Remove duplicates from HCMI

this resolves #397 because genes are not counted multiple times.

Author: sgosline

build/hcmi/02-getHCMIData.py

@@ -613,10 +613,13 @@ def write_dataframe_to_csv(dataframe, outname):
     -------
     None
     """
+    dataframe = dataframe.to_pandas()
+    dataframe = dataframe.drop_duplicates()
+
     if('gz' in outname):
-        dataframe.to_pandas().to_csv(outname,compression='gzip',index=False)
+        dataframe.to_csv(outname,compression='gzip',index=False)
     else:
-        dataframe.to_pandas().to_csv(outname,index=False)
+        dataframe.to_csv(outname,index=False)
     return
 
 def main():

build/utils/tpmFromCounts.py

@@ -78,7 +78,7 @@ def main(counts_data, genome_link, gene_column, exclude_columns, out_file):
 if __name__=='__main__':
     parser = argparse.ArgumentParser("Quick script to get TPM from counts matrix")
 
-    parser.add_argument('--counts', default=None, help='Transcriptomics counts matrix')
+    parser.add_argument('--counts', default=None, help='Transcriptomics counts matrix where rows represent gene values and columns represent samples')
     parser.add_argument('--genome_build', default="https://ftp.ensembl.org/pub/grch37/release-113/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz", help='Link to human genome build')
     parser.add_argument('--gene_col', default="stable_id", help='Name of column with gene names')
     parser.add_argument('--exclude_col', default="stable_id,display_label,description,biotype", help='Name of column with gene names')