to return.
+
+    """
+
+    #If sample phase is liquid, set pathnames accordingly
+    if sphase == "L":
+
+        pathFID = os.path.join(pathData,sname+sub_Dict['Liquid FID'][0])
+        pathMS = os.path.join(pathData,sname+sub_Dict['Liquid Labelled MS Peaks'][0])
+        pathFIDpMS = os.path.join(pathData,sname+sub_Dict['Liquid FID+MS'][0])
+        
+    #Else if sample phase is gas, set pathnames accordingly
+    elif sphase == "G":
+
+        pathFID = os.path.join(pathData,sname+sub_Dict['Gas TCD+FID'][0])
+        pathMS = os.path.join(pathData,sname+sub_Dict['Gas Labelled MS Peaks'][0])
+        pathFIDpMS = os.path.join(pathData,sname+sub_Dict['Gas FID+MS'][0])
+        
+    #Otherwise, set all paths to None
+    else:
+
+        pathFID = None
+        pathMS = None
+        pathFIDpMS = None
+        
+    paths = [pathFID,pathMS,pathFIDpMS]
+    
+    return paths
+    
+#Function for checking if FIDpMS file exists – creates it if necessary and imports/returns the data
+def checkFile(fpmDir,fDir):
+    """
+    Parameters
+    ----------
+    fpmDir : STR
+        A string containing the pathname of the FIDpMS file in question.
+    fDir : STR
+        A string containing the pathname of the FID file of the same sample/phase as the FIDpMS file.
+        
+    Returns
+    -------
+    fpmDF : DataFrame
+        A DataFrame containing the contents of the FIDpMS file.
+    exists : BOOL
+        A boolean describing whether or not the relevant file exists and has manually added peaks.
+
+    """
+
+    #If FIDpMS file does not exist in data file directory, create it and return False
+    if not os.path.exists(fpmDir):
+
+        #print that file wasn't found and a new one is being created
+        print('[fileChecks] FIDpMS file not found for sample and phase, creating new...')
+
+        #Read FID dataframe
+        fDF = pd.read_csv(fDir)
+
+        #Filter FID dataframe to only include FID rows, as gas samples may have TCD rows, and set to fpmDF
+        fpmDF = fDF.loc[fDF['Signal Name'] == 'FID1A'].copy()
+
+        #Rename FID RT and FID Area columns, as well as rename the Height column to MS RT
+        fpmDF = fpmDF.rename(columns={'RT':'FID RT','Area':'FID Area','Height':'MS RT'})
+
+        #Clear the contents of the MS RT column
+        fpmDF['MS RT'] = np.nan
+
+        #Create list of new columns to create
+        lnc = ['Formula','Match Factor','Compound Source','Compound Type Abbreviation']
+        
+        #Loop through lnc, adding nan columns for each entry
+        for i in lnc:
+            fpmDF[i] = np.nan
+        
+        #Remove the Injection Data File Name and Signal Name columns
+        fpmDF = fpmDF.drop(['Injection Data File Name','Signal Name'],axis=1).copy()
+
+        #Save fpmDF to provided pathname
+        fpmDF.to_csv(fpmDir, index=False)
+        
+        return fpmDF, False
+    
+    #Otherwise..
+    else:
+
+        fpmDF = pd.read_csv(fpmDir)
+
+        #If the FIDpMS exists and there exist any peaks..
+        if fpmDF['Compound Name'].any():
+
+            #Define a new dataframe which includes all rows with labelled peaks
+            fpmDF_labelled = fpmDF.loc[~fpmDF['Compound Name'].isna()]['Compound Source']
+
+            #If those peaks are manually assigned or have a blank source, return the dataframe and True
+            if 'Manual' in fpmDF_labelled.values.tolist() or pd.isna(fpmDF_labelled.values).any():
+
+                #Print
+                print('[fileChecks] FIDpMS file exists and contains manual and/or blank sourced entries')
+
+                return fpmDF, True
+            
+            #Otherwise, if there exist no manually assigned peaks or labelled peaks with a blank source, return False
+            else:
+
+                #Print
+                print('[fileChecks] FIDpMS file exists but does not contains manual or blank sourced entries')
+
+                return fpmDF, False
+            
+        #If the FIDpMS file exists but has no peaks, return False
+        else:
+
+            #Print
+            print('[fileChecks] FIDpMS file exists but contains no labelled peaks')
+
+            return fpmDF, False

chromaquant/Handle/handleDirectories.py

@@ -30,7 +30,7 @@ import getpass
 def handle(fileDir):
     #fileDir is the passed absolute directory of the currently running file
     
-    #Import sample information from json file
+    #Import file information from json file
     with open(os.path.join(fileDir,'properties.json'),'r') as props_f:
         props = json.load(props_f)
     

chromaquant/Hydro/__init__.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+ChromaQuant package initialization
+
+Julia Hancock
+Created 12-05-2024
+
+"""
+
+from .hydroMain import mainHydro