| Previous changeset 28:c0ecc31829bd (2016-12-07) Next changeset 30:33a7c49d48a7 (2016-12-12) |
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Commit message:
Uploaded |
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modified:
aa_histogram.r shm_csr.xml wrapper.sh |
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| diff -r c0ecc31829bd -r 80c4eebf7bc9 aa_histogram.r --- a/aa_histogram.r Wed Dec 07 08:17:09 2016 -0500 +++ b/aa_histogram.r Thu Dec 08 04:51:09 2016 -0500 |
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| @@ -16,15 +16,15 @@ for(gene in genes){ if(gene == ""){ - mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),] - absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),] + mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),] + absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),] } else { - mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),] - absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),] + mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),] + absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),] } print(paste("nrow", gene, nrow(absent.aa.by.id.gene))) if(nrow(mutations.by.id.gene) == 0){ - next + next } mutations.at.position = colSums(mutations.by.id.gene[,-c(1,2)]) |
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| diff -r c0ecc31829bd -r 80c4eebf7bc9 shm_csr.xml --- a/shm_csr.xml Wed Dec 07 08:17:09 2016 -0500 +++ b/shm_csr.xml Thu Dec 08 04:51:09 2016 -0500 |
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| @@ -27,7 +27,7 @@ <option value="CDR3.IMGT.AA,best_match_class">CDR3 (AA), C region</option> <option value="CDR3.IMGT.AA">CDR3 (AA)</option> - <option value="VGene,CDR3.IMGT.seq,best_match_class">Top.V.Gene, CDR3.nt.Seq, C region</option> + <option value="VGene,CDR3.IMGT.seq,best_match_class">Top.V.Gene, CDR3 (nt), C region</option> <option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3 (nt)</option> <option value="CDR3.IMGT.seq,best_match_class">CDR3 (nt), C region</option> <option value="CDR3.IMGT.seq">CDR3 (nt)</option> |
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| diff -r c0ecc31829bd -r 80c4eebf7bc9 wrapper.sh --- a/wrapper.sh Wed Dec 07 08:17:09 2016 -0500 +++ b/wrapper.sh Thu Dec 08 04:51:09 2016 -0500 |
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| @@ -187,6 +187,9 @@ if [ -e "$outdir/aa_histogram_.png" ]; then mv $outdir/aa_histogram_.png $outdir/aa_histogram.png mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt + mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt + mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt + mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt fi genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE) @@ -592,6 +595,12 @@ echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data used to generate the aa mutation frequency plot</td><td><a href='aa_histogram_sum.txt' download='aa_histogram_sum.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data used to generate the aa mutation frequency plot for IGA</td><td><a href='aa_histogram_sum_IGA.txt' download='aa_histogram_sum_IGA.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data used to generate the aa mutation frequency plot for IGG</td><td><a href='aa_histogram_sum_IGG.txt' download='aa_histogram_sum_IGG.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data used to generate the aa mutation frequency plot for IGM</td><td><a href='aa_histogram_sum_IGM.txt' download='aa_histogram_sum_IGM.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>The data used to generate the aa mutation frequency plot for IGE</td><td><a href='aa_histogram_sum_IGE.txt' download='aa_histogram_sum_IGE.txt' >Download</a></td></tr>" >> $output + echo "<tr><td>Baseline PDF (<a href='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf' download='baseline.pdf' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output |