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Optionally ignore errors #324

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Optionally ignore errors #324

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9fd46a5
Add option --ignore-report-errors to render a QC report even if plots…
bs-az Sep 10, 2024
9e2ac70
Bring formatting in line with other code
bs-az Sep 10, 2024
da7e946
Merge branch 'ConesaLab:master' into optionally-ignore-errors
bschiffthaler Sep 10, 2024
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5 changes: 3 additions & 2 deletions sqanti3_qc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2107,7 +2107,7 @@ def run(args):
## Generating report
if args.report != 'skip':
print("**** Generating SQANTI3 report....", file=sys.stderr)
cmd = RSCRIPTPATH + " {d}/{f} {c} {j} {p} {d} {a} {b}".format(d=utilitiesPath, f=RSCRIPT_REPORT, c=outputClassPath, j=outputJuncPath, p=args.doc, a=args.saturation, b=args.report)
cmd = RSCRIPTPATH + " {d}/{f} {c} {j} {p} {d} {a} {b} {i}".format(d=utilitiesPath, f=RSCRIPT_REPORT, c=outputClassPath, j=outputJuncPath, p=args.doc, a=args.saturation, b=args.report, i=args.ignore_report_errors)
if subprocess.check_call(cmd, shell=True)!=0:
print("ERROR running command: {0}".format(cmd), file=sys.stderr)
sys.exit(-1)
Expand Down Expand Up @@ -2384,7 +2384,7 @@ def combine_split_runs(args, split_dirs):

if args.report != 'skip':
print("**** Generating SQANTI3 report....", file=sys.stderr)
cmd = RSCRIPTPATH + " {d}/{f} {c} {j} {p} {d} {a} {b}".format(d=utilitiesPath, f=RSCRIPT_REPORT, c=outputClassPath, j=outputJuncPath, p=args.doc, a=args.saturation, b=args.report)
cmd = RSCRIPTPATH + " {d}/{f} {c} {j} {p} {d} {a} {b} {i}".format(d=utilitiesPath, f=RSCRIPT_REPORT, c=outputClassPath, j=outputJuncPath, p=args.doc, a=args.saturation, b=args.report, i=args.ignore_report_errors)
if subprocess.check_call(cmd, shell=True)!=0:
print("ERROR running command: {0}".format(cmd), file=sys.stderr)
sys.exit(-1)
Expand Down Expand Up @@ -2423,6 +2423,7 @@ def main():
parser.add_argument("-v", "--version", help="Display program version number.", action='version', version='SQANTI3 '+str(__version__))
parser.add_argument("--saturation", action="store_true", default=False, help='\t\tInclude saturation curves into report')
parser.add_argument("--report", choices=['html', 'pdf', 'both', 'skip'], default='html', help='\t\tselect report format\t\t--html\t\t--pdf\t\t--both\t\t--skip')
parser.add_argument("--ignore-report-errors", action="store_true", help='\t\tignore errors during the rendering of of the report')
parser.add_argument('--isoAnnotLite' , help='\t\tRun isoAnnot Lite to output a tappAS-compatible gff3 file',required=False, action='store_true' , default=False)
parser.add_argument('--gff3' , help='\t\tPrecomputed tappAS species specific GFF3 file. It will serve as reference to transfer functional attributes',required=False)
parser.add_argument('--short_reads', help='\t\tFile Of File Names (fofn, space separated) with paths to FASTA or FASTQ from Short-Read RNA-Seq. If expression or coverage files are not provided, Kallisto (just for pair-end data) and STAR, respectively, will be run to calculate them.', required=False)
Expand Down
13 changes: 11 additions & 2 deletions utilities/report_qc/SQANTI3_report.R
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Expand Up @@ -15,9 +15,10 @@ junc.file <- args[2]
utilities.path <- args[4]
saturation.curves <- args[5]
report.format <- args[6]
ignore.errors <- args[7]

if (length(args) < 6) {
stop("Incorrect number of arguments! Script usage is: [classification file] [junction file] [utilities directory path] [True/False for saturation curves] [pdf|html|both]. Abort!")
if (length(args) != 7) {
stop("Incorrect number of arguments! Script usage is: [classification file] [junction file] [utilities directory path] [True/False for saturation curves] [pdf|html|both] [True/False to ignore errors]. Abort!")
}

if (!(saturation.curves %in% c('True', 'False'))) {
Expand All @@ -28,6 +29,14 @@ if (!(report.format %in% c('pdf', 'html', 'both'))) {
stop("Report format needs to be: pdf, html, or both. Abort!")
}

if (!(ignore.errors %in% c('True', 'False'))) {
stop("Ignore errors needs to be 'True' or 'False'. Abort!")
}

if (ignore.errors == "True") {
options(error = function(){})
}

source(paste(utilities.path, "/report_qc/generatePDFreport.R", sep = "/"))

if (saturation.curves=='True'){
Expand Down
2 changes: 1 addition & 1 deletion utilities/report_qc/SQANTI3_report.Rmd
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Expand Up @@ -28,7 +28,7 @@ The code contains several parts:
<!---Basic setting-->

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, cache = FALSE, warning = FALSE, results = 'asis', echo=FALSE)
knitr::opts_chunk$set(cache = FALSE, warning = FALSE, results = 'asis', echo = FALSE, error = ignore.errors)

has_data <- function(df) {
if (!is.null(df) && length(df) > 0 && is.data.frame(df) && nrow(df) > 0) {
Expand Down