search

maurijlozano / ISCompare

ISCompare, an opensource program to identify Differentially Located Insertion Sequences
GNU General Public License v3.0
11 stars 1 forks source link

Error at step 5 #4

Closed mallen6 closed 2 years ago

mallen6 commented 2 years ago

Hi Mauricio,

ISCompare seems to be working happily but then fails at the stage of writing the final results. Do you have any suggestions how to fix this?

Thanks, M

I'm using python/3.9.9 with Biopython/1.79 DNAfeaturesviewer/3.1.0 Pandas/1.3.4 Numpy/1.21.4 Mechanize/0.4.7

My command and the command line output:

$ ISCompare.py -q R1S1.gbff -r Hlac.gbff -i Hlac_is.fna -o Hlac_v_R1S1_gbff -c -p

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

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 Hlac_v_R1S1_gbff created. Query: ['R1S1.gbff'] Ref: ['Hlac.gbff'] Copying files to Hlac_v_R1S1_gbff folder, and extracting fasta files from genbank. query.fasta generated. ref.fasta generated. 133 ISs found on the query genome... Step1: Removing identical scaffolds: Query --> Reference ... 93 identical scaffolds removed from the analysis... Step2: Testing for new IS on the query... 123 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 "/apps/iscompare/1.0.1/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 "/apps/python/3.9.9/lib/python3.9/site-packages/pandas/core/generic.py", line 5808, in astype results = [ File "/apps/python/3.9.9/lib/python3.9/site-packages/pandas/core/generic.py", line 5809, in self.iloc[:, i].astype(dtype, copy=copy) File "/apps/python/3.9.9/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 "/apps/python/3.9.9/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 "/apps/python/3.9.9/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 327, in apply applied = getattr(b, f)(**kwargs) File "/apps/python/3.9.9/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 "/apps/python/3.9.9/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 "/apps/python/3.9.9/lib/python3.9/site-packages/pandas/core/dtypes/cast.py", line 1257, in astype_array values = astype_nansafe(values, dtype, copy=copy) File "/apps/python/3.9.9/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 "/apps/python/3.9.9/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 "/apps/python/3.9.9/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

maurijlozano commented 2 years ago

Hi mallen6, the error was already corrected, but I forgot to make a new release of the code. Please try with version 1.0.3 https://github.com/maurijlozano/ISCompare/releases/tag/1.0.3 Thank's for reporting the bugs.