Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 43:2325074a8461 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 26 Oct 2017 09:58:05 -0400 |
| parents | 9a47d7a552d6 |
| children | 1d8728f3ff37 |
| files | report_clonality/RScript.r tool_dependencies.xml |
| diffstat | 2 files changed, 61 insertions(+), 20 deletions(-) [+] |
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--- a/report_clonality/RScript.r Thu Oct 26 09:08:37 2017 -0400 +++ b/report_clonality/RScript.r Thu Oct 26 09:58:05 2017 -0400 @@ -988,39 +988,44 @@ median.aa.l = data.frame(data.table(PRODF)[, list(median=as.double(median(as.numeric(.SD$CDR3.Length, na.rm=T), na.rm=T))), by=c("Sample")]) write.table(median.aa.l, "AAMedianBySample.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=F) - -#generate the "Sequences that are present in more than one replicate" dataset -clonaltype.in.replicates = inputdata -clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$Functionality %in% c("productive (see comment)","productive"),] -clonaltype.in.replicates = clonaltype.in.replicates[!(is.na(clonaltype.in.replicates$ID) | is.na(clonaltype.in.replicates$Top.V.Gene) | is.na(clonaltype.in.replicates$Top.J.Gene)),] -clonaltype = unlist(strsplit(clonaltype, ",")) +if(clonaltype != "none"){ + #generate the "Sequences that are present in more than one replicate" dataset + clonaltype.in.replicates = inputdata + clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$Functionality %in% c("productive (see comment)","productive"),] + clonaltype.in.replicates = clonaltype.in.replicates[!(is.na(clonaltype.in.replicates$ID) | is.na(clonaltype.in.replicates$Top.V.Gene) | is.na(clonaltype.in.replicates$Top.J.Gene)),] + clonaltype = unlist(strsplit(clonaltype, ",")) -clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[c(clonaltype, "Replicate")], sep = ":")) + clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[paste_columns], sep = ":")) -clonaltype.in.replicates = clonaltype.in.replicates[!duplicated(clonaltype.in.replicates$clonaltype),] + clonaltype.in.replicates = clonaltype.in.replicates[!duplicated(clonaltype.in.replicates$clonaltype),] -clonaltype = clonaltype[-which(clonaltype == "Sample")] + clonaltype = clonaltype[-which(clonaltype == "Sample")] -clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[clonaltype], sep = ":")) -clonaltype.in.replicates = clonaltype.in.replicates[,c("clonaltype","Replicate", "ID", "Sequence", "Sample")] + clonaltype.in.replicates$clonaltype = do.call(paste, c(clonaltype.in.replicates[clonaltype], sep = ":")) + clonaltype.in.replicates = clonaltype.in.replicates[,c("clonaltype","Replicate", "ID", "Sequence", "Sample")] -write.table(clonaltype.in.replicates, "clonaltypes_replicates_before_table.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) + write.table(clonaltype.in.replicates, "clonaltypes_replicates_before_table.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) -clonaltype.counts = data.frame(table(clonaltype.in.replicates$clonaltype)) + clonaltype.counts = data.frame(table(clonaltype.in.replicates$clonaltype)) -write.table(clonaltype.counts, "clonaltypes_counts.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) + write.table(clonaltype.counts, "clonaltypes_counts.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) -names(clonaltype.counts) = c("clonaltype", "coincidence") + names(clonaltype.counts) = c("clonaltype", "coincidence") -clonaltype.counts = clonaltype.counts[clonaltype.counts$coincidence > 1,] + clonaltype.counts = clonaltype.counts[clonaltype.counts$coincidence > 1,] -clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$clonaltype %in% clonaltype.counts$clonaltype,] -clonaltype.in.replicates = merge(clonaltype.in.replicates, clonaltype.counts, by="clonaltype") -clonaltype.in.replicates = clonaltype.in.replicates[order(-clonaltype.in.replicates$coincidence, clonaltype.in.replicates$clonaltype, clonaltype.in.replicates$Replicate),c("coincidence","clonaltype", "Sample", "Replicate", "ID", "Sequence")] + clonaltype.in.replicates = clonaltype.in.replicates[clonaltype.in.replicates$clonaltype %in% clonaltype.counts$clonaltype,] + clonaltype.in.replicates = merge(clonaltype.in.replicates, clonaltype.counts, by="clonaltype") + clonaltype.in.replicates = clonaltype.in.replicates[order(-clonaltype.in.replicates$coincidence, clonaltype.in.replicates$clonaltype, clonaltype.in.replicates$Replicate),c("coincidence","clonaltype", "Sample", "Replicate", "ID", "Sequence")] -write.table(clonaltype.in.replicates, "clonaltypes_replicates.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) + write.table(clonaltype.in.replicates, "clonaltypes_replicates.txt" , sep="\t",quote=F,na="-",row.names=F,col.names=T) +} else { + cat("No clonaltype", file="clonaltypes_replicates_before_table.txt") + cat("No clonaltype", file="clonaltypes_counts.txt") + cat("No clonaltype", file="clonaltypes_replicates.txt") +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Oct 26 09:58:05 2017 -0400 @@ -0,0 +1,36 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="igblastwrp" version="0.6"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://github.com/mikessh/higblast/releases/download/v0.6/igblastwrapper_linux64.tar.gz</action> + <action type="move_file"> + <source>bin</source> + <destination>$INSTALL_DIR/</destination> + </action> + <action type="move_file"> + <source>data</source> + <destination>$INSTALL_DIR/</destination> + </action> + <action type="move_file"> + <source>igblastwrp.jar</source> + <destination>$INSTALL_DIR/</destination> + </action> + <action type="set_environment"> + <environment_variable action="set_to" name="IGBLASTWRP">$INSTALL_DIR/</environment_variable> + </action> + </actions> + </install> + <readme> +Downloads https://github.com/mikessh/higblast/ + </readme> + </package> + <package name="weblogo" version="3.3"> + <repository changeset_revision="648e4b32f15c" name="package_weblogo_3_3" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <!-- + <package name="circostools" version="0.20"> + <repository name="package_circostools_0_20" owner="iuc" /> + </package> + --> +</tool_dependency>