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rajanil / msCentipede

A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
MIT License
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KeyError - Missing chromosome names #19

Open patrickCNMartin opened 4 years ago

patrickCNMartin commented 4 years ago

Hi,

I have been trying to use msCentipede on Drosophila data but to no avail. Once msCentipede tries to load my BAM files, I get the following error:

python msCentipede/call_binding.py --task learn motif_beaf.txt.gz ~/DNAaccess/cellAccess/S2_DNASE_harv/S2_Dnase_trim.bam 
loading motifs ... 
num of motif sites = 10000
loading read counts ... 
Traceback (most recent call last):
  File "msCentipede/call_binding.py", line 346, in <module>
    main()
  File "msCentipede/call_binding.py", line 339, in main
    learn_model(options)
  File "msCentipede/call_binding.py", line 72, in learn_model
    for bam_handle in bam_handles])
  File "/home/pm16057/proj/msCentipede/load_data.py", line 116, in get_read_counts
    right = min([center+width/2, self._ref_lengths[chrom]])
KeyError: '"chrX"'

From my understanding of the problem this is due to missing name 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?

Thank you!

Kind Regards

Patrick