- edited description
Error in pandas.parser.TextReader
Hi,
After running Mageck successfully, when I try to run the final command to display VISPR results, I encounter the following error:
BRBB138:Pool3_test paran$ vispr server results/*.vispr.yaml
Loading data.
Traceback (most recent call last):
File "/Users/paran/miniconda3/bin/vispr", line 6, in <module>
sys.exit(vispr.cli.main())
File "/Users/paran/miniconda3/lib/python3.5/site-packages/vispr/cli.py", line 195, in main
init_server(*args.config, port=args.port)
File "/Users/paran/miniconda3/lib/python3.5/site-packages/vispr/cli.py", line 41, in init_server
app.screens.add(config, parentdir=os.path.dirname(path))
File "/Users/paran/miniconda3/lib/python3.5/site-packages/vispr/results/__init__.py", line 28, in add
self.screens[screen] = Screen(config, parentdir=parentdir)
File "/Users/paran/miniconda3/lib/python3.5/site-packages/vispr/results/__init__.py", line 83, in __init__
posterior_results=get_path(config["sgrnas"].get("results", None)))
File "/Users/paran/miniconda3/lib/python3.5/site-packages/vispr/results/rna.py", line 36, in __init__
low_memory=False).iloc[:, :5]
File "/Users/paran/miniconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 562, in parser_f
return _read(filepath_or_buffer, kwds)
File "/Users/paran/miniconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 315, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/Users/paran/miniconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 645, in __init__
self._make_engine(self.engine)
File "/Users/paran/miniconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 799, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/Users/paran/miniconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 1213, in __init__
self._reader = _parser.TextReader(src, **kwds)
File "pandas/parser.pyx", line 523, in pandas.parser.TextReader.__cinit__ (pandas/parser.c:5214)
pandas.io.common.EmptyDataError: No columns to parse from file
I'm attaching the two config.yaml used to generate the results. Hope that someone can help me.
Thank you.
Comments (12)
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Thanks, and sorry for the bug. It looks like the file defined under sgrnas->results in the corresponding vispr config file contains something invalid or is even empty. Can you please post the first 10 lines of that file?
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Hi Johannes,
Here are the first 10 lines of the .vispr.yaml file in the results directory:
assembly: hg38
experiment: DMSO_14_Res_21
fastqc:
DMSO_14:
- qc/DMSO_14_0/Pool3_ABT199_DMSO_14_fastqc/fastqc_data.txt
Res_21:
- qc/Res_21_0/Pool3_ABT199_Res_21_fastqc/fastqc_data.txt
sgrnas:
annotation: sgrnas.bed
counts: count/all.count_normalized.txt
mapstats: count/all.countsummary.txt
results: test/DMSO_14_Res_21.sgrna_summary.txt
species: homo_sapiens
targets:
genes: true
results: test/DMSO_14_Res_21.gene_summary.txt
I noticed the sgrnas.bed file is empty in the results directory. However, there are definitely read matches because there were matches when I ran just Mageck.
Andrew
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Our sgrnas.log file outputs a "Warning: sequence not found" for every gene in our library, which I think causes the empty sgrnas.bed file. Do you know if the chromosomal location is required in the first column of the library csv file?
Thanks, Andrew
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Hi,
sorry, I meant the first 10 lines of the file mentioned under sgrnas->results. Here, this would be the file test/DMSO_14_Res_21.sgrna_summary.txt. Can you post these?The library csv file should contain only three columns: id, sequence, gene. Id is arbitrary, and sometimes people set it to the chromosomal location. This is not required though.
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Gene sgRNA eff
OR2C1 HGLibB_33731 1
OR2C1 HGLibA_33775 1
OR2C1 HGLibB_33730 1
OR2C1 HGLibB_33732 1
OR2C1 HGLibA_33776 1
OR2C1 HGLibA_33777 1
SBSPON HGLibB_42763 1
SBSPON HGLibA_42815 1
SBSPON HGLibA_42816 1
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Here are the first ten lines of the DMSO_14_Res_21_gene_summary.txt as well:
Gene sgRNA Res|beta Res|z Res|p-value Res|fdr Res|wald-p-value Res|wald-fdr
OR2C1 6 0.0069309 0.012054 0.73066 0.82313 0.99038 0.99639
SBSPON 6 -0.58971 -1.1612 0.30736 0.82313 0.24557 0.49254
RAB23 6 1.1897 4.1765 0.35626 0.82313 2.96E-05 0.00022816
ACTR10 6 -0.14591 -0.26308 0.67406 0.82313 0.79249 0.99639
SLC25A43 6 -0.39537 -0.75084 0.40177 0.82313 0.45275 0.77607
EBF4 6 0.72253 2.4889 0.55527 0.82313 0.012812 0.039274
FOXN1 6 1.2768 3.095 0.311 0.82313 0.0019681 0.0080094
PSMD7 6 0.81677 2.068 0.52105 0.82313 0.038642 0.10297
RPN2 6 -0.14591 -0.26308 0.67406 0.82313 0.79249 0.99639
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Thanks. I think I have narrowed it down to the file defined under sgrnas->annotation. It seems to be empty. The reason seems to be that non of your library sequences appears to be found in our annotation database. As a quick workaround, you can comment out the line
annotation: sgrnas.bed
in your vispr.yaml. -
I have just released version 0.4.13 of VISPR that should be able to deal with empty bed files. If you want, please try and let me know if it works.
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Hi Johannes,
You got it! I commented out the annotation: sgrnas.bed line in all vispr.yaml files, and I was able to successfully run VISPR and display the results.
I updated VISPR to 0.4.13 and removed the comments. No errors were generated.
Thank you for all the help!
Andrew
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I have to thank for reporting the problem!
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- changed status to resolved
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