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| Original file line number | Diff line number | Diff line change |
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| [loggers] | ||
| keys=root,pyCRISPRcleanR | ||
| keys=root,pyCRISPRcleanR,log02 | ||
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| [handlers] | ||
| keys=consoleHandler,fh01 | ||
| keys=fh01,hand02 | ||
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| [formatters] | ||
| keys=simpleFormatter | ||
| keys=simpleFormatter,form02 | ||
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| [logger_root] | ||
| level=DEBUG | ||
| handlers=consoleHandler | ||
| level=NOTSET | ||
| handlers=fh01,hand02 | ||
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| [logger_pyCRISPRcleanR] | ||
| level=DEBUG | ||
| handlers=fh01 | ||
| qualname=pyCRISPRcleanR | ||
| propagate=0 | ||
| propagate=1 | ||
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| [handler_fh01] | ||
| class=FileHandler | ||
| level=DEBUG | ||
| formatter=simpleFormatter | ||
| args=('log_pyCRISPRcleanR.log','w') | ||
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| [handler_consoleHandler] | ||
| [logger_log02] | ||
| level=INFO | ||
| handlers=hand02 | ||
| propagate=1 | ||
| qualname=compiler.parser | ||
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| [handler_hand02] | ||
| class=StreamHandler | ||
| level=DEBUG | ||
| formatter=simpleFormatter | ||
| level=INFO | ||
| formatter=form02 | ||
| args=(sys.stdout,) | ||
|
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| [formatter_simpleFormatter] | ||
| format=%(asctime)s - %(name)s - %(levelname)s - %(message)s:%(module)s:%(funcName)s:LINE#:%(lineno)d | ||
| datefmt=%Y-%m-%d %H:%M:%S | ||
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| [formatter_form02] | ||
| format=%(asctime)s - %(levelname)s - %(message)s | ||
| datefmt=%Y-%m-%d %H:%M:%S |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| { | ||
| "header" : ["<!DOCTYPE html> <html>", | ||
| "<head><style> #results {{border-collapse: collapse; width: 100%;}}", | ||
| "#results td, #results th {{ border: 1px solid #ddd; padding: 8px;}}", | ||
| "#results tr:nth-child(even){{background-color: #f2f2f2;}}", | ||
| "#results tr:hover {{background-color: #ddd;}}", | ||
| "#results th {{padding-top: 12px; padding-bottom: 12px; text-align: left; background-color: lightblue; color: black;}} </style></head>", | ||
| "<body> <h2>CRISPRcleanR Analysis Results [ <a href=\" ../{outdir}/{file_name}\">Download results.tar.bz2</a> ]</h2> <table style=\"width:100%\" id=\"results\">"], | ||
| "table_header": "<tr><th>{}</th><th>{}</th><th>Description</th></tr>", | ||
|
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| "table_row_images" : "<tr><td>{count}</td> <td><a href=\" ../{outdir}/{file_name}\" target=\"_blank\" >{file_name}</a></td><td>{description}</td></tr>", | ||
| "table_row_files" : "<tr><td>{count}</td> <td><a href=\" ../{outdir}/{file_name}\">{file_name}</a></td><td>{description}</td></tr>", | ||
| "table_row_folders" : "<tr><td>{count}</td> <td><a href=\" ../{outdir}/{file_name}\">{file_name}</a></td><td>{description}</td></tr>", | ||
|
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| "intermediate_row" : "<tr><th>{}</th></tr>", | ||
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| "footer" : "</table> </body> </html>", | ||
|
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| "images" : { | ||
| "01_raw_counts_boxplot.html" : ["Raw sgRNA counts"], | ||
| "01_raw_counts_correlation_matrix.html" : ["Raw sgRNA counts"], | ||
| "01_raw_counts_histogram.html" : ["Raw sgRNA counts"], | ||
| "02_normalised_counts_boxplot.html" : ["Normalised sgRNA counts (median-ratio normalisation of raw counts)"], | ||
| "02_normalised_counts_correlation_matrix.html": ["Normalised sgRNA counts (median-ratio normalisation of raw counts)"], | ||
| "02_normalised_counts_histogram.html" : ["Normalised sgRNA counts (median-ratio normalisation of raw counts)"], | ||
