conv tsv to csv before using sqllite utils

Dockerfile

@@ -15,7 +15,8 @@ ADD https://api.gbif.org/v1/occurrence/download/request/0032228-231002084531237.
 RUN ls -l /data
 RUN unzip /data/gbif-occs.zip -d /data
 RUN ls -l /data
-RUN csvs-to-sqlite /data/0032228-231002084531237.csv /code/gbifocc.db -s \$'\t'
+RUN python tab2csv.py /data/0032228-231002084531237.tsv /data/0032228-231002084531237.csv 
+RUN csvs-to-sqlite /data/0032228-231002084531237.csv /code/gbifocc.db
 RUN ls -l /code
 RUN sqlite-utils tables /code/gbifocc.db --counts
 

tab2csv.py

@@ -0,0 +1,11 @@
+import argparse
+import pandas as pd
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument("inputfile")
+    parser.add_argument("outputfile")    
+    args = parser.parse_args()
+
+    df = pd.read_csv(args.inputfile, encoding='utf8', keep_default_na=False, sep='\t')
+    df.to_csv(outputfile, index=False, sep=',')