Error with 'append' while running pychopper

[majdabdul]

Hello,

I encountered the following wrror while running pychopper on one of my samples:

$ pychopper ../PAK96837/01_raw_reads/10890_Control_IR_rep3_pass.fastq.gz pychopped/cont_ir_rep3_pychopped.fastq.gz Using kit: PCS109 Configurations to consider: "+:SSP,-VNP|-:VNP,-SSP" Counting fastq records in input file: ../PAK96837/01_raw_reads/10890_Control_IR_rep3_pass.fastq.gz Total fastq records in input file: 2304022 Tuning the cutoff parameter (q) on 10027 sampled reads (0.4%) passing quality filters (Q >= 7.0). Optimizing over 30 cutoff values. 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████| 30/30 [10:08<00:00, 20.02s/it] Best cutoff (q) value is 0.3448 with 86% of the reads classified. Processing the whole dataset using a batch size of 288002: 100%|████████████████████████████████████████████████████████████████████████████████████████| 2304022/2304022 [1:24:11<00:00, 456.11it/s] Finished processing file: ../PAK96837/01_raw_reads/10890_Control_IR_rep3_pass.fastq.gz Input reads failing mean quality filter (Q < 7.0): 0 (0.00%) Output fragments failing length filter (length < 50): 0 Traceback (most recent call last): File "/data/donc-panc-cancer-biomarker/ball5492/pychopper_env/bin/pychopper", line 10, in <module> sys.exit(main()) File "/data/donc-panc-cancer-biomarker/ball5492/pychopper_env/lib/python3.10/site-packages/pychopper/scripts/pychopper.py", line 542, in main stdf = stdf.append(pd.DataFrame(tune_df)) File "/data/donc-panc-cancer-biomarker/ball5492/pychopper_env/lib/python3.10/site-packages/pandas/core/generic.py", line 5989, in __getattr__ return object.__getattribute__(self, name) AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'?

As far as I can tell from Googling, it's an issue with Pandas versioning. I have version 2.0.2 (the latest version, as of writing this).

Can you please help me figure out how to fix it?

Thanks!

[nrhorner]

Hi @majdabdul You're right; pandas >=2.0 has done away with DataFrame.append() This is fixed in the latest Pychopper version (v0.2.5). Please try that.

[majdabdul]

Hi @majdabdul You're right; pandas >=2.0 has done away with DataFrame.append() This is fixed in the latest Pychopper version (v0.2.5). Please try that.

Thanks @nrhorner. Updating Pychopper got rid of this error indeed! But now I see this message: Finished processing file: /data/donc-panc-cancer-biomarker/ball5492/long/PromethIONRuns/combined/10890_Control_IR_rep1_combined_pass.fastq.gz Input reads failing mean quality filter (Q < 7.0): 0 (0.00%) Output fragments failing length filter (length < 50): 0 /data/donc-panc-cancer-biomarker/ball5492/pychopper_env/lib/python3.10/site-packages/pychopper/scripts/pychopper.py:184: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead found, rescue, unusable = float(rs.loc[rs.Name == "Primers_found", ].Value), float(rs.loc[rs.Name == "Rescue", ].Value), float(rs.loc[rs.Name == "Unusable", ].Value) /data/donc-panc-cancer-biomarker/ball5492/pychopper_env/lib/python3.10/site-packages/pychopper/scripts/pychopper.py:186: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead umi_detected = float(rs_stats.loc[rs_stats.Name == "Umi_detected", ].Value) /data/donc-panc-cancer-biomarker/ball5492/pychopper_env/lib/python3.10/site-packages/pychopper/scripts/pychopper.py:187: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead umi_detected_final = float(rs_stats.loc[rs_stats.Name == "Umi_detected_final", ].Value)

I'm not sure if it's related to the update, but can I assume that it doesn't affect the final output?

[nrhorner]

Hi @majdabdul This is a warning from a third party library, which will have no affect on the results. This will be addressed in the next release.

Could I ask you to use v0.2.6 now though as there was an introduced into v0.2.5 where things break when using the -m edlib option.

Thanks

[majdabdul]

Hi @majdabdul This is a warning from a third party library, which will have no affect on the results. This will be addressed in the next release.

Could I ask you to use v0.2.6 now though as there was an introduced into v0.2.5 where things break when using the -m edlib option.

Thanks

Wow @nrhorner, you work fast! Will update, thanks!