Mercurial > repos > davidvanzessen > change_o
changeset 1:326165da9ece draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 04 Aug 2016 08:59:47 -0400 |
| parents | dda9b2e72e2b |
| children | 6f57d43a1f4c |
| files | create_germlines.sh define_clones.r define_clones.sh define_clones.xml makedb.sh |
| diffstat | 5 files changed, 31 insertions(+), 7 deletions(-) [+] |
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--- a/create_germlines.sh Tue May 03 09:52:21 2016 -0400 +++ b/create_germlines.sh Thu Aug 04 08:59:47 2016 -0400 @@ -16,7 +16,7 @@ mkdir $PWD/outdir -#/home/galaxy/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $germline --outdir $PWD/outdir --outname output -g $type $cloned -/data/users/david/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned +/home/galaxy/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned +#/data/users/david/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned mv $PWD/outdir/output_germ-pass.tab $output
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/define_clones.r Thu Aug 04 08:59:47 2016 -0400 @@ -0,0 +1,14 @@ +args <- commandArgs(trailingOnly = TRUE) + +input=args[1] +output=args[2] + +change.o = read.table(input, header=T, sep="\t", quote="", stringsAsFactors=F) + +freq = data.frame(table(change.o$CLONE)) +freq2 = data.frame(table(freq$Freq)) +freq2$final = round(freq2$Freq / as.numeric(freq2$Var1), 2) + +names(freq2) = c("freq", "freq.of.freq", "divided") + +write.table(x=freq2, file=output, sep="\t",quote=F,row.names=F,col.names=T)
--- a/define_clones.sh Tue May 03 09:52:21 2016 -0400 +++ b/define_clones.sh Thu Aug 04 08:59:47 2016 -0400 @@ -19,13 +19,21 @@ link=$8 dist=$9 output=${10} + output2=${11} - /data/users/david/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link + #/data/users/david/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link + /home/galaxy/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link + + Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1 else method=$3 output=$4 + output2=$5 - /data/users/david/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method + #/data/users/david/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method + /home/galaxy/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method + + Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1 fi cp $PWD/outdir/output_clone-pass.tab $output
--- a/define_clones.xml Tue May 03 09:52:21 2016 -0400 +++ b/define_clones.xml Thu Aug 04 08:59:47 2016 -0400 @@ -2,9 +2,9 @@ <description>Change-O</description> <command interpreter="bash"> #if $input_type.input_type_select=="bygroup" - define_clones.sh bygroup $input $input_type.mode $input_type.act $input_type.model $input_type.norm $input_type.sym $input_type.link $input_type.dist $out_file + define_clones.sh bygroup $input $input_type.mode $input_type.act $input_type.model $input_type.norm $input_type.sym $input_type.link $input_type.dist $out_file $out_file2 #else - define_clones.sh hclust $input $input_type.method $out_file + define_clones.sh hclust $input $input_type.method $out_file $out_file2 #end if </command> <inputs> @@ -56,6 +56,7 @@ </inputs> <outputs> <data format="tabular" name="out_file" label = "Change-o DB clones ${input.name}"/> + <data format="tabular" name="out_file2" label = "Change-o DB clones info ${input.name}"/> </outputs> <citations> <citation type="doi">10.1093/bioinformatics/btv359</citation>
--- a/makedb.sh Tue May 03 09:52:21 2016 -0400 +++ b/makedb.sh Thu Aug 04 08:59:47 2016 -0400 @@ -27,6 +27,7 @@ mkdir $PWD/outdir -/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions +#/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions +/home/galaxy/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions mv $PWD/outdir/output_db-pass.tab $output