Mercurial > repos > davidvanzessen > mutation_analysis
changeset 108:6add3e66f4fa draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 13 Jul 2016 09:04:15 -0400 |
| parents | 01c9993865af |
| children | 0096cd454380 |
| files | aa_histogram.r mutation_analysis.py wrapper.sh |
| diffstat | 3 files changed, 10 insertions(+), 32 deletions(-) [+] |
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--- a/aa_histogram.r Wed Jul 13 08:04:13 2016 -0400 +++ b/aa_histogram.r Wed Jul 13 09:04:15 2016 -0400 @@ -26,7 +26,9 @@ if(nrow(mutations.by.id.gene) == 0){ next } - + + print(paste("nrow", gene, nrow(absent.aa.by.id.gene))) + mutations.at.position = colSums(mutations.by.id.gene[,-c(1,2)]) aa.at.position = colSums(absent.aa.by.id.gene[,-c(1,2,3,4)]) @@ -45,7 +47,12 @@ m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency")) print("---------------- write/print ----------------") - + + dat.sums = data.frame(index=1:length(mutations.at.position), mutations.at.position=mutations.at.position, aa.at.position=aa.at.position) + + write.table(dat.sums, paste(outdir, "/aa_histogram_sum_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) + write.table(mutations.by.id.gene, paste(outdir, "/aa_histogram_count_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) + write.table(absent.aa.by.id.gene, paste(outdir, "/aa_histogram_absent_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) write.table(dat_dt, paste(outdir, "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720) print(m)
--- a/mutation_analysis.py Wed Jul 13 08:04:13 2016 -0400 +++ b/mutation_analysis.py Wed Jul 13 09:04:15 2016 -0400 @@ -146,35 +146,6 @@ absentAAbyID[c] -= 1 o.write(ID + "\t" + str(cdr1Length) + "\t" + str(cdr2Length) + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in absentAAbyID]) + "\n") - - -aa_mutations_file = outfile[:outfile.rindex("/")] + "/aa_mutations.txt" -with open(aa_mutations_file, 'w') as o: - o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n") - o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation[1:]]) + "\n") - o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n") - - -aa_mutations_file_ca = outfile[:outfile.rindex("/")] + "/aa_mutations_ca.txt" -with open(aa_mutations_file_ca, 'w') as o: - o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n") - o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation_dic["ca"][1:]]) + "\n") - o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n") - - -aa_mutations_file_cg = outfile[:outfile.rindex("/")] + "/aa_mutations_cg.txt" -with open(aa_mutations_file_cg, 'w') as o: - o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n") - o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation_dic["cg"][1:]]) + "\n") - o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n") - - -aa_mutations_file_cm = outfile[:outfile.rindex("/")] + "/aa_mutations_cm.txt" -with open(aa_mutations_file_cm, 'w') as o: - o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n") - o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation_dic["cg"][1:]]) + "\n") - o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n") - if linecount == 0: print "No data, exiting" with open(outfile, 'w') as o:
--- a/wrapper.sh Wed Jul 13 08:04:13 2016 -0400 +++ b/wrapper.sh Wed Jul 13 09:04:15 2016 -0400 @@ -148,9 +148,9 @@ echo "---------------- aa_histogram.r ----------------" echo "---------------- aa_histogram.r ----------------<br />" >> $log -cp $outdir/aa_mutations.txt $outdir/aa_mutations_count.txt Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "ca,cg,cm" $outdir/ 2>&1 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png +mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt genes=(ca ca1 ca2 cg cg1 cg2 cg3 cg4 cm)