From 339ca84be94b76a9a22cbc12f0ff7c1f9011dfe7 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Wed, 11 Aug 2010 08:26:12 +0000
Subject: [PATCH] fix bug causing gff export to crash, missing styles list, fix
bugs in formatting _phase_ (not frame !).
---
src/zmapGFF/zmapGFF2Dumper.c | 77 ++++++++++++++++++++----------------
1 file changed, 43 insertions(+), 34 deletions(-)
diff --git a/src/zmapGFF/zmapGFF2Dumper.c b/src/zmapGFF/zmapGFF2Dumper.c
index a7dbdab2a..d5d6a32e1 100755
--- a/src/zmapGFF/zmapGFF2Dumper.c
+++ b/src/zmapGFF/zmapGFF2Dumper.c
@@ -21,25 +21,19 @@
* originated by
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk,
- * Malcolm Hinsley (Sanger Institute, UK) mh17@sanger.ac.uk
+ * Malcolm Hinsley (Sanger Institute, UK) mh17@sanger.ac.uk
*
* Description: Dumps the features within a given block as GFF v2
*
* Exported functions: See ZMap/zmapGFF.h
* HISTORY:
- * Last edited: Apr 22 14:46 2010 (edgrif)
+ * Last edited: Aug 11 09:09 2010 (edgrif)
* Created: Mon Nov 14 13:21:14 2005 (edgrif)
- * CVS info: $Id: zmapGFF2Dumper.c,v 1.21 2010-06-14 15:40:13 mh17 Exp $
+ * CVS info: $Id: zmapGFF2Dumper.c,v 1.22 2010-08-11 08:26:12 edgrif Exp $
*-------------------------------------------------------------------
*/
#include <ZMap/zmap.h>
-
-
-
-
-
-
#include <ZMap/zmapUtils.h>
#include <ZMap/zmapFeature.h>
#include <ZMap/zmapGFF.h>
@@ -54,7 +48,7 @@
#define GFF_END "%d"
#define GFF_SCORE "%g"
#define GFF_STRAND "%c"
-#define GFF_FRAME "%c"
+#define GFF_PHASE "%c"
#define GFF_ATTRIBUTES "%s"
#define GFF_ATTRIBUTE_SEPARATOR ';'
@@ -69,12 +63,13 @@ GFF_SOURCE GFF_SEPARATOR \
GFF_FEATURE GFF_SEPARATOR \
GFF_START GFF_SEPARATOR \
GFF_END
-#define GFF_SEP_SCORE GFF_SEPARATOR GFF_SCORE
-#define GFF_SEP_NOSCORE GFF_SEPARATOR "%c"
-#define GFF_STRAND_FRAME GFF_SEPARATOR GFF_STRAND GFF_SEPARATOR GFF_FRAME
+#define GFF_SEP_SCORE GFF_SEPARATOR GFF_SCORE
+#define GFF_SEP_NOSCORE GFF_SEPARATOR "%c"
+#define GFF_SEP_STRAND GFF_SEPARATOR GFF_STRAND
+#define GFF_SEP_PHASE GFF_SEPARATOR GFF_PHASE
#define GFF_SEP_ATTRIBUTES GFF_SEPARATOR GFF_ATTRIBUTES
-#define GFF_OBLIGATORY GFF_SEQ_SOURCE_FEAT_START_END GFF_SEP_SCORE GFF_STRAND_FRAME
-#define GFF_OBLIGATORY_NOSCORE GFF_SEQ_SOURCE_FEAT_START_END GFF_SEP_NOSCORE GFF_STRAND_FRAME
+#define GFF_OBLIGATORY GFF_SEQ_SOURCE_FEAT_START_END GFF_SEP_SCORE GFF_STRAND_FRAME
+#define GFF_OBLIGATORY_NOSCORE GFF_SEQ_SOURCE_FEAT_START_END GFF_SEP_NOSCORE GFF_SEP_STRAND GFF_SEP_PHASE
#define GFF_FULL_LINE GFF_SEQ_SOURCE_FEAT_START_END GFF_SEP_SCORE GFF_STRAND_FRAME GFF_SEP_ATTRIBUTES
typedef struct _GFFDumpDataStruct *GFFDumpData;
@@ -322,14 +317,14 @@ gboolean zMapGFFDumpForeachList(ZMapFeatureAny first_feature, GHashTable *styles
if ((result = dump_full_header(first_feature, file, error_out, &int_sequence)))
{
- GFFDumpData gff_data = NULL;
-
- gff_data = g_new0(GFFDumpDataStruct, 1);
+ GFFDumpData gff_data ;
- gff_data->basic = basic_funcs_G;
- gff_data->transcript = transcript_funcs_G;
