Mercurial > repos > davidvanzessen > change_o
changeset 6:3ddd933dd7a2 draft default tip
Uploaded
author | davidvanzessen |
---|---|
date | Thu, 15 Sep 2016 03:54:33 -0400 |
parents | 3d97839fda21 |
children | |
files | create_germlines.sh create_germlines.xml define_clones.r define_clones.sh define_clones.xml makedb.sh parsedb.sh |
diffstat | 7 files changed, 33 insertions(+), 37 deletions(-) [+] |
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--- a/create_germlines.sh Mon Aug 15 10:06:24 2016 -0400 +++ b/create_germlines.sh Thu Sep 15 03:54:33 2016 -0400 @@ -17,6 +17,7 @@ mkdir $PWD/outdir #/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 +#/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 +python3 $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 $output
--- a/create_germlines.xml Mon Aug 15 10:06:24 2016 -0400 +++ b/create_germlines.xml Thu Sep 15 03:54:33 2016 -0400 @@ -6,8 +6,8 @@ <inputs> <param name="input" type="data" label="Input IMGT zip file" /> <param name="type" type="select" label="Type" help="Specify type(s) of germlines to include full germline, germline with D-region masked, or germline for V-region only." > - <option value="dmask" selected="true">Full germline</option> - <option value="full">Masked D-region</option> + <option value="full" selected="true">Full germline</option> + <option value="dmask">Masked D-region</option> <option value="vonly" >V-region only</option> </param> <param name="cloned" type="select" label="Cloned" help="Create one germline per clone" >
--- a/define_clones.r Mon Aug 15 10:06:24 2016 -0400 +++ b/define_clones.r Thu Sep 15 03:54:33 2016 -0400 @@ -8,16 +8,8 @@ freq = data.frame(table(change.o$CLONE)) freq2 = data.frame(table(freq$Freq)) -print(freq) - -print(freq2$Freq) - -print(freq2$Var1) - freq2$final = as.numeric(freq2$Freq) * as.numeric(as.character(freq2$Var1)) -print(freq2) - names(freq2) = c("Clone size", "Nr of clones", "Nr of sequences") write.table(x=freq2, file=output, sep="\t",quote=F,row.names=F,col.names=T)
--- a/define_clones.sh Mon Aug 15 10:06:24 2016 -0400 +++ b/define_clones.sh Thu Sep 15 03:54:33 2016 -0400 @@ -6,7 +6,9 @@ type=$1 input=$2 -mkdir $PWD/outdir +mkdir -p $PWD/outdir + +echo "defineclones: $PWD/outdir" cp $input $PWD/input.tab #file has to have a ".tab" extension @@ -21,7 +23,7 @@ output=${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 + python3 $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 @@ -30,7 +32,7 @@ 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 + python3 $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
--- a/define_clones.xml Mon Aug 15 10:06:24 2016 -0400 +++ b/define_clones.xml Thu Sep 15 03:54:33 2016 -0400 @@ -11,7 +11,7 @@ <param name="input" type="data" format="tabular" label="A Change-O DB file" /> <conditional name="input_type"> <param name="input_type_select" type="select" label="Input type"> - <option value="bygroup">Define clones by V assignment, J assignment and junction length</option> + <option value="bygroup" selected="true">Define clones by V assignment, J assignment and junction length</option> <option value="hclust">Define clones by specified distance metric on CDR3s and cutting of hierarchical clustering tree</option> </param> <when value="bygroup"> @@ -20,29 +20,29 @@ <option value="gene" selected="true">Gene</option> </param> <param name="act" type="select" label="Specifies how to handle multiple V(D)J assignments for initial grouping."> - <option value="first">First</option> - <option value="set" selected="true">Set</option> + <option value="first" selected="true">First</option> + <option value="set">Set</option> </param> <param name="model" type="select" label="Specifies which substitution model to use for calculating distance between sequences."> <option value="aa">AA hamming distance</option> - <option value="ham">Nucleotide hamming distance</option> + <option value="ham" selected="true">Nucleotide hamming distance</option> <option value="m1n">Mouse single nucleotide (Smith et al, 1996)</option> - <option value="hs1f" selected="true">Human single nucleotide (Yaari et al, 2013)</option> + <option value="hs1f">Human single nucleotide (Yaari et al, 2013)</option> <option value="hs5f">Human S5F (Yaari et al, 2013)</option> </param> <param name="norm" type="select" label="Specifies how to normalize distances."> - <option value="none">Do not normalize</option> + <option value="none" selected="true">Do not normalize</option> <option value="mut">Normalize by number of mutations</option> - <option value="len" selected="true">Normalize by length</option> + <option value="len">Normalize by length</option> </param> <param name="sym" type="select" label="Specifies how to combine asymmetric distances."> - <option value="avg" selected="true">Average</option> - <option value="min">Minimum</option> + <option value="avg">Average</option> + <option value="min" selected="true">Minimum</option> </param> <param name="link" type="select" label="Type of linkage to use for hierarchical clustering."> - <option value="single" selected="true">Single</option> + <option value="single">Single</option> <option value="average">Average</option> - <option value="complete">Complete</option> + <option value="complete" selected="true">Complete</option> </param> <param name="dist" size="4" type="float" value="0.0" label="The distance threshold for clonal grouping" /> </when>
