From 84bfea53ec8f36e4af0a82d0f6863e7f8c490dab Mon Sep 17 00:00:00 2001
From: rds <rds>
Date: Thu, 2 Jul 2009 22:21:32 +0000
Subject: [PATCH] implement sequence fetching from gff file
---
src/include/ZMap/zmapGFF.h | 6 +-
src/zmapGFF/zmapGFF2parser.c | 155 ++++++++++++++++++++-------
src/zmapGFF/zmapGFF_P.h | 12 ++-
src/zmapServer/file/fileServer.c | 176 +++++++++++++++++++++++++++++--
4 files changed, 301 insertions(+), 48 deletions(-)
diff --git a/src/include/ZMap/zmapGFF.h b/src/include/ZMap/zmapGFF.h
index 67b1be32a..d2dc7a0e2 100755
--- a/src/include/ZMap/zmapGFF.h
+++ b/src/include/ZMap/zmapGFF.h
@@ -28,9 +28,9 @@
* of ZMapFeatureStruct's, one for each GFF source.
*
* HISTORY:
- * Last edited: Apr 24 11:01 2009 (edgrif)
+ * Last edited: Jul 2 21:26 2009 (rds)
* Created: Sat May 29 13:18:32 2004 (edgrif)
- * CVS info: $Id: zmapGFF.h,v 1.17 2009-04-24 10:36:18 edgrif Exp $
+ * CVS info: $Id: zmapGFF.h,v 1.18 2009-07-02 22:22:53 rds Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_GFF_H
@@ -101,6 +101,8 @@ typedef struct
ZMapGFFParser zMapGFFCreateParser(GData *sources, gboolean parse_only) ;
gboolean zMapGFFParseHeader(ZMapGFFParser parser, char *line, gboolean *header_finished) ;
gboolean zMapGFFParseLine(ZMapGFFParser parser, char *line) ;
+gboolean zMapGFFParserSetSequenceFlag(ZMapGFFParser parser);
+ZMapSequence zMapGFFGetSequence(ZMapGFFParser parser);
void zMapGFFParseSetSourceHash(ZMapGFFParser parser,
GHashTable *source_2_feature_set, GHashTable *source_2_sourcedata) ;
void zMapGFFSetStopOnError(ZMapGFFParser parser, gboolean stop_on_error) ;
diff --git a/src/zmapGFF/zmapGFF2parser.c b/src/zmapGFF/zmapGFF2parser.c
index a033cdf5a..914d4ecca 100755
--- a/src/zmapGFF/zmapGFF2parser.c
+++ b/src/zmapGFF/zmapGFF2parser.c
@@ -26,9 +26,9 @@
*
* Exported functions: See ZMap/zmapGFF.h
* HISTORY:
- * Last edited: Jun 25 15:51 2009 (edgrif)
+ * Last edited: Jul 2 21:27 2009 (rds)
* Created: Fri May 28 14:25:12 2004 (edgrif)
- * CVS info: $Id: zmapGFF2parser.c,v 1.92 2009-06-25 14:56:28 edgrif Exp $
+ * CVS info: $Id: zmapGFF2parser.c,v 1.93 2009-07-02 22:21:59 rds Exp $
*-------------------------------------------------------------------
*/
@@ -159,6 +159,9 @@ ZMapGFFParser zMapGFFCreateParser(GData *sources, gboolean parse_only)
}
+ parser->parsed_sequence.raw_line_data = g_string_sized_new(2000);
+ parser->parsed_sequence.finished = TRUE; /* default we don't parse the dna/protein */
+
/* Allocated dynamically as these fields in GFF can be big. */
parser->attributes_str = g_string_sized_new(GFF_MAX_FREETEXT_CHARS) ;
parser->comments_str = g_string_sized_new(GFF_MAX_FREETEXT_CHARS) ;
@@ -338,6 +341,38 @@ ZMapGFFHeader zMapGFFGetHeader(ZMapGFFParser parser)