- gff_data->homol = homol_funcs_G;
- gff_data->text = text_funcs_G;
+ gff_data = g_new0(GFFDumpDataStruct, 1);
+ gff_data->basic = basic_funcs_G ;
+ gff_data->transcript = transcript_funcs_G ;
+ gff_data->homol = homol_funcs_G ;
+ gff_data->text = text_funcs_G ;
+ gff_data->styles = styles ;
/* This might get overwritten later, but as DumpToFile uses
* Subset, there's a chance it wouldn't get set at all */
@@ -338,6 +333,8 @@ gboolean zMapGFFDumpForeachList(ZMapFeatureAny first_feature, GHashTable *styles
result = zMapFeatureListForeachDumperCreate(dump_gff_cb, styles, gff_data, g_free,
file, error_out,
list_func_out, list_data_out) ;
+
+
}
}
@@ -489,30 +486,42 @@ static gboolean dump_gff_cb(ZMapFeatureAny feature_any,
style = zMapFindStyle(gff_data->styles, feature->style_id) ;
- /* Output a record for the whole feature, fields are:
- * <seqname> <source> <feature> <start> <end> <score> <strand> <frame> */
- if(!(gff_data->gff_source = (char *)zMapStyleGetGFFSource(style)))
- gff_data->gff_source = (char *)zMapStyleGetName(style);
- if(!(gff_data->gff_feature = (char *)zMapStyleGetGFFFeature(style)))
- gff_data->gff_feature = (char *)g_quark_to_string(feature->ontology);
- /* Obligatory fields. */
+ /* Output a GFFv2 record for the whole feature, fields are:
+ *
+ * <seqname> <source> <feature> <start> <end> <score> <strand> <phase> [attributes]
+ *
+ * i.e. all but [attributes] are mandatory.
+ */
+
+ /* Mandatory fields. */
+
+ if (!(gff_data->gff_source = (char *)zMapStyleGetGFFSource(style)))
+ gff_data->gff_source = (char *)zMapStyleGetName(style) ;
+
+ if (!(gff_data->gff_feature = (char *)zMapStyleGetGFFFeature(style)))
+ gff_data->gff_feature = (char *)g_quark_to_string(feature->ontology) ;
+
g_string_append_printf(gff_string,
GFF_SEQ_SOURCE_FEAT_START_END,
gff_data->gff_sequence, /* saves feature->parent->parent->parent->original_id */
gff_data->gff_source,
gff_data->gff_feature,
feature->x1,
- feature->x2);
+ feature->x2) ;
if (feature->flags.has_score)
g_string_append_printf(gff_string, GFF_SEP_SCORE, feature->score) ;
else
g_string_append_printf(gff_string, GFF_SEP_NOSCORE, '.') ;
- g_string_append_printf(gff_string, GFF_STRAND_FRAME,
- strand2Char(feature->strand),
- phase2Char(feature->phase)) ;
+ g_string_append_printf(gff_string, GFF_SEP_STRAND, strand2Char(feature->strand)) ;
+
+ g_string_append_printf(gff_string, GFF_SEP_PHASE,
+ ((feature->type == ZMAPSTYLE_MODE_TRANSCRIPT && feature->feature.transcript.flags.cds)
+ ? phase2Char(feature->feature.transcript.start_phase)
+ : '.')) ;
+
/* Now to the attribute fields, and any subparts... */
@@ -699,7 +708,7 @@ static gboolean dump_transcript_subpart_lines(ZMapFeature feature,
transcript->cds_end,
'.',
strand2Char(feature->strand),
- phase2Char(feature->phase)) ;
+ phase2Char(transcript->start_phase)) ;
result = dump_transcript_identifier(feature, transcript,
gff_string, error,
--
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