Treeomics

Author: melkebir

result/sims/treeomics/convert_reads_to_treeomics.py

@@ -47,7 +47,9 @@ def write_reads(f, reads, nrMutations, loci):
     f.write("\t".join(["Chromosome", "Position", "Change", "Gene"] + samples) + "\n")
     f.write("\t".join(["#Purity", ".", ".", "."] + ["1.0"] * nrSamples) + "\n")
     for i in range(nrMutations):
-        f.write("\t".join(map(str, list(loci[i])) + [str(r[1][i]) for r in reads]) + "\n")
+        s = map(str, list(loci[i])) + [str(r[1][i]) for r in reads]
+        s[3] = 'mut' + str(i)
+        f.write("\t".join(s) + "\n")
 
 if __name__ == "__main__":
     if len(sys.argv) != 3:

result/sims/treeomics/generate_slurm.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+for p in {mS,S,M,R}
+do
+    for f in ../../../../data/sims/$p/reads_seed*.tsv
+    do
+	s=$(basename $f .tsv | sed -e s/reads_seed//g)
+	echo Generating TreeOmics slurm file for seed $s pattern $p...
+	
+	f="${p}_${s}.slurm"
+	echo "#!/bin/bash" > $f
+	echo "#SBATCH --job-name=\"${p}_${s}_treeomics\"" >> $f
+	echo "#SBATCH -c 16" >> $f
+	echo "#SBATCH -t 1:30:00" >> $f
+	echo "#SBATCH --mem=100G" >> $f
+        echo "cd /n/fs/ragr-data/projects/MACHINA/treeomics/src" >> $f
+        echo "source activate treeomics_env" >> $f
+	echo "python treeomics -r ../../machina/result/sims/treeomics/${p}_seed${s}_variant.txt -s ../../machina/result/sims/treeomics/${p}_seed${s}_coverage.txt -o output/${p}_seed${s} -l 100 -t 3600 " >> $f
+
+	ff="${p}_${s}_SUBCLONES.slurm"
+	echo "#!/bin/bash" > $ff
+	echo "#SBATCH --job-name=\"${p}_${s}_treeomics_SUBCLONES\"" >> $ff
+	echo "#SBATCH -c 16" >> $ff
+	echo "#SBATCH -t 1:30:00" >> $ff
+	echo "#SBATCH --mem=100G" >> $ff
+        echo "cd /n/fs/ragr-data/projects/MACHINA/treeomics/src" >> $ff
+        echo "source activate treeomics_env" >> $ff
+	echo "python treeomics -r ../../machina/result/sims/treeomics/${p}_seed${s}_variant.txt -s ../../machina/result/sims/treeomics/${p}_seed${s}_coverage.txt -o output/${p}_seed${s}_SUBCLONES -l 100 -u -t 3600" >> $ff
+    done
+done