return header ;
}
+gboolean zMapGFFParserSetSequenceFlag(ZMapGFFParser parser)
+{
+ gboolean set = TRUE;
+
+ parser->parsed_sequence.finished = FALSE;
+
+ return set;
+}
+
+ZMapSequence zMapGFFGetSequence(ZMapGFFParser parser)
+{
+ ZMapSequence sequence = NULL;
+
+ if(parser->done_header)
+ {
+ /* parsed_sequence.raw_line_data == NULL means we got to the end-XXXXXX */
+
+ if(parser->parsed_sequence.seq_data.type != ZMAPSEQUENCE_NONE &&
+ parser->parsed_sequence.seq_data.sequence != NULL &&
+ parser->parsed_sequence.raw_line_data == NULL)
+ {
+ sequence = g_new0(ZMapSequenceStruct, 1);
+ *sequence = parser->parsed_sequence.seq_data;
+ sequence->name = g_quark_from_string(parser->sequence_name);
+ /* So we don't copy empty data */
+ parser->parsed_sequence.seq_data.type = ZMAPSEQUENCE_NONE;
+ parser->parsed_sequence.seq_data.sequence = NULL; /* So it doesn't get free'd */
+ }
+ }
+
+ return sequence;
+}
void zMapGFFFreeHeader(ZMapGFFHeader header)
{
@@ -375,39 +410,6 @@ gboolean zMapGFFGetFeatures(ZMapGFFParser parser, ZMapFeatureBlock feature_block
}
-#ifdef RDS_NO_TO_HACKED_CODE
-/* HACKED CODE TO FIX UP LINKS IN BLOCK->SET->FEATURE */
-static void setBlock(GQuark key_id, gpointer data, gpointer user_data)
-{
- ZMapFeatureSet feature_set = (ZMapFeatureSet)data ;
-#ifdef RDS_DONT_INCLUDE
- ZMapFeatureBlock feature_block = (ZMapFeatureBlock)user_data ;
-
- feature_set->parent = (ZMapFeatureAny)feature_block ;
- zMapFeatureBlockAddFeatureSet(feature_block, feature_set);
-#endif
-
- g_datalist_foreach(&(feature_set->features), setSet, feature_set) ;
-
- return ;
-}
-
-static void setSet(GQuark key_id, gpointer data, gpointer user_data)
-{
- ZMapFeature feature = (ZMapFeature)data ;
- ZMapFeatureSet feature_set = (ZMapFeatureSet)user_data ;
-
-#ifdef RDS_DONT_INCLUDE
- feature->parent = (ZMapFeatureAny)feature_set ;
-#endif
- zMapFeatureSetAddFeature(feature_set, feature);
-
- return ;
-}
-/* END OF HACKED CODE TO FIX UP LINKS IN BLOCK->SET->FEATURE */
-#endif
-
-
/* Optionally set mappings that are keys from the GFF source to feature set and style names. */
void zMapGFFParseSetSourceHash(ZMapGFFParser parser,
GHashTable *source_2_feature_set, GHashTable *source_2_sourcedata)
@@ -722,9 +724,87 @@ static gboolean parseHeaderLine(ZMapGFFParser parser, char *line)
}
}
+ else if(!parser->parsed_sequence.finished)
+ {
+ if(g_str_has_prefix(line, "##Type"))
+ {
+ char seq_type[11] = {'\0'};
+ fields = 2;
+ format_str = "%*6s%10s";
+ if((fields = sscanf(line, format_str, &seq_type)) != 2)
+ {
+ parser->error = g_error_new(parser->error_domain, ZMAP_GFF_ERROR_HEADER,
+ "Bad ##Type line %d: \"%s\"",
+ parser->line_count, line);
+ }
+ else
+ {
+ if(g_ascii_strcasecmp(seq_type, "DNA") == 0)
