| Previous changeset 1:faae21ba5c63 (2016-10-25) Next changeset 3:275ab5175fd6 (2016-10-27) |
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merge_and_filter.r shm_csr.r wrapper.sh |
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| diff -r faae21ba5c63 -r e85fec274cde merge_and_filter.r --- a/merge_and_filter.r Tue Oct 25 07:28:43 2016 -0400 +++ b/merge_and_filter.r Thu Oct 27 07:26:45 2016 -0400 |
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| @@ -114,7 +114,7 @@ } print(paste("Number of sequences in result after CDR/FR filtering:", nrow(result))) -print(paste("Number of matched sequences in result after CDR/FR filtering:", nrow(result[!grepl("unmatched", result$best_match),]))) +print(paste("Number of sequences in result after CDR/FR filtering:", nrow(result[!grepl("unmatched", result$best_match),]))) if(empty.region.filter == "leader"){ result = result[!(grepl("n|N", result$FR1.IMGT.seq) | grepl("n|N", result$FR2.IMGT.seq) | grepl("n|N", result$FR3.IMGT.seq) | grepl("n|N", result$CDR1.IMGT.seq) | grepl("n|N", result$CDR2.IMGT.seq) | grepl("n|N", result$CDR3.IMGT.seq)),] @@ -123,7 +123,7 @@ } else if(empty.region.filter == "CDR1"){ result = result[!(grepl("n|N", result$FR2.IMGT.seq) | grepl("n|N", result$FR3.IMGT.seq) | grepl("n|N", result$CDR2.IMGT.seq) | grepl("n|N", result$CDR3.IMGT.seq)),] } else if(empty.region.filter == "FR2"){ - result = result[!(grepl("n|N", result$FR3.IMGT.seq) | grepl("n|N", result$CDR3.IMGT.seq)),] + result = result[!(grepl("n|N", result$FR3.IMGT.seq) | grepl("n|N", result$CDR2.IMGT.seq) | grepl("n|N", result$CDR3.IMGT.seq)),] } print(paste("Number of sequences in result after n filtering:", nrow(result))) @@ -183,15 +183,15 @@ chunk_hit_threshold = as.numeric(splt[1]) nt_hit_threshold = as.numeric(splt[2]) -higher_than=(summ$chunk_hit_percentage >= chunk_hit_threshold & summ$nt_hit_percentage >= nt_hit_threshold) +higher_than=(result$chunk_hit_percentage >= chunk_hit_threshold & result$nt_hit_percentage >= nt_hit_threshold) -unmatched=summ[NULL,c("Sequence.ID", "chunk_hit_percentage", "nt_hit_percentage", "start_locations", "best_match")] +unmatched=result[NULL,c("Sequence.ID", "chunk_hit_percentage", "nt_hit_percentage", "start_locations", "best_match")] -if(!all(higher_than, na.rm=T)){ #check for 'not all' because that would mean the unmatched set is empty - unmatched = summ[!higher_than,] +if(!all(higher_than, na.rm=T)){ #check for no unmatched + unmatched = result[!higher_than,] unmatched = unmatched[,c("Sequence.ID", "chunk_hit_percentage", "nt_hit_percentage", "start_locations", "best_match")] unmatched$best_match = paste("unmatched,", unmatched$best_match) - summ[!higher_than,"best_match"] = paste("unmatched,", summ[!higher_than,"best_match"]) + result[!higher_than,"best_match"] = paste("unmatched,", result[!higher_than,"best_match"]) } if(any(higher_than, na.rm=T)){ |
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| diff -r faae21ba5c63 -r e85fec274cde shm_csr.r --- a/shm_csr.r Tue Oct 25 07:28:43 2016 -0400 +++ b/shm_csr.r Thu Oct 27 07:26:45 2016 -0400 |
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| @@ -374,7 +374,7 @@ pc = pc + coord_polar(theta="y") + scale_y_continuous(breaks=NULL) pc = pc + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black")) pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IGA subclasses", "( n =", sum(genesForPlot$Freq), ")")) - write.table(genesForPlot, "IGA.txt", sep="\t",quote=F,row.names=F,col.names=T) + write.table(genesForPlot, "IGA_pie.txt", sep="\t",quote=F,row.names=F,col.names=T) png(filename="IGA.png") print(pc) @@ -395,7 +395,7 @@ pc = pc + coord_polar(theta="y") + scale_y_continuous(breaks=NULL) pc = pc + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black")) pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IGG subclasses", "( n =", sum(genesForPlot$Freq), ")")) - write.table(genesForPlot, "IGG.txt", sep="\t",quote=F,row.names=F,col.names=T) + write.table(genesForPlot, "IGG_pie.txt", sep="\t",quote=F,row.names=F,col.names=T) png(filename="IGG.png") print(pc) |
