From 6f6555a05f4505bcc327588e2186f8ebfa29d76e Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Wed, 18 Aug 2010 11:40:16 +0000
Subject: [PATCH] Add gffv3 format to blixem temp file formats, some
restructuring of code.
---
src/zmapView/zmapViewCallBlixem.c | 1392 +++++++++++++++++++----------
1 file changed, 944 insertions(+), 448 deletions(-)
diff --git a/src/zmapView/zmapViewCallBlixem.c b/src/zmapView/zmapViewCallBlixem.c
index c96a8060d..4abb65176 100755
--- a/src/zmapView/zmapViewCallBlixem.c
+++ b/src/zmapView/zmapViewCallBlixem.c
@@ -22,7 +22,7 @@
*
* 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: prepares input files in FASTA, seqbl and exblx format
* and then passes them to blixem for display.
@@ -30,33 +30,29 @@
* Exported functions: see zmapView_P.h
*
* HISTORY:
- * Last edited: Jul 29 12:33 2010 (edgrif)
+ * Last edited: Aug 18 11:55 2010 (edgrif)
* Created: Thu Jun 28 18:10:08 2007 (edgrif)
- * CVS info: $Id: zmapViewCallBlixem.c,v 1.33 2010-07-29 11:40:35 edgrif Exp $
+ * CVS info: $Id: zmapViewCallBlixem.c,v 1.34 2010-08-18 11:40:16 edgrif Exp $
*-------------------------------------------------------------------
*/
-#include <ZMap/zmap.h>
-
-
-
-
-
-
#include <unistd.h> /* for getlogin() */
#include <string.h> /* for memcpy */
#include <sys/types.h> /* for chmod() */
#include <sys/stat.h> /* for chmod() */
#include <glib.h>
+#include <ZMap/zmap.h>
#include <zmapView_P.h>
#include <ZMap/zmapUtils.h>
#include <ZMap/zmapGLibUtils.h>
#include <ZMap/zmapConfigIni.h>
#include <ZMap/zmapConfigStrings.h>
-
#include <ZMap/zmapThreads.h> // for thread lock functions
+
+
+
#define ZMAP_BLIXEM_CONFIG "blixem"
#define BLIX_NB_PAGE_GENERAL "General"
@@ -87,7 +83,24 @@ enum
BLX_ARGV_FASTA_FILE, /* [fasta file] */
BLX_ARGV_EXBLX_FILE, /* [exblx file] */
BLX_ARGV_ARGC /* argc ;) */
- };
+ } ;
+
+
+typedef enum {BLX_FILE_FORMAT_INVALID, BLX_FILE_FORMAT_EXBLX, BLX_FILE_FORMAT_GFF} BlixemFileFormat ;
+
+
+
+/* Data needed by GFF formatting routines. */
+typedef struct GFFFormatDataStructType
+{
+ gboolean use_SO_ids ; /* TRUE => use accession ids. */
+ gboolean maximise_ids ; /* Give every feature an id. */
+
+ int alignment_count ;
+ int transcript_count ;
+ int exon_count ;
+} GFFFormatDataStruct, *GFFFormatData ;
+
/* Control block for preparing data to call blixem. */
@@ -97,26 +110,27 @@ typedef struct BlixemDataStruct
gboolean kill_on_exit ; /* TRUE => remove this blixem on
program exit (default). */
- gchar *script; /* script to call blixem standalone */
+ gchar *script; /* script to call blixem standalone */
char *config_file ; /* Contains blixem config. information. */
- gchar *netid; /* eg pubseq */
- int port; /* eg 22100 */
+ gchar *netid; /* eg pubseq */
+ int port; /* eg 22100 */
- int scope; /* defaults to 40000 */
- int homol_max; /* score cutoff point */
+ int scope; /* defaults to 40000 */
+ int homol_max; /* score cutoff point */
char *opts;
+ void *format_data ; /* Some formats need "callback" data. */
+ BlixemFileFormat file_format ;
char *tmpDir ;
gboolean keep_tmpfiles ;
- GIOChannel *curr_channel;
-
char *fastAFile ;
GIOChannel *fasta_channel;
