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gersteinlab / HiC-spector

Spectral and reproducibility analysis of Hi-C contact maps
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ValueError: invalid literal for int() with base 10: 'HIC' #1

Closed jamesdalg closed 6 years ago

jamesdalg commented 6 years ago

Using HiC-spector, I really like the simple interface and how accessible it is from standard formats. In my case, I'm trying to use juicer output (.hic files) to get reproducibility statistics from HiC-spector, but I'm getting a python error. Is it my version of python? I looked through the supplementary information and the paper (https://academic.oup.com/bioinformatics/article/33/14/2199/3078603) and can't find specific information that would lead me to understand the source of this error.

(/data/CCRBioinfo/HiC-spector-env/) bash-4.1$ module show julialang

/usr/local/lmod/modulefiles/julialang/0.5.2.lua:

help([[This module sets up the environment for using XXXX. ]]) whatis("Julia: High level, dynamic language for techincal computing") whatis("Version: 0.5.2") prepend_path("PATH","/usr/local/apps/julialang/0.5.2/bin") load("git")

(/data/CCRBioinfo/HiC-spector-env/) bash-4.1$ python run_reproducibility.py -F hicrep1.hic hicrep2.hic Traceback (most recent call last): File "run_reproducibility.py", line 154, in main() File "run_reproducibility.py", line 139, in main M1, M2=Parse_matrix(sys.argv[2],sys.argv[3]) File "run_reproducibility.py", line 12, in Parse_matrix x,y,z=map(int, line.split()) ValueError: invalid literal for int() with base 10: 'HIC' (/data/CCRBioinfo/HiC-spector-env/) bash-4.1$ python Python 2.7.14 | packaged by conda-forge | (default, Oct 5 2017, 14:19:56) [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2 Type "help", "copyright", "credits" or "license" for more information.

import straw

jamesdalg commented 6 years ago

If you need, I can send the HiC files to you.

ChengfeiYan commented 6 years ago

Hi, For the .hic format, the command you should use it: "python run_reproducibility.py -f hic_file1 hic_file2 chrid resolution"

First, you should use "-F" rather than "-f". Second, you should include the chromosome id and the resolution of the HiC matrix. (Such as "10" for the chrid and "50000" for the resolution)

Hope this helps. Thanks, Chengfei Yan

jamesdalg commented 6 years ago

ChengfeiYan, I changed the chrid to "chr8" rather than "8", but it works perfectly now.

error: One of the chromosomes wasn't found in the file. Check that the chromosome name matches the genome.

Traceback (most recent call last): File "run_reproducibility.py", line 154, in main() File "run_reproducibility.py", line 142, in main M1, M2=Parse_matrix_hic(sys.argv[2],sys.argv[3],sys.argv[4],int(sys.argv[5])) File "run_reproducibility.py", line 41, in Parse_matrix_hic Table1=straw.straw("NONE",file1, chrn, chrn,"BP",resolution) File "/data/CCRBioinfo/dalgleishjl/HiC-spector/straw/python/straw.py", line 471, in straw master=list1[0] TypeError: 'int' object has no attribute 'getitem'

success after changing '8' to 'chr8': HiC version: 8 HiC version: 8 size of maps: 293 reproducibility score: 0.198