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biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
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where "chr1_before_find_islands.csv" file comes from? #70

Closed zhenyisong closed 6 years ago

zhenyisong commented 6 years ago

I installed the local version epic through bioconda. However, when task was competed, there was a file named "chr1_before_find_islands.csv" which was created along with expected cvs files. Here is my shell snippet:

    macs2 callpeak --treatment ${treat} --control ${control} \
          --format BAM --gsize mm --name ${base} --bdg --qvalue 0.01

here is the excerpt of this file ("chr1_before_find_islands.csv")

 Chromosome Bin ChIP Input Score
28 chr1 3007400 6 5.0 2.43113976041
134 chr1 3035800 6 4.0 2.43113976041
174 chr1 3046800 6 1.0 2.43113976041
177 chr1 3047400 6 3.0 2.43113976041

I am confused about this unwanted file. It seems that the run_epic.py will output this file. (at line 60)

dfs[0].to_csv("chr1_before_find_islands.csv", sep=" ")

Will you please clarify this chr1 output? Or it is just the temporary file and can be neglected whatever. Or the error message we should take care and tune the parameter in the command line?

endrebak commented 6 years ago

Thanks for reporting. I really appreciate it. The file was used for debugging and should not have been included in a release. Will fix tomorrow!

Endre

On Sunday, February 11, 2018, Yisong Zhen notifications@github.com wrote:

I installed the local version epic through bioconda. However, when task was competed, there was a file named "chr1_before_find_islands.csv" which was created along with expected cvs files. Here is my shell snippet:

macs2 callpeak --treatment ${treat} --control ${control} \
      --format BAM --gsize mm --name ${base} --bdg --qvalue 0.01

here is the excerpt of this file ("chr1_before_find_islands.csv")

Chromosome Bin ChIP Input Score 28 chr1 3007400 6 5.0 2.43113976041 134 chr1 3035800 6 4.0 2.43113976041 174 chr1 3046800 6 1.0 2.43113976041 177 chr1 3047400 6 3.0 2.43113976041

I am confused about this unwanted file. It seems that the run_epic.py will output this file. (at line 60)

dfs[0].to_csv("chr1_before_find_islands.csv", sep=" ")

Will you please clarify this chr1 output? Or it is just the temporary file and can be neglected whatever. Or the error message we should take care and tune the parameter in the command line?

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endrebak commented 6 years ago

This is fixed in 2.9 which is out on pypi but not bioconda yet. Will add it now :)