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morrislab / qapa

RNA-seq Quantification of Alternative Polyadenylation
GNU General Public License v3.0
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error about qapa build #50

Closed haojin9288 closed 1 year ago

haojin9288 commented 1 year ago

hello, i want to apply the software in species not human and mouse, but i meet some problems at the process of build 3′ UTRs from annotation. I am very grateful that you can give me some help! the code and error is in the below:

qapa build -N --db bos_ensembl_identifiers.txt bos_custom_genes_ensem109.genePred > bos_output.utrs.bedqapa.qapa - 2023-04-12 23:38:17,159 - INFO - Version 1.3.3 qapa.qapa - 2023-04-12 23:38:17,507 - INFO - Extracting 3' UTRs from bos_custom_genes_ensem109.genePred qapa.qapa - 2023-04-12 23:38:20,148 - INFO - Annotating 3' UTRs qapa.annotate - 2023-04-12 23:38:20,994 - INFO - Skipping annotation step qapa.qapa - 2023-04-12 23:38:22,170 - INFO - Checking 5' ends qapa.qapa - 2023-04-12 23:38:48,178 - INFO - Collapsing 3' ends qapa.collapse - 2023-04-12 23:38:48,218 - INFO - Sorting data frame by 3' end qapa.collapse - 2023-04-12 23:38:48,225 - INFO - Iterating and merging intervals by 3' end qapa.collapse - 2023-04-12 23:38:49,017 - INFO - Updating 5' end for each gene qapa.qapa - 2023-04-12 23:38:49,026 - ERROR - Error occurred in build: Traceback (most recent call last): File "/home/jh/mambaforge-pypy3/envs/qapa/lib/python3.10/site-packages/qapa/qapa.py", line 244, in build result = collapse.merge_bed(args, tf3.name) File "/home/jh/mambaforge-pypy3/envs/qapa/lib/python3.10/site-packages/qapa/collapse.py", line 147, in merge_bed forward = forward.drop('start_r', 1) TypeError: DataFrame.drop() takes from 1 to 2 positional arguments but 3 were given

hlldhy commented 1 year ago

I also encounter the same error,how to solve it?

IanLopesTeixeira commented 1 year ago

I also found it.

YaJiang233 commented 1 year ago

I also found this problem. I think this is because of the updates of panda package. To change the code in "collapse.py", line 147 to forward = forward.drop('start_r', axis=1) may fix it. But I don't know how to contact the developer.

olivertam commented 1 year ago

Changing these two lines: https://github.com/morrislab/qapa/blob/b7dd879edd063a114d9c5df9835d35c991390248/qapa/collapse.py#L147 https://github.com/morrislab/qapa/blob/b7dd879edd063a114d9c5df9835d35c991390248/qapa/collapse.py#L153 as described by @YaJiang233 (replacing 1 with axis=1 worked for me.

kcha commented 1 year ago

@olivertam @YaJiang233 thank you for catching this! A fix has been applied.