update

Author: Jon Palmer

setup.sh

@@ -204,7 +204,7 @@ if [ "$dep" = 'pass' ]; then
     fi
 
     check='pass'
-    for i in {blastp,hmmsearch,hmmscan,augustus,'gmes_petap.pl',mummer,nucmer,show-coords,exonerate,gmap,blat,RepeatModeler,RepeatMasker,pslCDnaFilter,bedtools,bamtools,'gag.py',tbl2asn,'braker.pl',funannotate,mafft,trimal,raxmlHPC-PTHREADS,tRNAscan-SE, 'rmOutToGFF3.pl'}; do
+    for i in {blastp,hmmsearch,hmmscan,augustus,'gmes_petap.pl',mummer,nucmer,show-coords,exonerate,gmap,blat,RepeatModeler,RepeatMasker,pslCDnaFilter,bedtools,bamtools,'gag.py',tbl2asn,'braker.pl',funannotate,mafft,trimal,raxmlHPC-PTHREADS,tRNAscan-SE,'rmOutToGFF3.pl'}; do
         var=$(command -v $i)
         if [ "$var" ]; then
             echo "$i installed.........$var"

util/fgenesh2gff3.py

@@ -37,17 +37,22 @@
         sys.stdout.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (scaffold, 'FGENESH', 'gene', genestart, genestop, '.', strand, '.', 'ID='+k+';'))
         sys.stdout.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (scaffold, 'FGENESH', 'mRNA', genestart, genestop, '.', strand, '.', 'ID='+k+'-T1;Parent='+k+';'))
         last_index = len(v)
-        for i in range(0,last_index):
-            start = v[i][0]
-            stop = v[i][1]
-            if i == 0: #first CDS, set phase to 0, calculate next phase
-                phase = '0'
+        phase = 0
+        if strand == '+':
+            for i in range(0,last_index):
+                start = v[i][0]
+                stop = v[i][1]
+                 sys.stdout.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (scaffold, 'FGENESH', 'exon', start, stop, '.', strand, '.', 'ID='+k+':exon'+str(i+1)+';Parent='+k+'-T1;'))
+                sys.stdout.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (scaffold, 'FGENESH', 'CDS', start, stop, '.', strand, str(phase), 'ID=cds.'+k+';Parent='+k+'-T1;'))
                 diff = int(stop) - int(start) + 1
                 next_phase = (int(phase) - diff) % 3
-            else:
-                phase = next_phase
+                phase = next_phase         
+        else:
+            for i in reversed(range(0,last_index)):
+                start = v[i][0]
+                stop = v[i][1]
+                sys.stdout.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (scaffold, 'FGENESH', 'exon', start, stop, '.', strand, '.', 'ID='+k+':exon'+str(i+1)+';Parent='+k+'-T1;'))
+                sys.stdout.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (scaffold, 'FGENESH', 'CDS', start, stop, '.', strand, phase, 'ID=cds.'+k+';Parent='+k+'-T1;'))
                 diff = int(stop) - int(start) + 1
                 next_phase = (int(phase) - diff) % 3
-
-            sys.stdout.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (scaffold, 'FGENESH', 'exon', start, stop, '.', strand, '.', 'ID='+k+':exon'+str(i+1)+';Parent='+k+'-T1;'))
-            sys.stdout.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (scaffold, 'FGENESH', 'CDS', start, stop, '.', strand, phase, 'ID=cds.'+k+';Parent='+k+'-T1;'))
+                phase = next_phase