| Previous changeset 30:33a7c49d48a7 (2016-12-12) Next changeset 32:4c5ba6b5d10d (2016-12-15) |
|
Commit message:
Uploaded |
|
modified:
new_imgt.r sequence_overview.r shm_csr.xml wrapper.sh |
| b |
| diff -r 33a7c49d48a7 -r fe44a905aee9 new_imgt.r --- a/new_imgt.r Mon Dec 12 05:19:58 2016 -0500 +++ b/new_imgt.r Tue Dec 13 10:06:49 2016 -0500 |
| [ |
| @@ -4,7 +4,7 @@ merged.file = args[2] gene = args[3] -merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F) +merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F, comment.char="") if(gene != "-"){ merged = merged[grepl(paste("^", gene, sep=""), merged$best_match),] @@ -17,7 +17,7 @@ for(f in list.files(imgt.dir, pattern="*.txt$")){ #print(paste("filtering", f)) path = paste(imgt.dir, f, sep="") - dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F, check.names=FALSE) + dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F, check.names=FALSE, comment.char="") dat = dat[dat[,"Sequence ID"] %in% merged$Sequence.ID,] |
| b |
| diff -r 33a7c49d48a7 -r fe44a905aee9 sequence_overview.r --- a/sequence_overview.r Mon Dec 12 05:19:58 2016 -0500 +++ b/sequence_overview.r Tue Dec 13 10:06:49 2016 -0500 |
| [ |
| @@ -22,13 +22,13 @@ #before.unique = before.unique[!grepl("unmatched", before.unique$best_match),] if(empty.region.filter == "leader"){ - before.unique$seq_conc = paste(before.unique$FR1.IMGT.seq, before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq) + before.unique$seq_conc = paste(before.unique$FR1.IMGT.seq, before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq) } else if(empty.region.filter == "FR1"){ - before.unique$seq_conc = paste(before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq) + before.unique$seq_conc = paste(before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq) } else if(empty.region.filter == "CDR1"){ - before.unique$seq_conc = paste(before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq) + before.unique$seq_conc = paste(before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq) } else if(empty.region.filter == "FR2"){ - before.unique$seq_conc = paste(before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq) + before.unique$seq_conc = paste(before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq) } IDs = before.unique[,c("Sequence.ID", "seq_conc", "best_match", "Functionality")] |
| b |
| diff -r 33a7c49d48a7 -r fe44a905aee9 shm_csr.xml --- a/shm_csr.xml Mon Dec 12 05:19:58 2016 -0500 +++ b/shm_csr.xml Tue Dec 13 10:06:49 2016 -0500 |
| [ |
| @@ -55,23 +55,23 @@ </inputs> <outputs> <data format="html" name="out_file" label = "SHM & CSR on ${in_file.name}"/> - <data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" > + <data format="imgt_archive" name="naive_output_ca" label = "Filtered IMGT IGA: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> </data> - <data format="imgt_archive" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" > + <data format="imgt_archive" name="naive_output_cg" label = "Filtered IMGT IGG: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> </data> - <data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" > + <data format="imgt_archive" name="naive_output_cm" label = "Filtered IMGT IGM: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> </data> - <data format="imgt_archive" name="naive_output_ce" label = "Naive CE input data from ${in_file.name}" > + <data format="imgt_archive" name="naive_output_ce" label = "Filtered IMGT IGE: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> </data> - <data format="imgt_archive" name="naive_output_all" label = "Naive input data from ${in_file.name}" > + <data format="imgt_archive" name="naive_output_all" label = "Filtered IMGT all: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] == "101_101"</filter> </data> |
| b |
| diff -r 33a7c49d48a7 -r fe44a905aee9 wrapper.sh --- a/wrapper.sh Mon Dec 12 05:19:58 2016 -0500 +++ b/wrapper.sh Tue Dec 13 10:06:49 2016 -0500 |
| b |
| @@ -546,7 +546,7 @@ echo "</div>" >> $output echo "<div class='tabbertab' title='Overlap'>" >> $output - cat "$outdir/sequence_overview/index.html" >> $output + cat "$outdir/sequence_overview/index.html" | sed "s%href='\(.*\).html%href='sequence_overview/\1.html%g" >> $output # rewrite href to 'sequence_overview/..." echo "</div>" >> $output @@ -609,6 +609,7 @@ echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output +echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output @@ -639,7 +640,7 @@ echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='new_IMGT_IGG3.txz' download='new_IMGT_IGG3.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='new_IMGT_IGG4.txz' download='new_IMGT_IGG4.txz' >Download</a></td></tr>" >> $output echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output -echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output +echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGE.txz' >Download</a></td></tr>" >> $output echo "</table>" >> $output |