ValueError: not enough values to unpack (expected 2, got 1)

[yr542]

I get the error ValueError: not enough values to unpack (expected 2, got 1) but I do not know why as my metadata is tab separated. I have removed my paths as I am working on an HPC and they do not allow us to disclose any paths on the HPC.

My variables are

• tsv_file = /path/to/rmats_JCEC_results.tsv
• meta_file = /path/to/Timepoint_1_Case_Control_Samples.tsv
• p_value=0.05
• q_value=0.05
• Jutils_Cloned_Directory = /path/to/Jutils/directory
• jutils_script_path="${Jutils_Cloned_Directory}/jutils.py"

The relevant section of my script:

python3 "$jutils_script_path" heatmap \
    --tsv-file "$tsv_file" \
    --meta-file "$meta_file" \
    --p-value "$p_value" \
    --q-value "$q_value"

My metadata:

C-01  Control
C-02  Control
C-03  Control
KO-01  Case
KO-02  Case
KO-03  Case

My full error:

Traceback (most recent call last):
  File "/path/to/jutils.py", line 149, in <module>
    main()
  File "/path/to/jutils.py", line 142, in main
    run_heatmap_module(args, parser_dict)
  File "/path/to/jutils.py", line 108, in run_heatmap_module
    plot_heatmap(Path(args.tsv_file), Path(args.meta_file), Path(args.out_dir), args.p_value,
  File "/path/to/heatmap_utils.py", line 63, in plot_heatmap
    sample, cond = line.strip().split('\t')
ValueError: not enough values to unpack (expected 2, got 1)

How do I get around this error. I ran rMats from fastq files and used a Refseq gtf and rMats ran well. Therefore, I believe is an issue here with the heat map. The conversion to tsv script ran without error.

[edwwlui]

Thanks for reporting this! Based on the error message, I believe it is due to the meta file not being tab-separated. My guess is your "tab" became two spaces, please let me know if this is not the case.

[yr542]

Applying Your Suggestion/Solution:

To get around this issue I wrote it out in Excel and saves as a a tab separated file.

The new error:

Traceback (most recent call last):
  File "/path/to/jutils.py", line 149, in <module>
    main()
  File "/path/to/jutils.py", line 142, in main
    run_heatmap_module(args, parser_dict)
  File "/path/to/jutils.py", line 108, in run_heatmap_module
    plot_heatmap(Path(args.tsv_file), Path(args.meta_file), Path(args.out_dir), args.p_value,
  File "/path/to/heatmap_utils.py", line 72, in plot_heatmap
    data_df['GeneName'] = data_df['GeneName'].apply(truncate_gene_name)
  File "/path/to/pandas/series.py", line 4630, in apply
    return SeriesApply(self, func, convert_dtype, args, kwargs).apply()
  File "/path/tp/pandas/apply.py", line 1025, in apply
    return self.apply_standard()
  File "/path/to/pandas/apply.py", line 1076, in apply_standard
    mapped = lib.map_infer(
  File "pandas/_libs/lib.pyx", line 2834, in pandas._libs.lib.map_infer
  File "/path/to/heatmap_utils.py", line 92, in truncate_gene_name
    gene_names = string.split(',')
AttributeError: 'float' object has no attribute 'split'

How would I resolve this error?

[edwwlui]

Thanks for catching this error, it is due to the 'GeneName' column being read as numbers instead of strings.

I have specified 'GeneName' to be strings only, please kindly git pull to update the code and try again. Let me know if there are any issues.

[yr542]

When I run this I still get the same error. I have deleted the cloned directory and then re-cloned using git clone why is this not working?

[splicebox]

Hello - unfortunately with the information we have so far we cannot reproduce the error. Would you be able to send us a portion of your TSV file (the first 10-20 lines would suffice) and the metadata file? You can email them to florea@jhu.edu if you prefer. Thank you.

[deb0612]

Dear sir,
I also got thte same error.

[edwwlui]

Hi @deb0612

Thanks for letting us know! Based on the error message, I think it comes from the meta file being not tab-separated either.