+ {
+ parser->parsed_sequence.seq_data.type = ZMAPSEQUENCE_DNA;
+ }
+ else if(g_ascii_strcasecmp(seq_type, "Protein"))
+ {
+ parser->parsed_sequence.seq_data.type = ZMAPSEQUENCE_PEPTIDE;
+ }
+ }
+ }
- if (parser->done_version && parser->done_source && parser->done_sequence_region)
- parser->done_header = TRUE ;
+ if(!parser->parsed_sequence.in_sequence_block)
+ {
+ gboolean in_block = FALSE;
+
+ if((parser->parsed_sequence.seq_data.type == ZMAPSEQUENCE_NONE))
+ {
+ if(g_str_has_prefix(line, "##DNA"))
+ parser->parsed_sequence.seq_data.type = ZMAPSEQUENCE_DNA;
+ else if(g_str_has_prefix(line, "##Protein"))
+ parser->parsed_sequence.seq_data.type = ZMAPSEQUENCE_PEPTIDE;
+ }
+
+ if(g_str_has_prefix(line, "##DNA") && parser->parsed_sequence.seq_data.type == ZMAPSEQUENCE_DNA)
+ {
+ in_block = TRUE;
+ }
+ else if(g_str_has_prefix(line, "##Protein") && parser->parsed_sequence.seq_data.type == ZMAPSEQUENCE_PEPTIDE)
+ {
+ in_block = TRUE;
+ }
+
+ parser->parsed_sequence.in_sequence_block = in_block;
+ }
+ else if(g_str_has_prefix(line, "##end-")) /* I don't think we really need to care about matching type */
+ {
+ parser->parsed_sequence.seq_data.length = parser->parsed_sequence.raw_line_data->len;
+ parser->parsed_sequence.seq_data.sequence = g_string_free(parser->parsed_sequence.raw_line_data, FALSE);
+ parser->parsed_sequence.raw_line_data = NULL;
+ parser->parsed_sequence.finished = TRUE;
+ }
+ else
+ {
+ char *line_ptr = line;
+ /* must be sequence */
+ line_ptr+=2; /* move past ## */
+ /* save the string */
+ g_string_append(parser->parsed_sequence.raw_line_data, line_ptr);
+ }
+ }
+
+ if (parser->done_version && parser->done_source && parser->done_sequence_region &&
+ parser->parsed_sequence.finished)
+ {
+ parser->done_header = TRUE ;
+
+ if((parser->parsed_sequence.seq_data.type == ZMAPSEQUENCE_DNA) &&
+ (parser->features_end - parser->features_start + 1) != parser->parsed_sequence.seq_data.length)
+ {
+ parser->error = g_error_new(parser->error_domain, ZMAP_GFF_ERROR_HEADER,
+ "##sequence-region length [%d] does not match DNA base count [%d].",
+ (parser->features_end - parser->features_start + 1),
+ parser->parsed_sequence.seq_data.length);
+ }
+
+ }
}
@@ -1805,7 +1885,6 @@ static gboolean getAssemblyPathAttrs(char *attributes, char **assembly_name_unus
{
gboolean result = TRUE ;
char *tag_pos ;
- int start = 0, end = 0 ;
ZMapStrand strand ;
int length = 0 ;
GArray *path = NULL ;
diff --git a/src/zmapGFF/zmapGFF_P.h b/src/zmapGFF/zmapGFF_P.h
index a099777d4..815e86074 100755
--- a/src/zmapGFF/zmapGFF_P.h
+++ b/src/zmapGFF/zmapGFF_P.h
@@ -25,9 +25,9 @@
* Description: Internal types, functions etc. for the GFF parser,
* currently this parser only does GFF v2.
