Commits on Aug 8, 2024

1. Replace zcat (#94) …

   * D3-Enhancements (#78)
   
   * Sam/try plots (#71)
   
   * Fix batch mode pandas warning. (#70)
   
   * refactor to call method on DataFrame, rather than Series.
   Removes warning.
   
   * Fix pandas future warning in CRISPRessoWGS
   
   ---------
   
   Co-authored-by: Cole Lyman <[email protected]>
   
   * Functional
   
   * Cole/fix status file name (#69)
   
   * 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 <[email protected]>
   
   * Try catch all futures
   
   * Fix test fail plots
   
   * Point test to try-plots
   
   * Fix d3 not showing and plotly mixing with matplotlib
   
   * Use logger for warnings and debug statements
   
   * Point tests back at master
   
   ---------
   
   Co-authored-by: mbowcut2 <[email protected]>
   Co-authored-by: Cole Lyman <[email protected]>
   
   * Sam/fix plots (#72)
   
   * Fix batch mode pandas warning. (#70)
   
   * refactor to call method on DataFrame, rather than Series.
   Removes warning.
   
   * Fix pandas future warning in CRISPRessoWGS
   
   ---------
   
   Co-authored-by: Cole Lyman <[email protected]>
   
   * Functional
   
   * Cole/fix status file name (#69)
   
   * 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 <[email protected]>
   
   * Try catch all futures
   
   * Fix test fail plots
   
   * Fix d3 not showing and plotly mixing with matplotlib
   
   ---------
   
   Co-authored-by: mbowcut2 <[email protected]>
   Co-authored-by: Cole Lyman <[email protected]>
   
   * Remove token from integration tests file
   
   * Provide sgRNA_sequences to plot_nucleotide_quilt plots
   
   * Passing sgRNA_sequences to plot
   
   * Refactor check for determining when to use CRISPREssoPro or matplotlib for Batch plots
   
   * Add max-height to Batch report samples
   
   * Change testing branch
   
   * Fix wrong check for large Batch plots
   
   * Fix typo and move flexiguide to debug (#77)
   
   * Change flexiguide output to debug level
   
   * Fix typo in fastp merged output file name
   
   * Adding id tags for d3 script enhancements
   
   * pointing to test branch
   
   * Add amplicon_name parameter to allele heatmap and line plots
   
   * Add function to extract quantification window regions from include_idxs
   
   * Scale the quantification window according to the coordinates of the sgRNA plot
   
   * added c2pro check, added space in args.json
   
   * Correct the quantification window indexes for multiple guides
   
   * Fix name of nucleotide conversion plot when guides are not the same
   
   * Fix jinja variables that aren't found
   
   * Fix multiple guide errors where the wrong sgRNA sequence was associated in d3 plot
   
   * Remove unneeded variable and extra whitespace
   
   * Switch test branch to master
   
   ---------
   
   Co-authored-by: Samuel Nichols <[email protected]>
   Co-authored-by: mbowcut2 <[email protected]>
   Co-authored-by: Cole Lyman <[email protected]>
   
   * Replace zcat with gunzip -c in `get_most_frequent_reads`
   
   ---------
   
   Co-authored-by: Trevor Martin <[email protected]>
   Co-authored-by: Samuel Nichols <[email protected]>
   Co-authored-by: mbowcut2 <[email protected]>

   

   

   4 people authored Aug 8, 2024
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