Fix import statement and typos for genomemap

diff --git a/htsworkflow/pipelines/genomemap.py b/htsworkflow/pipelines/genomemap.py
index 0dc4919aaff4208c2254e77ba6d178caa6515f65..f39df7914723afb4cf654c5d7c2c4ee63e6f8896 100644 (file)
--- a/htsworkflow/pipelines/genomemap.py
+++ b/htsworkflow/pipelines/genomemap.py
@@ -3,6 +3,7 @@
 from glob import glob
 import os
 import collections
+from htsworkflow.pipelines.runfolder import ElementTree
 
 vldInfo = collections.namedtuple('vldInfo', 'name is_link')
 
@@ -78,7 +79,7 @@ def guess_genome(contig_sizes):
     genomes = {'chr1': {197195432: 'mm9',
                         247249719: 'hg19',
                         },
-               'chrI': {230218, 'sacCer3'},
+               'chrI': {230218: 'sacCer3'},
                }
 
     for key in genomes:

diff --git a/htsworkflow/pipelines/test/test_genomemap.py b/htsworkflow/pipelines/test/test_genomemap.py
index 8dc64d0e6b619dc0cac4a5cdc1c4c10a587805fb..421308d9bdbce0f6cc9c8873d6a84c8e72f863c2 100644 (file)
--- a/htsworkflow/pipelines/test/test_genomemap.py
+++ b/htsworkflow/pipelines/test/test_genomemap.py
@@ -57,5 +57,7 @@ class TestGenomeMap(unittest.TestCase):
         self.assertTrue('chr1.fa' in g)
         self.assertEqual(len(g), 3)
         self.assertEqual(g['chr1.fa'], '{0}/chr1.fa'.format(tempgenome))
+
+
 if __name__ == "__main__":
     unittest.main()