Mercurial > repos > davidvanzessen > mutation_analysis
changeset 85:07f7da724a77 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 26 May 2016 08:18:13 -0400 |
| parents | 041f94f50b34 |
| children | 0011a0597685 |
| files | merge_and_filter.r mutation_analysis.py wrapper.sh |
| diffstat | 2 files changed, 6 insertions(+), 10 deletions(-) [+] |
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--- a/mutation_analysis.py Tue May 24 03:59:44 2016 -0400 +++ b/mutation_analysis.py Thu May 26 08:18:13 2016 -0400 @@ -49,8 +49,8 @@ fr2Index = linesplt.index("FR2.IMGT") cdr2Index = linesplt.index("CDR2.IMGT") fr3Index = linesplt.index("FR3.IMGT") - cdr1LengthIndex = linesplt.index("CDR1.IMGT.Nb.of.nucleotides") - cdr2LengthIndex = linesplt.index("CDR2.IMGT.Nb.of.nucleotides") + cdr1LengthIndex = linesplt.index("CDR1.IMGT.length") + cdr2LengthIndex = linesplt.index("CDR2.IMGT.length") first = False continue linecount += 1 @@ -73,9 +73,9 @@ cdr1Length = linesplt[cdr1LengthIndex] cdr2Length = linesplt[cdr2LengthIndex] - cdr1LengthDic[ID] = int(cdr1Length) / 3 - cdr2LengthDic[ID] = int(cdr2Length) / 3 - + cdr1LengthDic[ID] = int(cdr1Length) if cdr1Length != "X" else 0 + cdr2LengthDic[ID] = int(cdr2Length) if cdr2Length != "X" else 0 + IDlist += [ID] AALength = (int(max(mutationList, key=lambda i: int(i[4]) if i[4] else 0)[4]) + 1) # [4] is the position of the AA mutation, None if silent
--- a/wrapper.sh Tue May 24 03:59:44 2016 -0400 +++ b/wrapper.sh Thu May 26 08:18:13 2016 -0400 @@ -90,10 +90,6 @@ echo "R mutation analysis" Rscript $dir/mutation_analysis.r $outdir/merged.txt $classes $outdir ${include_fr1} 2>&1 -#echo "." > $output -#exit 0 - - echo "---------------- mutation_analysis.py ----------------" echo "---------------- mutation_analysis.py ----------------<br />" >> $output @@ -119,7 +115,7 @@ while read ID class seq A C G T do - echo "<tr><td>$ID</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html + echo "<tr><td>$ID</td><td>$seq</td><td>$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