Fix issues with file_prefix
#430
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* Update config file logging messages This removes printing the exception (which is essentially a duplicate), and adds a condition if no config file was provided. Also changes `json` to `config` so that it is more clear. * Fix divide by zero when no amplicons are present in Batch mode * Don't append file_prefix to status file name * Place status files in output directories * Update tests branch for file_prefix addition * Load D3 and plotly figures with pro with multiple amplicons * Update batch * Fix bug in CRISPRessoCompare with pointing to report datas with file_prefix Before this fix, when using a file_prefix the second run that was compared would not be displayed as a data in the first figure of the report. * Import CRISPRessoPro instead of importing the version When installed via conda, the version is not available * Remove `get_amplicon_output` unused function from CRISPRessoCompare Also remove unused argparse import * Implement `get_matching_allele_files` in CRISPRessoCompare and accompanying unit tests * Allow for matching of multiple guides in the same amplicon * Fix pandas FutureWarning * Change test branch back to master --------- Co-authored-by: Sam <snic9004@gmail.com>
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This PR includes:
This removes printing the exception (which is essentially a duplicate), and adds a condition if no config file was provided. Also changes
jsontoconfigso that it is more clear.Fix divide by zero when no amplicons are present in Batch mode
Don't append file_prefix to status file name
Place status files in output directories
Update tests branch for file_prefix addition
Load D3 and plotly figures with pro with multiple amplicons
Fix bug in CRISPRessoCompare with pointing to report datas with file_prefix
Before this fix, when using a file_prefix the second run that was compared would not be displayed as a data in the first figure of the report.
When installed via conda, the version is not available
get_amplicon_outputunused function from CRISPRessoCompareAlso remove unused argparse import
get_matching_allele_filesin CRISPRessoCompare and accompanying unit testsThis now enables CRISPRessoCompare to ensure that the amplicon sequences are the same (instead of just comparing the amplicon names) and that at least one guide matches and that the quantification windows are the same before comparing.
Allow for matching of multiple guides in the same amplicon
Fix pandas FutureWarning