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| diff -r faae21ba5c63 -r e85fec274cde wrapper.sh --- a/wrapper.sh Tue Oct 25 07:28:43 2016 -0400 +++ b/wrapper.sh Thu Oct 27 07:26:45 2016 -0400 |
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| b'@@ -478,24 +478,37 @@\n echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output\n echo "<tr><td>The complete dataset</td><td><a href=\'merged.txt\' download=\'merged.txt\' >Download</a></td></tr>" >> $output\n echo "<tr><td>The filtered dataset</td><td><a href=\'filtered.txt\' download=\'filtered.txt\' >Download</a></td></tr>" >> $output\n-echo "<tr><td>The SHM Overview table as a dataset</td><td><a href=\'data_sum.txt\' download=\'data_sum.txt\' >Download</a></td></tr>" >> $output\n-echo "<tr><td>The data used to generate the first SHM Overview plot</td><td><a href=\'plot1.txt\' download=\'plot1.txt\' >Download</a></td></tr>" >> $output\n-echo "<tr><td>The data used to generate the second SHM Overview plot</td><td><a href=\'plot2.txt\' download=\'plot2.txt\' >Download</a></td></tr>" >> $output\n-echo "<tr><td>The data used to generate the third SHM Overview plot</td><td><a href=\'plot3.txt\' download=\'plot3.txt\' >Download</a></td></tr>" >> $output\n echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href=\'unmatched.txt\' download=\'unmatched.txt\' >Download</a></td></tr>" >> $output\n \n+echo "<tr><td colspan=\'2\' style=\'background-color:#E0E0E0;\'>SHM Overview</td></tr>" >> $output\n+echo "<tr><td>The SHM Overview table as a dataset</td><td><a href=\'data_sum.txt\' download=\'data_sum.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>Motif data per sequence ID</td><td><a href=\'motif_per_seq.txt\' download=\'motif_per_seq.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>Mutation data per sequence ID</td><td><a href=\'mutation_by_id.txt\' download=\'mutation_by_id.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>Base count for every sequence</td><td><a href=\'base_overview.html\'>View</a></td></tr>" >> $output\n+echo "<tr><td>The data used to generate the RGYW/WRCY and TW/WA plot</td><td><a href=\'plot1.txt\' download=\'plot1.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>The data used to generate the relative transition and transversion plot</td><td><a href=\'plot2.txt\' download=\'plot2.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>The data used to generate the absolute transition and transversion plot</td><td><a href=\'plot3.txt\' download=\'plot3.txt\' >Download</a></td></tr>" >> $output\n+\n+echo "<tr><td colspan=\'2\' style=\'background-color:#E0E0E0;\'>SHM Frequency</td></tr>" >> $output\n echo "<tr><td>The data generate the frequency scatter plot</td><td><a href=\'scatter.txt\' download=\'scatter.txt\' >Download</a></td></tr>" >> $output\n echo "<tr><td>The data used to generate the frequency by class plot</td><td><a href=\'frequency_ranges_classes.txt\' download=\'frequency_ranges_classes.txt\' >Download</a></td></tr>" >> $output\n echo "<tr><td>The data for frequency by subclass</td><td><a href=\'frequency_ranges_subclasses.txt\' download=\'frequency_ranges_subclasses.txt\' >Download</a></td></tr>" >> $output\n \n+echo "<tr><td colspan=\'2\' style=\'background-color:#E0E0E0;\'>Transition Tables</td></tr>" >> $output\n+echo "<tr><td>The data for the \'all\' transition plot</td><td><a href=\'transition_all_sum.txt\' download=\'transition_all_sum.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>The data for the \'IGA\' transition plot</td><td><a href=\'transition_IGA_sum.txt\' download=\'transition_all_sum.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>The data for the \'IGA1\' transition plot</td><td><a href=\'transition_IGA1_sum.txt\' download=\'transition_IGA1_sum.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>The data for the \'IGA1\' transition plot</td><td><a href=\'transition_IGA1_sum.txt\' download=\'transition_IGA1_sum.