char *errorMsg;
+
char *exblxFile ;
GIOChannel *exblx_channel;
char *exblx_errorMsg;
@@ -124,10 +138,12 @@ typedef struct BlixemDataStruct
GIOChannel *seqbl_channel ;
char *seqbl_errorMsg ;
+ char *gff_file ;
+ GIOChannel *gff_channel ;
+ char *gff_errorMsg ;
ZMapView view;
-
ZMapFeature feature ;
ZMapFeatureBlock block ;
GHashTable *known_sequences ; /* Used to check if we already have a sequence. */
@@ -179,6 +195,8 @@ typedef struct
collected to send to blixem, defaults to 40000 */
int homol_max ; /* defines max. number of aligns sent
to blixem. */
+
+ BlixemFileFormat file_format ;
gboolean keep_tmpfiles ;
/* Not user configurable */
@@ -194,7 +212,7 @@ typedef struct
static gboolean initBlixemData(ZMapView view, ZMapFeature feature, blixemData blixem_data, char **err_msg) ;
static gboolean addFeatureDetails(blixemData blixem_data) ;
static gboolean buildParamString (blixemData blixem_data, char **paramString);
-static void freeBlixemData (blixemData blixem_data);
+static void freeBlixemData(blixemData blixem_data);
static void setPrefs(BlixemConfigData curr_prefs, blixemData blixem_data) ;
static gboolean getUserPrefs(BlixemConfigData prefs) ;
@@ -210,15 +228,41 @@ static void writeHashEntry(gpointer key, gpointer data, gpointer user_data) ;
static void writeListEntry(gpointer data, gpointer user_data) ;
static gboolean writeFastAFile(blixemData blixem_data);
+static gboolean writeFeatureFiles(blixemData blixem_data);
+static gboolean initFeatureFile(char *filename, char *file_header, GString *buffer,
+ GIOChannel **gio_channel_out, blixemData blixem_data) ;
-static gboolean writeExblxSeqblFiles(blixemData blixem_data);
-
-static void writeExblxSeqblLine(ZMapFeature feature, blixemData blixem_data) ;
-
+static void writeFeatureLine(ZMapFeature feature, blixemData blixem_data) ;
static gboolean printAlignment(ZMapFeature feature, blixemData blixem_data) ;
+static gboolean formatAlignmentExbl(GString *line,
+ int min_range, int max_range,
+ char *match_name,
+ int qstart, int qend, ZMapStrand q_strand, int qframe,
+ int sstart, int send, ZMapStrand s_strand, int sframe,
+ float score, GArray *gaps, char *sequence, char *description) ;
+static gboolean formatAlignmentGFF(GFFFormatData gff_data, GString *line,
+ int min_range, int max_range,
+ char *ref_name, char *match_name, char *source_name, ZMapHomolType homol_type,
+ int qstart, int qend, ZMapStrand q_strand,
+ int sstart, int send, ZMapStrand s_strand,
+ float score, GArray *gaps, char *sequence, char *description) ;
static gboolean printTranscript(ZMapFeature feature, blixemData blixem_data) ;
-static gboolean printLine(blixemData blixem_data, char *line) ;
static gboolean processExons(blixemData blixem_data, ZMapFeature feature, gboolean cds_only) ;
+static gboolean formatTranscriptExblx(GString *line, int min, int max,
+ char *transcript_name,
+ float score,
+ int exon_base, int exon_start, int exon_end,
+ int qstart, int qend, int qstrand,
+ int sstart, int send) ;
+static gboolean formatTranscriptGFF(GFFFormatData gff_data, GString *line, int min, int max,
+ char *ref_name, char *source_name,
