fix colums for webserver output

PatrickRWright · Oct 27, 2017 · 175d827 · 175d827
1 parent 670f9db
commit 175d827
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Showing 4 changed files with 28 additions and 30 deletions.
diff --git a/CopraRNA2.pl b/CopraRNA2.pl
@@ -97,6 +97,8 @@
 
 # v2.1.1   : added input exceptions
 #            DAVID python code now py2 and py3 compatible
+#            changed coloring in evolutionary heatmap
+#            fixed issue for regions plots for sequences with non ATGC alphabet
 #
 # v2.1.0   : topcount default 200
 #            stopped tracking edits manually
@@ -436,19 +438,6 @@
 system "convert -density '300' -resize '700' -flatten -rotate 90 sRNA_regions_with_histogram.ps sRNA_regions_with_histogram.png";
 system "convert -density '300' -resize '700' -flatten -rotate 90 mRNA_regions_with_histogram.ps mRNA_regions_with_histogram.png";
 
-# trim off last column (initial_sorting) if CopraRNA 2 prediction mode
-unless ($cop1) {
-     system "awk -F, -vOFS=, '{NF-=1;print}' CopraRNA_result.csv > CopraRNA_result_temp.csv";
-     system "mv CopraRNA_result_temp.csv CopraRNA_result.csv";
-     system "awk -F, -vOFS=, '{NF-=1;print}' CopraRNA_result_all.csv > CopraRNA_result_all_temp.csv";
-     system "mv CopraRNA_result_all_temp.csv CopraRNA_result_all.csv";
-     # change header
-     system "sed -i 's/,Additional.homologs,/,Additional homologs,/g' CopraRNA_result.csv";
-     system "sed -i 's/,Amount.sampled/,Amount sampled/g' CopraRNA_result.csv";
-     system "sed -i 's/,Additional.homologs,/,Additional homologs,/g' CopraRNA_result_all.csv";
-     system "sed -i 's/,Amount.sampled/,Amount sampled/g' CopraRNA_result_all.csv";
-}
-
 # clean up
 unless ($noclean) {
 
@@ -466,7 +455,7 @@
     system "rm input_sRNA.fa merged_refseq_ids.txt";    
     system "rm CopraRNA2_prep*";
     system "rm fasta_temp_file fasta_temp_file_out";
-    system "rm conservation_table.Rdata" unless ($cop1);
+    #system "rm conservation_table.Rdata" unless ($cop1);
 
     # fix warning "rm: missing operand Try 'rm --help' for more information." ## edit 2.0.1
     my $temp_fasta_check = `find -regex ".*fa[0-9]+\$"`;

diff --git a/coprarna_aux/homology_intaRNA.pl b/coprarna_aux/homology_intaRNA.pl
@@ -394,6 +394,20 @@
     print ERRORLOG "Error: No predictions in CopraRNA_result.csv. CopraRNA run failed.\n"; ## edit 2.0.2
 }
 
+# trim off last column (initial_sorting) if CopraRNA 2 prediction mode
+unless ($cop1) {
+     system "awk -F, -vOFS=, '{NF-=1;print}' CopraRNA_result.csv > CopraRNA_result_temp.csv";
+     system "mv CopraRNA_result_temp.csv CopraRNA_result.csv";
+     system "awk -F, -vOFS=, '{NF-=1;print}' CopraRNA_result_all.csv > CopraRNA_result_all_temp.csv";
+     system "mv CopraRNA_result_all_temp.csv CopraRNA_result_all.csv";
+     # change header
+     system "sed -i 's/,Additional.homologs,/,Additional homologs,/g' CopraRNA_result.csv";
+     system "sed -i 's/,Amount.sampled/,Amount sampled/g' CopraRNA_result.csv";
+     system "sed -i 's/,Additional.homologs,/,Additional homologs,/g' CopraRNA_result_all.csv";
+     system "sed -i 's/,Amount.sampled/,Amount sampled/g' CopraRNA_result_all.csv";
+}
+
+
 if ($websrv) { # only if webserver output is requested via -websrv ## edit 2.0.5.1
 
     my $allrefs = $refseqaffiliations{$ARGV[4]};

diff --git a/coprarna_aux/prepare_output_for_websrv_new.pl b/coprarna_aux/prepare_output_for_websrv_new.pl
@@ -63,21 +63,13 @@
         my $intncRNA = $split_ooi[6] . " -- " . $split_ooi[7];
         print WRITEINTERNAL $split_ooi[6] . " -- " . $split_ooi[7] . ",";
 
-        if ($cop1) {
-            # annotation
-            print WRITEINTERNAL $split[-3] . ","; ## edit 2.0.1
-            # additional homologs
-            my $temp = $split[-2]; ## edit 2.0.1
-            chomp $temp;
-            print WRITEINTERNAL $temp . ",";
-        } else { ## edit 2.0.6
-            # annotation
-            print WRITEINTERNAL $split[-2] . ",";
-            # additional homologs
-            my $temp = $split[-1];
-            chomp $temp;
-            print WRITEINTERNAL $temp . ",";
-        }
+        # annotation
+        print WRITEINTERNAL $split[-3] . ","; ## edit 2.0.1
+        # additional homologs
+        my $temp = $split[-2]; ## edit 2.0.1
+        chomp $temp;
+        print WRITEINTERNAL $temp . ",";
+
         my $GID = "";
         if ($split_ooi[8] =~ m/GeneID:(\d+)\)/) {
             $GID = $1;

diff --git a/coprarna_aux/print_archive_README.pl b/coprarna_aux/print_archive_README.pl
@@ -111,9 +111,12 @@
 sequences with an annotation to visualize the interaction sites and consensus
 interaction regions in Jalview.
 
-all_predictions (not made if -cop1) :
+all_predictions (not made if -cop1):
 This directory contains the results for all modes available in CopraRNA 2. 
 
+conservation_table.Rdata:
+Precomputed R data environment for evolutionary heatmap. 
+
 README.txt:
 This file.