Merge pull request #4 from filipsPL/float-in-names

Float as a name, fix issue
filipsPL · Aug 5, 2022 · d30c371 · d30c371
2 parents a573e48 + dc56ce8
commit d30c371
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/.github/workflows/thefirst.yml b/.github/workflows/thefirst.yml
@@ -11,7 +11,7 @@ jobs:
       matrix:
         # os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
         # align-it in conda is only for linux 64 bit https://anaconda.org/bioconda/align_it/files
-        os: ['ubuntu-16.04', 'ubuntu-18.04', 'ubuntu-20.04']
+        os: ['ubuntu-18.04', 'ubuntu-20.04']
     runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout

diff --git a/annapurna.py b/annapurna.py
@@ -1266,15 +1266,15 @@ def scoreLoop(infile, outputFilename, models, sdffile, ClusteringMethod, Cluster
       '''For each supplied model in models[] loop over data form infile, predict probabilities and save it in outputFilename '''
       printMemInfo()
       print info.info + "Reading statistics file..."
-      statComplex = pd.read_csv(infile, delimiter="\t")
+      statComplex = pd.read_csv(infile, delimiter="\t", dtype={"compound": 'str'})
       printMemInfo()
       print info.info + "Grouping..."
       statComplexGrouped = statComplex.groupby(['base', 'at2', 'atom_type'])
       del statComplex
       printMemInfo()
 
       print info.info + "Reading Energy data..."
-      E_ligand = pd.read_csv(outputFilename + ".ligand_energy.csv.bz2", delimiter=",")
+      E_ligand = pd.read_csv(outputFilename + ".ligand_energy.csv.bz2", delimiter=",", dtype={"compound": 'str'})
 
 
       for modelName in models:
@@ -1289,7 +1289,7 @@ def scoreLoop(infile, outputFilename, models, sdffile, ClusteringMethod, Cluster
           score(statComplexGrouped, modelName, tempFilename = outputFilename + ".scores.tmp")
 
           # WARNING - tu może zrobić chunks?
-          output = pd.read_csv(outputFilename + ".scores.tmp", delimiter=",")
+          output = pd.read_csv(outputFilename + ".scores.tmp", delimiter=",", dtype={"compound": 'str'}) # address the issue #3
 
           os.remove(outputFilename + ".scores.tmp") # delete the temp file
 
@@ -1529,7 +1529,7 @@ def mergeOutputFiles(outputFilename, models, groupByName = False):
       for modelName in models:
           outfile = outputFilename + "." + modelName + ".csv"
           print info.info + "Processing file:", outfile
-          data = pd.read_csv(outfile, delimiter="\t")
+          data = pd.read_csv(outfile, delimiter="\t", dtype={"compound": 'str'})
           data = data.ix[:, ['compoundId', 'compound', 'score'] ]			# last number - the column with the actual score
           data = data.rename(columns={'score': 'AnnapuRNA Score:' + modelName})
 
@@ -1543,7 +1543,7 @@ def mergeOutputFiles(outputFilename, models, groupByName = False):
           if groupByName == True:
                 outfileGrouped = outputFilename + "." + modelName + ".grouped.csv"
                 print info.info + "Processing file:", outfileGrouped
-                dataGrouped = pd.read_csv(outfileGrouped, delimiter="\t")
+                dataGrouped = pd.read_csv(outfileGrouped, delimiter="\t", dtype={"compound": 'str'})
                 dataGrouped = dataGrouped.ix[:, ['compoundId', 'compound', 'score'] ]
                 dataGrouped = dataGrouped.reindex_axis(['compound', 'compoundId', 'score'], axis=1)