Mercurial > repos > davidvanzessen > mutation_analysis
diff wrapper.sh @ 82:564c4f6da203 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 24 May 2016 03:52:14 -0400 |
| parents | a778156dad3d |
| children | 041f94f50b34 |
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--- a/wrapper.sh Tue May 17 04:17:38 2016 -0400 +++ b/wrapper.sh Tue May 24 03:52:14 2016 -0400 @@ -86,9 +86,9 @@ echo "---------------- mutation_analysis.r ----------------" echo "---------------- mutation_analysis.r ----------------<br />" >> $output -genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched" +classes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm,unmatched" echo "R mutation analysis" -Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1 +Rscript $dir/mutation_analysis.r $outdir/merged.txt $classes $outdir ${include_fr1} 2>&1 #echo "." > $output #exit 0 @@ -98,7 +98,7 @@ echo "---------------- mutation_analysis.py ----------------" echo "---------------- mutation_analysis.py ----------------<br />" >> $output -python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt +python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt echo "---------------- aa_histogram.r ----------------" echo "---------------- aa_histogram.r ----------------<br />" >> $output @@ -109,6 +109,19 @@ funcs=(sum mean median) +echo "---------------- sequence_overview.r ----------------" + +mkdir $outdir/sequence_overview + +Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1 + +echo "<table border='1'>" > $outdir/base_overview.html + +while read ID class seq A C G T +do + echo "<tr><td>$ID</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html +done < $outdir/sequence_overview/ntoverview.txt + echo "<html><center><h1>$title</h1></center>" > $output @@ -222,7 +235,7 @@ #optional output for naive -echo "---------------- aa_histogram.r ----------------" +echo "---------------- naive_output.r ----------------" if [[ "$naive_output" != "None" ]] then @@ -233,19 +246,6 @@ Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} $outdir/ntoverview.txt $outdir/ntsum.txt 2>&1 fi -echo "---------------- sequence_overview.r ----------------" - -mkdir $outdir/sequence_overview - -Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/sequence_overview 2>&1 - -echo "<table border='1'>" > $outdir/base_overview.html - -while read ID class seq A C G T -do - echo "<tr><td>$ID</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html -done < $outdir/sequence_overview/ntoverview.txt - echo "</table>" >> $outdir/base_overview.html echo "---------------- Done! ----------------"