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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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Zcat error on OSX #7

Closed DoaneAS closed 8 years ago

DoaneAS commented 8 years ago

Hi,

Attempting to run the demo, and it seems there is an error related to zcat behavior on OSX.

python call_binding.py --task learn test/CTCF_chr10_motifs.txt.gz test/Gm12878_Rep1.bam test/Gm12878_Rep2.bam

loading motifs ... zcat: can't stat: Ctcf.test.txt (Ctcf.test.txt.Z): No such file or directory Traceback (most recent call last): File "call_binding.py", line 344, in <module> main() File "call_binding.py", line 337, in main learn_model(options) File "call_binding.py", line 32, in learn_model motif_handle = load_data.ZipFile(options.motif_file) File "/Users/asd2007/Tools/msCentipede/load_data.py", line 31, in __init__ header = self.handle.next() StopIteration

It turns out this is a known issue with differences in zcat on OSX

Possible solutions are to use gunzip -c in the code, or just add this gnu-tools-for-mac.sh

Or for OSX users, install GNU coreutils, and add /usr/local/opt/coreutils/libexec/gnubin to your PATH

EricDeveaud commented 8 years ago

instead of using zcat, gunzip or whatever just use plain python gzip support