From 6c2f902fd21b18fe28c86d44e7dcdb8fda646959 Mon Sep 17 00:00:00 2001 From: thomasmanke Date: Sun, 1 Dec 2024 17:56:30 +0100 Subject: [PATCH 1/2] update install docu --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7250caf..2f574a5 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ Clone this repository, create the environment and pip install > git clone git@github.com:maxplanck-ie/dissectBCL.git > cd dissectBCL - > conda create -f env.yml --name dissectBCL + > conda env create -f env.yml --name dissectBCL > conda activate dissectBCL > pip install ./ From a803bc3e7e1bfaca66fb547a6a8aa05c33358471 Mon Sep 17 00:00:00 2001 From: thomasmanke Date: Sun, 1 Dec 2024 17:57:44 +0100 Subject: [PATCH 2/2] fix parkour organism as list --- src/dissectBCL/fakeNews.py | 4 ++-- src/dissectBCL/misc.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/dissectBCL/fakeNews.py b/src/dissectBCL/fakeNews.py index 3b2f7da..9848c8a 100644 --- a/src/dissectBCL/fakeNews.py +++ b/src/dissectBCL/fakeNews.py @@ -443,7 +443,7 @@ def gatherFinalMetrics(outLane, flowcell): # hence the try / except. # 'mouse (GRCm39)' -> 'mouse' parkourOrg = str( # To string since NA is a float - ssdf[ssdf["Sample_ID"] == sampleID]['Organism'].values[0] + ssdf[ssdf["Sample_ID"] == sampleID]['Organism'].values[0][0] ).split(' ')[0] try: screenDF = pd.read_csv( @@ -478,4 +478,4 @@ def gatherFinalMetrics(outLane, flowcell): 'transferTime': flowcell.transferTime, 'exitStats': flowcell.exitStats, 'P5RC':ssDic['P5RC'] - } \ No newline at end of file + } diff --git a/src/dissectBCL/misc.py b/src/dissectBCL/misc.py index f244e12..e82cbb9 100644 --- a/src/dissectBCL/misc.py +++ b/src/dissectBCL/misc.py @@ -510,7 +510,7 @@ def multiQC_yaml(flowcell, project, laneFolder): )) # Organisms orgs = ', '.join(list( - ssdf["Organism"].fillna('None').unique() + ssdf["Organism"].str[0].fillna('None').unique() )) # Resequencing runs are screwed up (e.g. don't contain the samples) # switch total requested to NA @@ -663,4 +663,4 @@ def matchOptdupsReqs(optDups, ssdf): int(got) ] ) - return (sorted(_optDups, key=lambda x: x[1])) \ No newline at end of file + return (sorted(_optDups, key=lambda x: x[1]))