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bug in the plot_homer_annotatepeaks.r script #86

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anvlasova opened this issue Feb 27, 2020 · 5 comments
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bug in the plot_homer_annotatepeaks.r script #86

anvlasova opened this issue Feb 27, 2020 · 5 comments
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@anvlasova
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Hi,

Some annotations containing special characters in the gene names, for example in dm3 genome some genes have " ' '' symbol in the gene name.

Function 'read.table' in the script plot_homer_annotatepeaks.r can't properly read such files and the whole pipeline crashes in the 'merge_library_macs_qc' step. While function read.csv can process those files without problems. Guess this is because of default quote and comment char options that are different between these two functions: https://stackoverflow.com/questions/12828438/read-csv-vs-read-table

Can you please fix it?

thanks,
Anna

@drpatelh drpatelh added the bug Something isn't working label Feb 27, 2020
@drpatelh
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Hi @anvlasova Thanks for reporting this 👍

Would you mind uploading a file I can use to test this please? Alternatively, please feel free to submit a PR with a fix to the dev branch. The pipeline is pretty much ready for the next release so it will be fixed in the next version.

@anvlasova
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Hi @drpatelh,

we found this problem with this annotation file ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.57_FB2014_03/gff/dmel-all-filtered-r5.57.gff.gz
Some genes have a " ' " character in their names, i.e. gene "Name=beta'COP " on the chr 2L:13378902-13382382 and this causes the problem.
i will try to contribute to the dev branch,

thanks,
Anna

@drpatelh
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Thanks @anvlasova . Just to clarify this is the change you had to make in order to get things working?
cf6c5c3

@anvlasova
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hi @drpatelh ,
yes, it is, thank you! hope it will not break smth else.
thanks,
Anna

@drpatelh
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I hope not! I remember specifically adding in quote="" to fix another bug. Hopefully should be fine ;)

Fixed in #92

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