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Issue warning for possible duplicate analysis files #175

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Issue warning for possible duplicate analysis files #175

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10fb2e5
Issue warning for possible duplicate analysis files
cadley-nyulangone Mar 26, 2020
553bf14
Check for dups in the "data" matrix, rather than in filenames.
cadley-nyulangone Mar 26, 2020
b2a9162
Fixed some tabs
cadley-nyulangone Mar 26, 2020
3bf3344
Changed if from != to >
cadley-nyulangone Mar 30, 2020
c2fa72b
Added flowcell ID to Group when processing tracks byLocus.
cadley-nyulangone Mar 31, 2020
3fb0e3f
Add a FlowCellID column to samplesforTrackhub.R output
cadley-nyulangone Apr 6, 2020
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11 changes: 7 additions & 4 deletions dnase/trackhub/MakeTrackhub.py
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Original file line number Diff line number Diff line change
Expand Up @@ -312,9 +312,12 @@ def shortest_unique_strings(array, minlength=1):
# So sampleName_trackname is increased by 4+8+9=21 characters.
# If sampleName_trackname starts with 107 characters, then 128 characters get sent to the server. This causes an error.
# So sampleName_trackname needs to be 106 characters or less.
sampleName_trackname = cleanTrackName(sampleNameGenome + "_" + curGroup + "_" + curSample['SampleID'])


if args.supertrack == "By_Locus":
# curGroup does not contain the flowcell ID here.
sampleName_trackname = cleanTrackName(sampleNameGenome + "_" + curGroup + "_" + curSample['FlowCellID'] + "_" + curSample['SampleID'])
else:
sampleName_trackname = cleanTrackName(sampleNameGenome + "_" + curGroup + "_" + curSample['SampleID'])

# Make sure there are no duplicate track names.
if sampleName_trackname in sampleName_dict:
if args.verbose:
Expand Down Expand Up @@ -411,7 +414,7 @@ def shortest_unique_strings(array, minlength=1):
visibility="full",
parentonoff=DensCovTracksDefaultDisplayMode,
tracktype="bigWig",
viewLimits="0:500",
viewLimits="0:500", #Keep high since it becomes a hard limit in the UI
autoScale='on',
alwaysZero='on',
maxHeightPixels="100:30:10",
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17 changes: 16 additions & 1 deletion dnase/trackhub/samplesforTrackhub.R
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Original file line number Diff line number Diff line change
Expand Up @@ -166,11 +166,12 @@ colorAssignments <- NULL


# Initialize "data" with just column names. We'll be adding rows to this later on in the code.
outputCols <- c("Name", "SampleID", "Assay", "Group", "filebase", "Mapped_Genome", "Annotation_Genome", "Color", "analyzed_reads", "Genomic_coverage", "SPOT", "Num_hotspots", "Exclude", "Age", "Institution", "Replicate", "Bait_set", "Genetic_Modification")
outputCols <- c("Name", "SampleID", "Assay", "Group", "filebase", "Mapped_Genome", "Annotation_Genome", "Color", "analyzed_reads", "Genomic_coverage", "SPOT", "Num_hotspots", "Exclude", "Age", "Institution", "Replicate", "Bait_set", "Genetic_Modification", "FlowCellID")
if(opt$project == "CEGS_byLocus") {
outputCols <- c(outputCols, "Study", "Project", "Assembly", "Type")
}

data_keys <- vector()
data <- data.frame(matrix(ncol=length(outputCols), nrow=1))
colnames(data) <- outputCols
i <- 0 # This will be our "data" output variable index.
Expand Down Expand Up @@ -421,6 +422,20 @@ for(curdir in mappeddirs) {
}

data$filebase[i] <- paste0(curdir, "/", paste0(unlist(strsplit(basename(analysisFile), "\\."))[2:3], collapse="."))

# Check for duplicate analysisFiles, possibly left over from a previous run.
# Note: "data$Group" does not contain flowcell ID info when opt$project=CEGS_byLocus, so we need to get it from curdir.
# FlowCellID will also be used in MakeTrackhub.py to create unique byLocus tracknames.
data$FlowCellID[i] <- strsplit(curdir, "/", fixed=TRUE)[[1]][1]
data_key <- paste(data$SampleID[i], data$Mapped_Genome[i], data$FlowCellID[i], sep="")
if(i > 1) {
if(data_key %in% data_keys){
message("[samplesforTrackhub] ", "WARNING Possible duplicate analysis files found in ", curdir)
msg <- paste("See: SampleID:", data$SampleID[i], "Mapped_Genome:", data$Mapped_Genome[i], "FlowCellID:", data$FlowCellID[i], sep=" ")
message("[samplesforTrackhub] ", msg)
}
}
data_keys[i] <- data_key
}
}

Expand Down