--- a/makedb.sh Mon Aug 15 10:06:24 2016 -0400 +++ b/makedb.sh Thu Sep 15 03:54:33 2016 -0400 @@ -27,7 +27,8 @@ mkdir $PWD/outdir -/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions +python3 $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
--- a/parsedb.sh Mon Aug 15 10:06:24 2016 -0400 +++ b/parsedb.sh Thu Sep 15 03:54:33 2016 -0400 @@ -12,21 +12,21 @@ mkdir $PWD/outdir if [ "fasta" == "$action" ] ; then - /data/users/david/anaconda3/bin/python $dir/ParseDb.py fasta -d $input --outdir $PWD/outdir --outname output + python3 $dir/ParseDb.py fasta -d $input --outdir $PWD/outdir --outname output mv $PWD/outdir/output_sequences.fasta $output elif [ "clip" == "$action" ] ; then - /data/users/david/anaconda3/bin/python $dir/ParseDb.py clip -d $input --outdir $PWD/outdir --outname output + python3 $dir/ParseDb.py clip -d $input --outdir $PWD/outdir --outname output mv $PWD/outdir/output_sequences.fasta $output elif [ "split" == "$action" ] ; then field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`" label=$5 mkdir $PWD/split - /data/users/david/anaconda3/bin/python $dir/ParseDb.py split -d $input --outdir $PWD/split --outname output -f $field + python3 $dir/ParseDb.py split -d $input --outdir $PWD/split --outname output -f $field #rename "s/output_${field}/$label/" $PWD/split/* elif [ "add" == "$action" ] ; then field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`" value=$5 - /data/users/david/anaconda3/bin/python $dir/ParseDb.py add -d $input --outdir $PWD/outdir --outname output -f $field -u $value + python3 $dir/ParseDb.py add -d $input --outdir $PWD/outdir --outname output -f $field -u $value mv $PWD/outdir/output_parse-add.tab $output elif [ "delete" == "$action" ] ; then field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`" @@ -37,20 +37,20 @@ else regex="" fi - /data/users/david/anaconda3/bin/python $dir/ParseDb.py delete -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex + python3 $dir/ParseDb.py delete -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex mv $PWD/outdir/output_parse-delete.tab $output elif [ "drop" == "$action" ] ; then field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`" - /data/users/david/anaconda3/bin/python $dir/ParseDb.py drop -d $input --outdir $PWD/outdir --outname output -f $field + python3 $dir/ParseDb.py drop -d $input --outdir $PWD/outdir --outname output -f $field mv $PWD/outdir/output_parse-drop.tab $output elif [ "index" == "$action" ] ; then field=$4 - /data/users/david/anaconda3/bin/python $dir/ParseDb.py index -d $input --outdir $PWD/outdir --outname output -f $field + python3 $dir/ParseDb.py index -d $input --outdir $PWD/outdir --outname output -f $field mv $PWD/outdir/output_parse-index.tab $output elif [ "rename" == "$action" ] ; then field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`" newname=$5 - /data/users/david/anaconda3/bin/python $dir/ParseDb.py rename -d $input --outdir $PWD/outdir --outname output -f $field -k $newname + python3 $dir/ParseDb.py rename -d $input --outdir $PWD/outdir --outname output -f $field -k $newname mv $PWD/outdir/output_parse-rename.tab $output elif [ "select" == "$action" ] ; then field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`" @@ -61,7 +61,7 @@ else regex="" fi - /data/users/david/anaconda3/bin/python $dir/ParseDb.py select -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex + python3 $dir/ParseDb.py select -d $input --outdir $PWD/outdir --outname output -f $field -u $value --logic any $regex mv $PWD/outdir/output_parse-select.tab $output elif [ "sort" == "$action" ] ; then field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`" @@ -74,7 +74,7 @@ if [ "true" == "$desc" ] ; then tmp="--descend $tmp" fi - /data/users/david/anaconda3/bin/python $dir/ParseDb.py sort -d $input --outdir $PWD/outdir --outname output -f $field $tmp + python3 $dir/ParseDb.py sort -d $input --outdir $PWD/outdir --outname output -f $field $tmp mv $PWD/outdir/output_parse-sort.tab $output elif [ "update" == "$action" ] ; then field="`cat $input 2> /dev/null | head -n 1 | cut -f$4 | tr '\n\r' ' '`" @@ -86,7 +86,7 @@ else regex="" fi - /data/users/david/anaconda3/bin/python $dir/ParseDb.py update -d $input --outdir $PWD/outdir --outname output -f $field -u $value -t $replace $regex + python3 $dir/ParseDb.py update -d $input --outdir $PWD/outdir --outname output -f $field -u $value -t $replace $regex mv $PWD/outdir/output_parse-update.tab $output fi