Problem with TypeError: ...FloatingDType

[JD2112]

@maurijlozano

What is the

` **** ISCompare Version: 1.0.1 Developed by Mauricio J. Lozano github.com/maurijlozano

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Please cite:

Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare. E.G. Mogro, N. Ambrosis, M.J. Lozano doi: https://doi.org/10.1101/2020.10.16.342287 Instituto de Biotecnología y Biología Molecular CONICET - CCT La Plata - UNLP - FCE

Downloaded from: https://github.com/maurijlozano/ISCompare

Directory consensusMap already exists. Query: ['MT-1_consensus_seqret.genbank'] Ref: ['MT-2_consensus_seqret.genbank'] Copying files to consensusMap folder, and extracting fasta files from genbank. query.fasta generated. ref.fasta generated. 6 ISs found on the query genome... Step1: Removing identical scaffolds: Query --> Reference ... 0 identical scaffolds removed from the analysis... Step2: Testing for new IS on the query... 6 ISs found on the reference genome... Step3: Removing identical scaffolds: Reference --> Query ... 0 identical scaffolds removed from the analysis... Step4: Testing for IS missing on the query... Step5: Consolidating results and annotating data... Traceback (most recent call last): File "/mnt/SD2/Jyotirmoys/Backup_20211108/BIN21P012_MT/ISCompare/./ISCompare.py", line 2297, in FinalResults[['ISstart', 'ISend', 'Start1', 'End1', 'REF.Start1','REF.End1','Start2', 'End2', 'REF.Start2','REF.End2']] = FinalResults[['ISstart', 'ISend', 'Start1', 'End1', 'REF.Start1','REF.End1','Start2', 'End2', 'REF.Start2','REF.End2']].astype("Float32") File "/opt/sw/bioinfo-tools/sources/anaconda3/envs/multiqc/lib/python3.9/site-packages/pandas/core/generic.py", line 5808, in astype results = [ File "/opt/sw/bioinfo-tools/sources/anaconda3/envs/multiqc/lib/python3.9/site-packages/pandas/core/generic.py", line 5809, in self.iloc[:, i].astype(dtype, copy=copy) File "/opt/sw/bioinfo-tools/sources/anaconda3/envs/multiqc/lib/python3.9/site-packages/pandas/core/generic.py", line 5815, in astype new_data = self._mgr.astype(dtype=dtype, copy=copy, errors=errors) File "/opt/sw/bioinfo-tools/sources/anaconda3/envs/multiqc/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 418, in astype return self.apply("astype", dtype=dtype, copy=copy, errors=errors) File "/opt/sw/bioinfo-tools/sources/anaconda3/envs/multiqc/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 327, in apply applied = getattr(b, f)(**kwargs) File "/opt/sw/bioinfo-tools/sources/anaconda3/envs/multiqc/lib/python3.9/site-packages/pandas/core/internals/blocks.py", line 591, in astype new_values = astype_array_safe(values, dtype, copy=copy, errors=errors) File "/opt/sw/bioinfo-tools/sources/anaconda3/envs/multiqc/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 1309, in astype_array_safe new_values = astype_array(values, dtype, copy=copy) File "/opt/sw/bioinfo-tools/sources/anaconda3/envs/multiqc/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 1257, in astype_array values = astype_nansafe(values, dtype, copy=copy) File "/opt/sw/bioinfo-tools/sources/anaconda3/envs/multiqc/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 1105, in astype_nansafe return dtype.construct_array_type()._from_sequence(arr, dtype=dtype, copy=copy) File "/opt/sw/bioinfo-tools/sources/anaconda3/envs/multiqc/lib/python3.9/site-packages/pandas/core/arrays/floating.py", line 261, in _from_sequence values, mask = coerce_to_array(scalars, dtype=dtype, copy=copy) File "/opt/sw/bioinfo-tools/sources/anaconda3/envs/multiqc/lib/python3.9/site-packages/pandas/core/arrays/floating.py", line 143, in coerce_to_array raise TypeError(f"{values.dtype} cannot be converted to a FloatingDtype") TypeError: object cannot be converted to a FloatingDtype `

How to solve

I solved this by changing the line# 2297 of ISCompare.py from .astype("Float32") to .astype("float32")

[maurijlozano]

Thank you for your comment. I'm already correcting the code. Kind regards