Narrow peak debug #127
Narrow peak debug #127
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* added info in the doc of get_scores * integrate the cases when there is no item in the region * updated output of make_tracks_file
* added info in the doc of get_scores * integrate the cases when there is no item in the region * updated output of make_tracks_file * bedgraph inherit the init from GenomeTracks to have self.log
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Hi,
I think we should agree on the return of get_score.
Initially, when the chromosome was not on the file it was raising an error and when it was part of the file but there was no item in the region it was returning [nan], (start_region, end_region).
I guess this was to be able to make bedgraph to plot correctly.
So, if we keep this behaviour, when the chromosome is not part of the file, it should return [nan], (start_region, end_region).
The class which use this function are:
bedgraph ok
bedgraphmatrix ok
epilogos ok
narrowPeaks.
In the case of narrowPeaks, for idx, peak in enumerate(score_list): will go once except if we test before that the score_list is not [nan]...
| @@ -174,7 +175,7 @@ def get_scores(self, chrom_region, start_region, end_region, return_nans=True): | |||
| "chromosome name inside the bedgraph " | |||
| "file. This will generate an empty " | |||
| "track!!\n") | |||
| return | |||
| return score_list, pos_list | |||
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I think you should return the same thing line 161.
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right, I need to change that error message to warning too.
I will check for them, thanks! |
Narrow peak debug ld
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Hi, I thought you would prefer that the default is an empty list. |
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Either is fine by me, I would leave it be as long as it works fine. Thanks for the clarification! |
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I prefer to let it empty this way we do not need to import numpy to check if it is equal to |
fixed a bug in narrowPeaks which brought to us by #120