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>The data for the \'IGG\' transition plot</td><td><a href=\'transition_IGG_sum.txt\' download=\'transition_IGG_sum.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>The data for the \'IGG1\' transition plot</td><td><a href=\'transition_IGG1_sum.txt\' download=\'transition_IGG1_sum.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>The data for the \''..b'tput\n+echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href=\'change_o/change-o-defined_clones-summary-IGA.txt\' download=\'change_o/change-o-defined_clones-summary-IGA.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>The Change-O DB file with defined clones of IGG</td><td><a href=\'change_o/change-o-db-defined_clones-IGG.txt\' download=\'change_o/change-o-db-defined_clones-IGG.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href=\'change_o/change-o-defined_clones-summary-IGG.txt\' download=\'change_o/change-o-defined_clones-summary-IGG.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href=\'change_o/change-o-db-defined_clones-IGM.txt\' download=\'change_o/change-o-db-defined_clones-IGM.txt\' >Download</a></td></tr>" >> $output\n+echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href=\'change_o/change-o-defined_clones-summary-IGM.txt\' download=\'change_o/change-o-defined_clones-summary-IGM.txt\' >Download</a></td></tr>" >> $output\n+\n+echo "<tr><td colspan=\'2\' style=\'background-color:#E0E0E0;\'>Filtered IMGT output files</td></tr>" >> $output\n echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href=\'new_IMGT.txz\' download=\'new_IMGT.txz\' >Download</a></td></tr>" >> $output\n echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href=\'new_IMGT_IGA.txz\' download=\'new_IMGT_IGA.txz\' >Download</a></td></tr>" >> $output\n echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href=\'new_IMGT_IGA1.txz\' download=\'new_IMGT_IGA1.txz\' >Download</a></td></tr>" >> $output\n@@ -517,15 +546,6 @@\n 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\n 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\n \n-echo "<tr><td>The Change-O DB file with defined clones and subclass annotation</td><td><a href=\'change_o/change-o-db-defined_clones.txt\' download=\'change_o/change-o-db-defined_clones.txt\' >Download</a></td></tr>" >> $output\n-echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href=\'change_o/change-o-defined_clones-summary.txt\' download=\'change_o/change-o-defined_clones-summary.txt\' >Download</a></td></tr>" >> $output\n-echo "<tr><td>The Change-O DB file with defined clones of IGA</td><td><a href=\'change_o/change-o-db-defined_clones-IGA.txt\' download=\'change_o/change-o-db-defined_clones-IGA.txt\' >Download</a></td></tr>" >> $output\n-echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href=\'change_o/change-o-defined_clones-summary-IGA.txt\' download=\'change_o/change-o-defined_clones-summary-IGA.txt\' >Download</a></td></tr>" >> $output\n-echo "<tr><td>The Change-O DB file with defined clones of IGG</td><td><a href=\'change_o/change-o-db-defined_clones-IGG.txt\' download=\'change_o/change-o-db-defined_clones-IGG.txt\' >Download</a></td></tr>" >> $output\n-echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href=\'change_o/change-o-defined_clones-summary-IGG.txt\' download=\'change_o/change-o-defined_clones-summary-IGG.txt\' >Download</a></td></tr>" >> $output\n-echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href=\'change_o/change-o-db-defined_clones-IGM.txt\' download=\'change_o/change-o-db-defined_clones-IGM.txt\' >Download</a></td></tr>" >> $output\n-echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href=\'change_o/change-o-defined_clones-summary-IGM.txt\' download=\'change_o/change-o-defined_clones-summary-IGM.txt\' >Download</a></td></tr>" >> $output\n-\n echo "</table>" >> $output\n \n echo "</div>" >> $output #downloads tab end\n' |