search

zavolanlab / MIRZAG

MIRZA-G - Pipeline and model for miRNA target prediction
5 stars 3 forks source link

rg_calculate_MIRZA.py crashes in snakemake version when custom tree is provided #9

Closed fgypas closed 6 years ago

fgypas commented 6 years ago

Traceback (most recent call last): File "../../docker/scripts/rg_calculate_MIRZA.py", line 786, in main(options) File "../../docker/scripts/rg_calculate_MIRZA.py", line 192, in main mrna_len=options.contextLen) File "../../docker/scripts/rg_calculate_MIRZA.py", line 520, in calculate_conservation min_score.retain_taxa_with_labels([ref_org]) File "/usr/local/lib/python2.7/site-packages/dendropy/datamodel/treemodel.py", line 5390, in retain_taxa_with_labels suppress_unifurcations=suppress_unifurcations) File "/usr/local/lib/python2.7/site-packages/dendropy/datamodel/treemodel.py", line 5377, in retain_taxa suppress_unifurcations=suppress_unifurcations) File "/usr/local/lib/python2.7/site-packages/dendropy/datamodel/treemodel.py", line 5346, in prune_taxa suppress_unifurcations=suppress_unifurcations) File "/usr/local/lib/python2.7/site-packages/dendropy/datamodel/treemodel.py", line 5307, in prune_leaves_without_taxa nd.edge.tail_node.remove_child(nd) AttributeError: 'NoneType' object has no attribute 'remove_child'

fgypas commented 6 years ago

The problem is that the organism that I currently use is not hg19 but hg38.

parser.add_argument('--reforg',
                     dest='reforg',
                     action="store",
                     default="hg19",
                     help="Reference organism to which alignments are performed: default: hg19")

So i just have to expose this in the config.

fgypas commented 6 years ago

Indeed this fixes the issue.

fgypas commented 6 years ago

fixed in 136ad38a54291d85ac313e5c6385f4b263ce58ba