* HISTORY:
- * Last edited: Mar 30 11:11 2009 (edgrif)
+ * Last edited: Jul 2 12:06 2009 (rds)
* Created: Sat May 29 13:18:32 2004 (edgrif)
- * CVS info: $Id: zmapGFF_P.h,v 1.18 2009-04-06 13:10:53 edgrif Exp $
+ * CVS info: $Id: zmapGFF_P.h,v 1.19 2009-07-02 22:22:08 rds Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_GFF_P_H
@@ -141,6 +141,14 @@ typedef struct ZMapGFFParserStruct_
GString *attributes_str ;
GString *comments_str ;
+ struct
+ {
+ GString *raw_line_data;
+ ZMapSequenceStruct seq_data;
+ unsigned int in_sequence_block : 1;
+ unsigned int finished :1;
+ }parsed_sequence;
+
} ZMapGFFParserStruct ;
diff --git a/src/zmapServer/file/fileServer.c b/src/zmapServer/file/fileServer.c
index 14eb9b6cf..048e43736 100755
--- a/src/zmapServer/file/fileServer.c
+++ b/src/zmapServer/file/fileServer.c
@@ -30,9 +30,9 @@
*
* Exported functions: See ZMap/zmapServerPrototype.h
* HISTORY:
- * Last edited: Jun 12 10:52 2009 (edgrif)
+ * Last edited: Jul 2 21:56 2009 (rds)
* Created: Fri Sep 10 18:29:18 2004 (edgrif)
- * CVS info: $Id: fileServer.c,v 1.38 2009-06-12 13:57:07 edgrif Exp $
+ * CVS info: $Id: fileServer.c,v 1.39 2009-07-02 22:21:32 rds Exp $
*-------------------------------------------------------------------
*/
@@ -452,17 +452,180 @@ static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFe
}
+static void eachBlockSequence(gpointer key, gpointer data, gpointer user_data)
+{
+ ZMapFeatureBlock feature_block = (ZMapFeatureBlock)data ;
+ GetFeatures get_features = (GetFeatures)user_data ;
+
+ if (get_features->result == ZMAP_SERVERRESPONSE_OK)
+ {
+ ZMapSequence sequence;
+ if(!(sequence = zMapGFFGetSequence(get_features->parser)))
+ {
+ GError *error;
+ error = zMapGFFGetError(get_features->parser);
+ setErrMsg(get_features->server,
+ g_strdup_printf("zMapGFFGetSequence() failed, error=%s",
+ error->message));
+ ZMAPSERVER_LOG(Warning, FILE_PROTOCOL_STR,
+ get_features->server->file_path,
+ "%s", get_features->server->last_err_msg);
+ }
+ else
+ {
+ ZMapFeatureContext context;
+ ZMapFeatureSet feature_set;
+
+ if(zMapFeatureDNACreateFeatureSet(feature_block, &feature_set))
+ {
+ ZMapFeatureTypeStyle dna_style = NULL;
+ ZMapFeature feature;
+
+ /* This temp style creation feels wrong, and probably is,
+ * but we don't have the merged in default styles in here,
+ * or so it seems... */
+ dna_style = zMapStyleCreate(ZMAP_FIXED_STYLE_DNA_NAME,
+ ZMAP_FIXED_STYLE_DNA_NAME_TEXT);
+
+ feature = zMapFeatureDNACreateFeature(feature_block, dna_style,
+ sequence->sequence, sequence->length);
+
+ zMapStyleDestroy(dna_style);
+ }
+
+ context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)feature_block,
+ ZMAPFEATURE_STRUCT_CONTEXT) ;
+
+ /* I'm going to create the three frame translation up front! */
+ if (zMap_g_list_find_quark(context->feature_set_names, zMapStyleCreateID(ZMAP_FIXED_STYLE_3FT_NAME)))
+ {
+ if ((zMapFeature3FrameTranslationCreateSet(feature_block, &feature_set)))
+ {
+ ZMapFeatureTypeStyle frame_style = NULL;
+
+ frame_style = zMapStyleCreate(ZMAP_FIXED_STYLE_DNA_NAME,
+ ZMAP_FIXED_STYLE_DNA_NAME_TEXT);
+
+ zMapFeature3FrameTranslationSetCreateFeatures(feature_set, frame_style);
+
+ zMapStyleDestroy(frame_style);
+ }
+ }
+
+ g_free(sequence);
+ }
+ }
+
+ return ;
+}
+
+/* Process all the alignments in a context. */
+static void eachAlignmentSequence(gpointer key, gpointer data, gpointer user_data)
+{
+ ZMapFeatureAlignment alignment = (ZMapFeatureAlignment)data ;
+ GetFeatures get_features = (GetFeatures)user_data ;
+
+ if (get_features->result == ZMAP_SERVERRESPONSE_OK)
+ g_hash_table_foreach(alignment->blocks, eachBlockSequence, (gpointer)get_features) ;
+
+ return ;
+}
/* We don't support this for now... */
