From 0010b9d697aac6e1a8be989736a4da58d2aeec01 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Fri, 20 Aug 2010 16:25:56 +0000
Subject: [PATCH] fix bug in cds finding function.
---
src/include/ZMap/zmapFeature.h | 7 ++--
src/zmapFeature/zmapFeatureUtils.c | 63 +++++++++++++++++++++---------
2 files changed, 47 insertions(+), 23 deletions(-)
diff --git a/src/include/ZMap/zmapFeature.h b/src/include/ZMap/zmapFeature.h
index 26b42c99e..7f3faafaa 100755
--- a/src/include/ZMap/zmapFeature.h
+++ b/src/include/ZMap/zmapFeature.h
@@ -25,9 +25,9 @@
* Description: Data structures describing a sequence feature.
*
* HISTORY:
- * Last edited: Aug 18 12:30 2010 (edgrif)
+ * Last edited: Aug 18 12:52 2010 (edgrif)
* Created: Fri Jun 11 08:37:19 2004 (edgrif)
- * CVS info: $Id: zmapFeature.h,v 1.180 2010-08-18 11:31:41 edgrif Exp $
+ * CVS info: $Id: zmapFeature.h,v 1.181 2010-08-20 16:25:56 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_FEATURE_H
@@ -544,7 +544,6 @@ typedef struct ZMapFeatureStruct_
ZMapFeatureID db_id ; /* unique DB identifier, currently
unused but will be..... */
- /* THIS NEEDS TO GO.....AND ONLY BE HELD IN THE STYLE... */
ZMapStyleMode type ; /* Basic, transcript, alignment. */
@@ -553,7 +552,7 @@ typedef struct ZMapFeatureStruct_
"trans_splice_acceptor_site", this
might be recognised SO term or not. */
- // style id tp be removed when style fully working
+ // style id tp be removed when style fully working
GQuark style_id ; /* Style defining how this feature is processed.
(use Styles _unique_ id.) */
diff --git a/src/zmapFeature/zmapFeatureUtils.c b/src/zmapFeature/zmapFeatureUtils.c
index 9eb38e47c..b824c6cbe 100755
--- a/src/zmapFeature/zmapFeatureUtils.c
+++ b/src/zmapFeature/zmapFeatureUtils.c
@@ -27,9 +27,9 @@
*
* Exported functions: See ZMap/zmapFeature.h
* HISTORY:
- * Last edited: Aug 16 14:39 2010 (edgrif)
+ * Last edited: Aug 20 17:25 2010 (edgrif)
* Created: Tue Nov 2 2004 (rnc)
- * CVS info: $Id: zmapFeatureUtils.c,v 1.73 2010-08-18 11:31:41 edgrif Exp $
+ * CVS info: $Id: zmapFeatureUtils.c,v 1.74 2010-08-20 16:25:56 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -943,12 +943,8 @@ gboolean zMapFeatureExon2CDS(ZMapFeature feature,
cds_start = feature->feature.transcript.cds_start ;
cds_end = feature->feature.transcript.cds_end ;
-
- if (cds_start > exon_end || cds_end < exon_start)
- {
- ;
- }
- else
+
+ if (!(cds_start > exon_end || cds_end < exon_start))
{
/* Exon has a cds section so calculate it and find the exons phase. */
int start, end, phase ;
@@ -958,7 +954,7 @@ gboolean zMapFeatureExon2CDS(ZMapFeature feature,
*exon_cds_start = start ;
*exon_cds_end = end ;
*phase_out = phase ;
-
+
is_cds_exon = TRUE ;
}
}
@@ -1220,7 +1216,7 @@ static int findExon(ZMapFeature feature, int exon_start, int exon_end)
}
-/* Returns the coords (in reference coords) of the cds section of the given exon
+/* Returns the coords (in reference sequence coords) of the cds section of the given exon
* and also it's phase. */
static gboolean calcExonPhase(ZMapFeature feature, int exon_index,
int *exon_cds_start_out, int *exon_cds_end_out, int *phase_out)
@@ -1228,15 +1224,34 @@ static gboolean calcExonPhase(ZMapFeature feature, int exon_index,
gboolean result = FALSE ;
int cds_start, cds_end ;
GArray *exons ;
- int i ;
+ int i, incr, end ;
int cds_bases ;
+ gboolean first_exon ;
cds_start = feature->feature.transcript.cds_start ;
cds_end = feature->feature.transcript.cds_end ;
+ cds_bases = 0 ;
exons = feature->feature.transcript.exons ;
- cds_bases = 0 ;
- for (i = 0 ; i < exons->len && i <= exon_index ; i++)
+ first_exon = FALSE ;
+
+
+ /* Go forwards through exons for forward strand genes and backwards for
+ * reverse strand genes. */
+ if (feature->strand == ZMAPSTRAND_FORWARD)
+ {
+ i = 0 ;
+ end = feature->feature.transcript.exons->len - 1 ;
+ incr = 1 ;
+ }
+ else
+ {
+ i = exons->len - 1 ;
+ end = 0 ;
+ incr = -1 ;
+ }
+
+ for ( ; i != end ; i += incr)
{
ZMapSpan next_exon ;
@@ -1249,7 +1264,6 @@ static gboolean calcExonPhase(ZMapFeature feature, int exon_index,
else
{
int start, end, phase ;
- gboolean first_exon = FALSE ;
start = next_exon->x1 ;
end = next_exon->x2 ;
@@ -1257,18 +1271,27 @@ static gboolean calcExonPhase(ZMapFeature feature, int exon_index,
if (cds_start >= start && cds_start <= end)
{
start = cds_start ;
- first_exon = TRUE ;
+
+ if (feature->strand == ZMAPSTRAND_FORWARD)
+ first_exon = TRUE ;
}
if (cds_end >= start && cds_end <= end)
- end = cds_end ;
+ {
+ end = cds_end ;
+
+ if (feature->strand == ZMAPSTRAND_REVERSE)
+ first_exon = TRUE ;
+ }
if (i == exon_index)
{
+ /* The first exon must have phase 0 unless it has been annotated as
+ * starting with a different phase, all others are calculated from
+ * CDS bases so far. */
+
if (first_exon)
{
- /* The first exon must have phase 0 unless it has been annotated as
- * starting with a different phase. */
if (feature->feature.transcript.flags.start_not_found)
phase = feature->feature.transcript.start_phase ;
else
@@ -1276,7 +1299,7 @@ static gboolean calcExonPhase(ZMapFeature feature, int exon_index,
}
else
{
- phase = cds_bases % 3 ;
+ phase = (3 - (cds_bases % 3)) % 3 ;
}
*exon_cds_start_out = start ;
@@ -1290,6 +1313,8 @@ static gboolean calcExonPhase(ZMapFeature feature, int exon_index,
/* Keep a running count of bases so far, caculate phase of next exon from this. */
cds_bases += (end - start) + 1 ;
+
+ first_exon = FALSE ;
}
}
--
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