Error in pandas.parser.TextReader

[Former user]

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.

[Johannes Köster]

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?

[parkapdx]

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

[parkapdx]

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

[Johannes Köster]

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.

[parkapdx]

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

[parkapdx]

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

[Johannes Köster]

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.

[Johannes Köster]

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.

[parkapdx]

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

[Johannes Köster]

I have to thank for reporting the problem!