From 74f04060670e058e5fd3c968a4aa9f65420c4416 Mon Sep 17 00:00:00 2001
From: WardDeb <ward@deboutte.be>
Date: Wed, 26 Apr 2023 11:49:03 +0200
Subject: [PATCH] flake minor formatting

---
 src/dissectBCL/classes.py | 10 +++++++---
 src/dissectBCL/demux.py   | 19 ++++++++++---------
 src/dissectBCL/drHouse.py | 29 +++++++++++++++--------------
 3 files changed, 32 insertions(+), 26 deletions(-)

diff --git a/src/dissectBCL/classes.py b/src/dissectBCL/classes.py
index 7900ae9..389e79d 100644
--- a/src/dissectBCL/classes.py
+++ b/src/dissectBCL/classes.py
@@ -482,9 +482,13 @@ def optDupRet(optDup):
         if not self.P5RC:
             P5RCstr = ''
         else:
-            P5RCstr = '\n\nNote that the <FONT COLOR=red><strong>P5s have been reverse complemented automatically</strong></FONT> !'
-            P5RCstr += '\nThe multiQC report contains the barcodes as they are used for demultiplexing.\n'
-        
+            P5RCstr = '\n\n <FONT COLOR=red> '
+            P5RCstr += 'Note that the P5s have been reverse complemented '
+            P5RCstr += 'automatically. </strong></FONT> \n\n'
+            P5RCstr += 'The multiqc report contains '
+            P5RCstr += 'the index sequences '
+            P5RCstr += 'as they are used for demultiplexing.'
+
         msg = _html.render() +\
             P5RCstr +\
             '<h3>Top unknown barcodes</h3>' +\
diff --git a/src/dissectBCL/demux.py b/src/dissectBCL/demux.py
index 0de26bc..572824c 100644
--- a/src/dissectBCL/demux.py
+++ b/src/dissectBCL/demux.py
@@ -322,7 +322,7 @@ def writeDemuxSheet(demuxOut, ssDic, laneSplitStatus):
             f.write('{}\n'.format(line))
 
 
-def readDemuxSheet(demuxSheet):
+def readDemuxSheet(demuxSheet, what='all'):
     '''
     In case of manual intervention.
     We want to have the correct info in reports / emails.
@@ -371,7 +371,10 @@ def readDemuxSheet(demuxSheet):
         mask
     except NameError:
         mask = None
-    return (mask, df, dualIx, mmdic)
+    if what == 'all':
+        return (mask, df, dualIx, mmdic)
+    elif what == 'df':
+        return (df)
 
 
 def parseStats(outputFolder, ssdf):
@@ -538,7 +541,7 @@ def demux(sampleSheet, flowcell, config):
                 Path(
                     os.path.join(outputFolder, 'bclconvert.done')
                 ).touch()
-                if flowcell.sequencer ==  'MiSeq':
+                if flowcell.sequencer == 'MiSeq':
                     if differentialDiagnosis(
                         outputFolder,
                         sampleSheet.ssDic[outLane]['dualIx'],
@@ -549,7 +552,6 @@ def demux(sampleSheet, flowcell, config):
                         shutil.rmtree(
                             os.path.join(outputFolder, 'Reports')
                         )
-                        # 
                         bclRunner = Popen(
                             bclOpts,
                             stdout=PIPE
@@ -559,12 +561,11 @@ def demux(sampleSheet, flowcell, config):
                             "bclConvert P5fix exit {}".format(exitcode)
                         )
                         # Update the sampleSheet with proper RC'ed indices.
-                        manual_mask, manual_df, manual_dualIx, man_mmdic = readDemuxSheet(
-                            demuxOut
-                        )
-                        sampleSheet.ssDic[outLane]['sampleSheet'] = matchingSheets(
+                        sampleSheet.ssDic[outLane][
+                            'sampleSheet'
+                        ] = matchingSheets(
                             sampleSheet.ssDic[outLane]['sampleSheet'],
-                            manual_df
+                            readDemuxSheet(demuxOut, what='df')
                         )
                         sampleSheet.ssDic[outLane]['P5RC'] = True
                 else:
diff --git a/src/dissectBCL/drHouse.py b/src/dissectBCL/drHouse.py
index 1f98a40..533cb5e 100644
--- a/src/dissectBCL/drHouse.py
+++ b/src/dissectBCL/drHouse.py
@@ -6,7 +6,6 @@
 import glob
 import datetime
 import logging
-import sys
 from Bio.Seq import Seq
 
 
@@ -90,39 +89,41 @@ def differentialDiagnosis(outPath, dualIx):
     logging.warning(
         'More then 90% samples empty. Attempting to salvage by RC the P5.'
     )
-    if not dualIx: # Only RC P5 operations for now.
+    if not dualIx:  # Only RC P5 operations for now.
         return (False)
 
     # Read demuxSheet
     demuxSheetPath = os.path.join(
         outPath, 'demuxSheet.csv'
     )
-    demuxHeaders = []
     demuxSheet = []
     with open(demuxSheetPath) as f:
         headStatus = True
         for line in f:
-            if headStatus:
-                demuxHeaders.append(line.strip().split(','))
-            else:                    
-                demuxSheetLine = line.strip().split(',')
-                ixPos = colnames.index('index2')
-                oldIx = demuxSheetLine[ixPos]
-                newIx = str(Seq(oldIx).reverse_complement())
-                demuxSheetLine[ixPos] = newIx
-                demuxSheet.append(demuxSheetLine)
             if 'Sample_ID' in line.strip():
                 headStatus = False
                 colnames = line.strip().split(',')
+                demuxSheet.append(colnames)
+            if headStatus:
+                demuxSheet.append(line.strip().split(','))
+            else:
+                if 'Sample_ID' not in line.strip():
+                    demuxSheetLine = line.strip().split(',')
+                    ixPos = colnames.index('index2')
+                    oldIx = demuxSheetLine[ixPos]
+                    newIx = str(Seq(oldIx).reverse_complement())
+                    demuxSheetLine[ixPos] = newIx
+                    demuxSheet.append(demuxSheetLine)
     shutil.move(
         demuxSheetPath,
         demuxSheetPath+'.bak'
     )
     with open(demuxSheetPath, 'w') as f:
-        for l in demuxHeaders + demuxSheet:
-            f.write(','.join(l) +'\n')
+        for _l in demuxSheet:
+            f.write(','.join(_l) + '\n')
     return (True)
 
+
 def initClass(
     outPath, initTime, flowcellID, ssDic, transferTime, exitStats, solPath
         ):