uci-cbcl / factornet Goto Github PK

Hi,

I have been trying to use FactorNet on Drosophila data but to no avail. I have been getting the following error:

python FactorNet-master/train.py -i Training/TrainingScores_chr3R.bed -vi Validation/Validation_Peaks_chr2R.bed -k 128 -r 128 -d 256 -oc Training_output
Multi-task training
output directory (Training_output) already exists so it will be clobbered
Loading genome
Traceback (most recent call last):
  File "FactorNet-master/train.py", line 301, in <module>
    main()
  File "FactorNet-master/train.py", line 190, in main
    genome = utils.load_genome()
  File "/home/pm16057/FactorNet/FactorNet-master/utils.py", line 349, in load_genome
    onehot_chroms = parmap.map(get_onehot_chrom, chroms)
  File "/usr/lib/python2.7/site-packages/parmap/parmap.py", line 304, in map
    return _map_or_starmap(function, iterable, args, kwargs, "map")
  File "/usr/lib/python2.7/site-packages/parmap/parmap.py", line 248, in _map_or_starmap
    output = result.get()
  File "/usr/lib64/python2.7/multiprocessing/pool.py", line 554, in get
    raise self._value
KeyError: 'chr2RHet'

From my understanding of the problem this is due to missing names is some python dictionary.

I was wondering if it could be that some dependency does not support chromosome names from other species or if there is a way around this issue that I have not been able to find?

I have changes files in the resources folder and made changes to utils/.py but to no avail.

Thank you!

Kind Regards

Patrick

executing the testcases results in the following error:
Traceback (most recent call last):
File "train.py", line 301, in
main()
File "train.py", line 197, in main
utils.load_chip_singleTask(input_dirs, tf)
File "/home/hpc/t1172/di36dih/bin/FactorNet-master/utils.py", line 462, in load_chip_singleTask
blacklist = make_blacklist()
File "/home/hpc/t1172/di36dih/bin/FactorNet-master/utils.py", line 373, in make_blacklist
blacklist = blacklist.cat(blacklist2)
File "/home/hpc/t1172/di36dih/anaconda2/envs/env1/lib/python2.7/site-packages/pybedtools/bedtool.py", line 840, in decorated
result = method(self, *args, **kwargs)
File "/home/hpc/t1172/di36dih/anaconda2/envs/env1/lib/python2.7/site-packages/pybedtools/bedtool.py", line 3064, in cat
for f in self:
File "pybedtools/cbedtools.pyx", line 798, in pybedtools.cbedtools.IntervalIterator.next
File "pybedtools/cbedtools.pyx", line 698, in pybedtools.cbedtools.create_interval_from_list
pybedtools.cbedtools.MalformedBedLineError: Unable to detect format from ['chr17_ctg5_hap1', '-1', '1255794']

Even after updating pybedtools or changing of the genome the error still occurs.

I feel like matplotlib should be added as an additional requirement for FactorNet, since without it I received errors when trying to run predict.py.
(Error was relating to missing pylab)