| "03_fold_changes_boxplot.html" : ["sgRNA fold changes with respect to plasmid sgRNA normalised count)"], | ||
| "03_fold_changes_correlation_matrix.html" :[ "sgRNA fold changes with respect to plasmid sgRNA normalised count"], | ||
| "03_fold_changes_histogram.html" : ["sgRNA fold changes with respect to plasmid sgRNA normalised count"], | ||
| "04_pr_rc_curve_sgRNA.html" : ["Precision/Recall(PrRc) evaluation curve quantifying the performances in classifying the considered reference sets based on their logFCs"], | ||
| "04_roc_curve_sgRNA.html" : ["ROC curve quantifying the performances in classifying the user defined reference sets based on their logFCs"], | ||
| "05_pr_rc_curve_gene.html" : ["Precision/Recall(PrRc) evaluation curve quantifying the performances in classifying the considered reference sets based on their logFCs"], | ||
| "05_roc_curve_gene.html" :["ROC curve quantifying the performances in classifying the user defined reference sets based on their logFCs"], | ||
| "06_depletion_profile_genes.html" : ["Shows visual inspection of enrichments of predefined sets of core-fitness essential genes", | ||
| "near the top of the genome wide essentiality profiles (composed of sgRNA or gene depletion logFCs ranked in increasing order),", | ||
| "and to compute their classification recall at a fixed FDR(e.g., 5%)"], | ||
|
|
||
| "07_CRISPRcleanR_corrected_count_boxplot.html" : ["Corrected counts are calculated using a unsupervised approach and correcting chromosomal segments of", | ||
| "equal sgRNA log fold-changes if they include sgRNAs targeting at least 3 different", | ||
| "genes, and without making any assumption on gene essentiality, nor knowing", | ||
| "a priori the copy number status of the included genes"], | ||
| "07_CRISPRcleanR_corrected_count_correlation_matrix.html" : ["see description for 07_CRISPRcleanR_corrected_count_boxplot.html "], | ||
| "07_CRISPRcleanR_corrected_count_histogram.html" : ["see description for 07_CRISPRcleanR_corrected_count_boxplot.html"], | ||
| "08_CRISPRcleanR_corrected_fold_changes_boxplot.html" : ["see description for 07_CRISPRcleanR_corrected_count_boxplot.html"], | ||
| "08_CRISPRcleanR_corrected_foldchanges_correlation_matrix.ht" : ["see description for 07_CRISPRcleanR_corrected_count_boxplot.html"], | ||
| "08_CRISPRcleanR_corrected_fold_changes_histogram.html" : ["see description for 07_CRISPRcleanR_corrected_count_boxplot.html"], | ||
| "09_Raw_vs_postCRISPRcleanR_segmentation_fold_changes.pdf" :["one plot per chromosome, with segments of sgRNAs' equal log fold-change before and after the correction"], | ||
| "10_density_plots_pre_and_post_CRISPRcleanR.html" : ["Shows the variation induced by the CRISPRcleanR correction on thelogFCs’", | ||
| "distributions of sgRNAs targeting defined sets of genes prior/post CRISPRcleanR correction"], | ||
| "11_impact_on_phenotype_barchart.html" : ["Evaluates the effect of the CRISPRcleanR correction on the genes showing a significant loss/gain-of-fitness", | ||
| "effect (fitness genes) in the uncorrected data, a comparison of fitness gene sets (computed with MAGeCK) before/after CRISPRcleanR correction"], | ||
| "11_impact_on_phenotype_piechart.html" : ["see description for 11_impact_on_phenotype_barchart.html"] | ||
| }, | ||
| "files" : { | ||
| "01_normalised_counts.tsv" : ["Normalised sgRNA counts (median-ratio normalisation of raw counts)"], | ||
| "02_normalised_fold_changes.tsv" : ["sgRNA fold changes with respect to plasmid sgRNA normalised count"], | ||
| "03_crispr_cleanr_corrected_counts.tsv" : ["see description for 07_CRISPRcleanR_corrected_count_boxplot.html"], | ||
| "04_crispr_cleanr_fold_changes.tsv" : ["see description for 07_CRISPRcleanR_corrected_count_boxplot.html"], | ||
| "05_alldata.tsv" : ["Includes all data along with filtered raw counts"] | ||
| }, | ||
| "folders" : { | ||
| "mageckOut" : ["results from MAGeCK algorithm "], | ||
| "bagelOut" : ["results from BAGEL algorithm"] | ||
| } | ||
| } |
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