Add test for csv2db (#360)

*  revert #358 and add small test for csv2db

*  pep8

* avoid using customised .sqliterc for sqlite output

CGAT/CSV2DB.py

@@ -507,8 +507,7 @@ def row_iter(rows, reader):
 
         while 1:
             try:
-                if isinstance(dbhandle, str):
-                    dbhandle.executemany(statement, data)
+                dbhandle.executemany(statement, data)
             except error as msg:
                 E.warn("import failed: msg=%s, statement=\n  %s" %
                        (msg, statement))

tests/csv2db.py/csvdb.ref

@@ -0,0 +1,2 @@
+|transcribed_unprocessed_pseudogene|ENSG00000223972|DDX11L1|havana|5|OTTHUMG00000000961|2|OTTHUMT00000362751|1|basic|processed_transcript|havana|1|2
+1|transcribed_unprocessed_pseudogene|ENSG00000223972|DDX11L1|havana|5|OTTHUMG00000000961|2|OTTHUMT00000362751|1|basic|processed_transcript|havana|1|2

tests/csv2db.py/table.csv

@@ -0,0 +1,3 @@
+gene_id	exon_version	gene_biotype	gene_name	gene_source	gene_version	havana_gene	havana_gene_version	havana_transcript	havana_transcript_version	tag	transcript_biotype	transcript_source	transcript_support_level	transcript_version
+ENSG00000223972		transcribed_unprocessed_pseudogene	DDX11L1	havana	5	OTTHUMG00000000961	2	OTTHUMT00000362751	1	basic	processed_transcript	havana	1	2
+ENSG00000223972	1	transcribed_unprocessed_pseudogene	DDX11L1	havana	5	OTTHUMG00000000961	2	OTTHUMT00000362751	1	basic	processed_transcript	havana	1	2

tests/csv2db.py/tests.yaml

@@ -4,3 +4,9 @@ version:
     outputs: [stdout]
     references: []
     options: --version
+
+simple_query:
+    stdin: table.csv
+    outputs: [stdout]
+    references: [csvdb.ref]
+    options: --retry --database-backend=sqlite --database-name=csvdb --table=gene_info -L /dev/null -S /dev/null -E /dev/null && sqlite3 <TMP>/csvdb "select * from gene_info;" 2> /dev/null