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Fix batch mode pandas warning. #70

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merged 2 commits into from
Apr 26, 2024
Merged

Fix batch mode pandas warning. #70

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7abf6b5
refactor to call method on DataFrame, rather than Series.
mbowcut2 Apr 25, 2024
63d7ade
Fix pandas future warning in CRISPRessoWGS
Colelyman Apr 26, 2024
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2 changes: 1 addition & 1 deletion CRISPResso2/CRISPRessoBatchCORE.py
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Expand Up @@ -196,7 +196,7 @@ def main():
batch_params[arg] = getattr(args, arg)
else:
if (getattr(args, arg) is not None):
batch_params[arg].fillna(value=getattr(args, arg), inplace=True)
batch_params.fillna(value={arg: getattr(args, arg)}, inplace=True)

# assert that all names are unique
# and clean names
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2 changes: 1 addition & 1 deletion CRISPResso2/CRISPRessoWGSCORE.py
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Expand Up @@ -582,7 +582,7 @@ def set_filenames(row):
cols_to_print = ["chr_id", "bpstart", "bpend", "sgRNA", "Expected_HDR", "Coding_sequence", "sequence", "n_reads", "bam_file_with_reads_in_region", "fastq_file_trimmed_reads_in_region"]
if args.gene_annotations:
cols_to_print.append('gene_overlapping')
df_regions.fillna('NA').to_csv(report_reads_aligned_filename, sep='\t', columns = cols_to_print, index_label="Name")
df_regions.infer_objects(copy=False).fillna('NA').to_csv(report_reads_aligned_filename, sep='\t', columns = cols_to_print, index_label="Name")

#save progress
crispresso2_info['running_info']['finished_steps']['generation_of_fastq_files_for_each_amplicon'] = True
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