static ZMapServerResponseType getContextSequence(void *server_in, GData *styles, ZMapFeatureContext feature_context_out)
{
- ZMapServerResponseType result = ZMAP_SERVERRESPONSE_OK ;
+ FileServer server = (FileServer)server_in ;
+ GetFeaturesStruct get_features ;
+ GIOStatus status ;
+ gsize terminator_pos = 0 ;
+ GError *gff_file_err = NULL ;
+ GError *error = NULL ;
+ get_features.result = ZMAP_SERVERRESPONSE_OK ;
+ get_features.server = (FileServer)server_in ;
- result = ZMAP_SERVERRESPONSE_UNSUPPORTED ;
+ get_features.parser = zMapGFFCreateParser(styles, FALSE) ;
+ /* FALSE => do the real parse. */
+ zMapGFFParserSetSequenceFlag(get_features.parser);
+ get_features.gff_line = g_string_sized_new(2000) ; /* Probably not many lines will be >
+ 2k chars. */
+ g_io_channel_seek_position(server->gff_file, 0, G_SEEK_SET, &gff_file_err);
- return result ;
+ /* Read the header, needed for feature coord range. */
+ while ((status = g_io_channel_read_line_string(server->gff_file, get_features.gff_line,
+ &terminator_pos,
+ &gff_file_err)) == G_IO_STATUS_NORMAL)
+ {
+ gboolean done_header = FALSE ;
+
+ *(get_features.gff_line->str + terminator_pos) = '\0' ; /* Remove terminating newline. */
+
+ if (zMapGFFParseHeader(get_features.parser, get_features.gff_line->str, &done_header))
+ {
+ if (done_header)
+ break ;
+ else
+ get_features.gff_line = g_string_truncate(get_features.gff_line, 0) ;
+ /* Reset line to empty. */
+ }
+ else
+ {
+ if (!done_header)
+ {
+ error = zMapGFFGetError(get_features.parser) ;
+
+ if (!error)
+ {
+ /* SHOULD ABORT HERE.... */
+ setErrMsg(server,
+ g_strdup_printf("zMapGFFParseLine() failed with no GError for line %d: %s",
+ zMapGFFGetLineNumber(get_features.parser), get_features.gff_line->str)) ;
+ ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
+ "%s", server->last_err_msg) ;
+ }
+ else
+ {
+ /* If the error was serious we stop processing and return the error,
+ * otherwise we just log the error. */
+ if (zMapGFFTerminated(get_features.parser))
+ {
+ get_features.result = ZMAP_SERVERRESPONSE_REQFAIL ;
+ setErrMsg(server, g_strdup_printf("GFFTerminated! %s", error->message)) ;
+ ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
+ "%s", server->last_err_msg) ; }
+ else
+ {
+ setErrMsg(server,
+ g_strdup_printf("zMapGFFParseHeader() failed for line %d: %s",
+ zMapGFFGetLineNumber(get_features.parser),
+ get_features.gff_line->str)) ;
+ ZMAPSERVER_LOG(Critical, FILE_PROTOCOL_STR, server->file_path,
+ "%s", server->last_err_msg) ;
+ }
+ }
+ get_features.result = ZMAP_SERVERRESPONSE_REQFAIL ;
+ }
+
+ break ;
+ }
+ }
+
+ if (get_features.result == ZMAP_SERVERRESPONSE_OK)
+ {
+ /* Fetch all the alignment blocks for all the sequences, this all hacky right now as really.
+ * we would have to parse and reparse the file....can be done but not needed this second. */
+ g_hash_table_foreach(feature_context_out->alignments, eachAlignmentSequence, (gpointer)&get_features) ;
+
+ }
+
+
+ /* Clear up. */
+ zMapGFFDestroyParser(get_features.parser) ;
+ g_string_free(get_features.gff_line, TRUE) ;
+
+
+ return get_features.result ;
}
@@ -556,6 +719,8 @@ static void addMapping(ZMapFeatureContext feature_context, ZMapGFFHeader header)
feature_context->sequence_to_parent.p2 = feature_context->sequence_to_parent.c2
= feature_block->block_to_sequence.q2 = feature_block->block_to_sequence.t2 ;
+
+ feature_context->length = feature_context->sequence_to_parent.c2 - feature_context->sequence_to_parent.c1 + 1;
return ;
}
@@ -618,7 +783,6 @@ static void eachBlock(gpointer key, gpointer data, gpointer user_data)
}
-
static gboolean sequenceRequest(FileServer server, ZMapGFFParser parser, GString* gff_line,
ZMapFeatureBlock feature_block)
{
--
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