fix bug (when summit in merged peaks is None)

[leepc12]

I got errors when running pipelines for some samples from Butcher's lab. This PR is a fix for it.

                Traceback (most recent call last):
                  File "/software/miniconda3/envs/bds_atac_py3/bin/idr", line 4, in <module>
                    __import__('pkg_resources').run_script('idr==2.0.3', 'idr')
                  File "/software/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 744, in run_script
                  File "/software/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 1499, in run_script
                  File "/software/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/EGG-INFO/scripts/idr", line 10, in <module>
                    idr.idr.main()
                  File "/software/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 899, in main
                    useBackwardsCompatibleOutput=args.use_old_output_format)
                  File "/software/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 486, in write_results_to_file
                    merged_peak, IDR, localIDR, output_file_type, signal_type)
                  File "/software/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 352, in build_idr_output_line_with_bed6
                    mean(x.summit-x.start for x in m_pk.pks[key])
                  File "/software/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 15, in mean
                    items = list(items)
                  File "/software/miniconda3/envs/bds_atac_py3/lib/python3.5/site-packages/idr-2.0.3-py3.5-linux-x86_64.egg/idr/idr.py", line 352, in <genexpr>
                    mean(x.summit-x.start for x in m_pk.pks[key])
                TypeError: unsupported operand type(s) for -: 'NoneType' and 'int'

[huanhuantai]

Hi, may I ask how the peak summit position is calculated in IDR pipeline? after IDR, I got chromosome start and end position per peak but the peak summit position looks like a relative position relative to the peak length. How can I get the absolute peak summit position relative to chromosome? The absolute peak summit position is important for me to perform the downstream analysis. Many thanks!

[YogiOnBioinformatics]

@leepc12 will you ever be merging this changes? I ask since I am experiencing this issue currently.

[leepc12]

@YogiOnBioinformatics: This repo has been deprecated. This is already fixed in the new repo: https://github.com/kundajelab/idr

[YogiOnBioinformatics]

@leepc12 I really appreciate your quick response! Thanks!