bcgsc / chopstitch Goto Github PK

>gi|239619018|gb|FJ830670.1|_1_53
ATGTTCACCTTGAAGAAATCCCTGTTGCTCCTTTTCTTTCTTGGGACCATCTC
>gi|239619018|gb|FJ830670.1|_54_73
ATTATCTCTCTGTGAGCAAG
>gi|239619018|gb|FJ830670.1|_74_283
AGAGAGATGCCGATGGAGATGAAGGGGAAGTTGAAGAAGTAAAAAGAGGTTTCCTGGATATCATCAAGGATACGGGGAAGGAATTTGCTGTGAAAATTTTGAATAATTTAAAATGTAAATTGGCTGGAGGATGTCCACCCTGAATCAGAGGTCATCTCATGTGGAATATCACTTAGCTAAATCTGTAATGTCTTATTAAAAAATAAAAAT
>gi|239619018|gb|FJ830670.1|_294_321
AGAAAAAAAAAAAAAAAAAAAAAAAAAA

T1<tab>G1
T2<tab>G1
T3<tab>G1
T4<tab>G2
T5<tab>G2
...

$ python FindSubcomponents.py -g ./test.dot -m
Warning: syntax error in line 2 near ''
Traceback (most recent call last):
  File "/home/kmnip/programs/chopstitch/ChopStitch/FindSubcomponents.py", line 120, in <module>
    main()
  File "/home/kmnip/programs/chopstitch/ChopStitch/FindSubcomponents.py", line 108, in main
    cc_subgraph = obj.findcc()
  File "/home/kmnip/programs/chopstitch/ChopStitch/FindSubcomponents.py", line 24, in findcc
    G = nx.drawing.nx_agraph.read_dot(self.dotfile)
  File "/home/kmnip/lib/python2.7/site-packages/networkx/drawing/nx_agraph.py", line 197, in read_dot
    A=pygraphviz.AGraph(file=path)
  File "/home/kmnip/lib/python2.7/site-packages/pygraphviz/agraph.py", line 158, in __init__
    self.read(filename)
  File "/home/kmnip/lib/python2.7/site-packages/pygraphviz/agraph.py", line 1228, in read
    raise DotError("Invalid Input")
pygraphviz.agraph.DotError: Invalid Input

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