Roitools module error when running psite: "ValueError: too many values to unpack (expected 2)"

[marcasriv]

Hi,

I am getting this error when running psite :

psite -q my_rois.txt test --min_length 22 --max_length 34 --require_upstream --count_files harr.bam

psite [2020-10-30 10:19:10]: Opening count files harr.bam ...
psite [2020-10-30 10:19:10]: Counted 942136 total reads.
psite [2020-10-30 10:19:10]: Counted 1 ROIs ...
psite [2020-10-30 10:19:11]: Counted 1001 ROIs ...
psite [2020-10-30 10:19:11]: Counted 2001 ROIs ...
psite [2020-10-30 10:19:12]: Counted 3001 ROIs ...
psite [2020-10-30 10:19:13]: Counted 4001 ROIs ...
psite [2020-10-30 10:19:13]: Counted 5001 ROIs ...
psite [2020-10-30 10:19:14]: Counted 6001 ROIs ...
psite [2020-10-30 10:19:15]: Counted 7001 ROIs ...
psite [2020-10-30 10:19:15]: Counted 8001 ROIs ...
psite [2020-10-30 10:19:16]: Counted 9001 ROIs ...
psite [2020-10-30 10:19:17]: Counted 10001 ROIs ...
psite [2020-10-30 10:19:18]: Counted 11001 ROIs ...
psite [2020-10-30 10:19:18]: Counted 12001 ROIs ...
Traceback (most recent call last):
File "/home/user/anaconda2/envs/bin/psite", line 8, in
sys.exit(main())
File "/home/user/anaconda2/envs/lib/python2.7/site-packages/plastid/bin/psite.py", line 345, in main
printer=printer)
File "/home/user/anaconda2/envs/lib/python2.7/site-packages/plastid/bin/psite.py", line 157, in do_count
roi = SegmentChain.from_str(row["region"])
File "plastid/genomics/roitools.pyx", line 3311, in plastid.genomics.roitools.SegmentChain.from_str
ValueError: too many values to unpack (expected 2)

I've found this error when running Plastid 0.5.1, went back to Plastid 0.4.7 and still happened. I have installed plastid through conda, and this is my environment:

• _libgcc_mutex 0.1 conda_forge conda-forge
• _openmp_mutex 4.5 1_gnu conda-forge
• biopython 1.77 pypi_0 pypi
• bowtie 1.3.0 py38hed8969a_1 bioconda
• bzip2 1.0.8 h516909a_3 conda-forge
• c-ares 1.11.0 h470a237_1 bioconda
• ca-certificates 2020.6.20 hecda079_0 conda-forge
• certifi 2020.6.20 py38h924ce5b_2 conda-forge
• cycler 0.10.0 py_2 conda-forge
• cython 0.29.21 py38h348cfbe_1 conda-forge
• fastx_toolkit 0.0.14 0 bioconda
• freetype 2.10.4 he06d7ca_0 conda-forge
• jpeg 9d h516909a_0 conda-forge
• kiwisolver 1.2.0 py38hbf85e49_1 conda-forge
• krb5 1.17.1 hfafb76e_3 conda-forge
• lcms2 2.11 hbd6801e_0 conda-forge
• ld_impl_linux-64 2.35 h769bd43_9 conda-forge
• libblas 3.9.0 2_openblas conda-forge
• libcblas 3.9.0 2_openblas conda-forge
• libcurl 7.71.1 hcdd3856_8 conda-forge
• libdeflate 1.6 h516909a_0 conda-forge
• libedit 3.1.20191231 he28a2e2_2 conda-forge
• libev 4.33 h516909a_1 conda-forge
• libffi 3.2.1 he1b5a44_1007 conda-forge
• libgcc-ng 9.3.0 h5dbcf3e_17 conda-forge
• libgfortran-ng 9.3.0 he4bcb1c_17 conda-forge
• libgfortran5 9.3.0 he4bcb1c_17 conda-forge
• libgomp 9.3.0 h5dbcf3e_17 conda-forge
• libgtextutils 0.7 he1b5a44_6 bioconda
• liblapack 3.9.0 2_openblas conda-forge
• libnghttp2 1.41.0 hab1572f_1 conda-forge
• libopenblas 0.3.12 pthreads_h4812303_1 conda-forge
• libpng 1.6.37 hed695b0_2 conda-forge
• libssh2 1.9.0 hab1572f_5 conda-forge
• libstdcxx-ng 9.3.0 h2ae2ef3_17 conda-forge
• libtiff 4.1.0 hc7e4089_6 conda-forge
• libwebp-base 1.1.0 h516909a_3 conda-forge
• lz4-c 1.9.2 he1b5a44_3 conda-forge
• matplotlib-base 3.3.2 py38h4d1ce4f_1 conda-forge
• ncurses 6.2 he1b5a44_2 conda-forge
• nose 1.3.7 py_1006 conda-forge
• numpy 1.19.2 py38hf89b668_1 conda-forge
• olefile 0.46 pyh9f0ad1d_1 conda-forge
• openssl 1.1.1h h516909a_0 conda-forge
• pandas 1.1.3 py38hddd6c8b_2 conda-forge
• perl 5.30.3 h516909a_1 conda-forge
• pillow 8.0.1 py38h9776b28_0 conda-forge
• pip 20.2.4 py_0 conda-forge
• plastid 0.5.1 py38h197edbe_1 bioconda
• pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
• pysam 0.16.0.1 py38hbdc2ae9_1 bioconda
• python 3.8.6 h852b56e_0_cpython conda-forge
• python-dateutil 2.8.1 py_0 conda-forge
• python_abi 3.8 1_cp38 conda-forge
• pytz 2020.1 pyh9f0ad1d_0 conda-forge
• readline 8.0 he28a2e2_2 conda-forge
• scipy 1.5.2 py38hd9480d8_2 conda-forge
• setuptools 49.6.0 py38h924ce5b_2 conda-forge
• six 1.15.0 pyh9f0ad1d_0 conda-forge
• sqlite 3.33.0 h4cf870e_1 conda-forge
• tbb 2020.2 hc9558a2_0 conda-forge
• termcolor 1.1.0 py_2 conda-forge
• tk 8.6.10 hed695b0_1 conda-forge
• tornado 6.0.4 py38h1e0a361_2 conda-forge
• twobitreader 3.1.7 pyh864c0ab_1 bioconda
• wheel 0.35.1 pyh9f0ad1d_0 conda-forge
• xz 5.2.5 h516909a_1 conda-forge
• zlib 1.2.11 h516909a_1010 conda-forge
• zstd 1.4.5 h6597ccf_2 conda-forge

Thank you!