+ ZMapFeature feature, char *transcript_name,
+ int exon_start, int exon_end,
+ int qstart, int qend, int qstrand,
+ int sstart, int send) ;
+static gboolean printTranscriptExtrasExblx(ZMapFeature feature, blixemData blixem_data, gboolean cds_only) ;
+
+static gboolean printLine(GIOChannel *gio_channel, char **err_msg_out, char *line) ;
static int findFeature(gconstpointer a, gconstpointer b) ;
static void freeSequences(gpointer data, gpointer user_data_unused) ;
@@ -234,49 +278,22 @@ static void getFeatureCB(gpointer key, gpointer data, gpointer user_data) ;
static gint scoreOrderCB(gconstpointer a, gconstpointer b) ;
+/*
+ * Globals
+ */
/* Global for hanging on to current configuration. */
static BlixemConfigDataStruct blixem_config_curr_G = {FALSE} ;
-
static gboolean debug_G = TRUE ;
-/* Returns a ZMapGuiNotebookChapter containing all user settable blixem resources. */
-ZMapGuiNotebookChapter zMapViewBlixemGetConfigChapter(ZMapGuiNotebook note_book_parent)
-{
- ZMapGuiNotebookChapter chapter = NULL ;
- gboolean status = TRUE ;
-
-
- /* If the current configuration has not been set yet then read stuff from the config file. */
- if (!blixem_config_curr_G.init)
- {
- status = getUserPrefs(&blixem_config_curr_G);
- if(!status)
- {
- /* ensure data struct is safe
- * -> if read fails then options are zero
- * -> if option not configured likewise
- * make the dialog even if options not set so that they can fix it
- */
-
- // null values for strings should be ok, they are programmed by low level cGUINotebook functions
-
- }
- }
-
- chapter = makeChapter(note_book_parent) ; // mh17: this uses blixen_config_curr_G
- return chapter ;
-}
-gboolean zMapViewBlixemGetConfigFunctions(ZMapView view, gpointer *edit_func,
- gpointer *apply_func, gpointer save_func, gpointer *data)
-{
+/*
+ * External routines
+ */
- return TRUE;
-}
gboolean zmapViewBlixemLocalSequences(ZMapView view, ZMapFeature feature, GList **local_sequences_out)
{
@@ -363,6 +380,7 @@ gboolean zmapViewCallBlixem(ZMapView view, ZMapFeature feature, GList *local_seq
{
gboolean status = TRUE ;
char *argv[BLX_ARGV_ARGC + 1] = {NULL} ;
+ GFFFormatDataStruct gff_data = {FALSE} ;
blixemDataStruct blixem_data = {0} ;
char *err_msg = "error in zmapViewCallBlixem()" ;
@@ -371,6 +389,9 @@ gboolean zmapViewCallBlixem(ZMapView view, ZMapFeature feature, GList *local_seq
status = initBlixemData(view, feature, &blixem_data, &err_msg) ;
+ if (blixem_data.file_format == BLX_FILE_FORMAT_GFF)
+ blixem_data.format_data = &gff_data ;
+
blixem_data.local_sequences = local_sequences ;
blixem_data.align_set = align_set;
@@ -384,7 +405,7 @@ gboolean zmapViewCallBlixem(ZMapView view, ZMapFeature feature, GList *local_seq
}
if (status)
- status = writeExblxSeqblFiles(&blixem_data);
+ status = writeFeatureFiles(&blixem_data);
if (status)
status = writeFastAFile(&blixem_data);
@@ -419,15 +440,16 @@ gboolean zmapViewCallBlixem(ZMapView view, ZMapFeature feature, GList *local_seq
printf("\n") ;
}
- zMapThreadForkLock();
- if(!(g_spawn_async(cwd, &argv[0], envp, flags, pre_exec, pre_exec_data, &spawned_pid, &error)))
+ if (!(g_spawn_async(cwd, &argv[0], envp, flags, pre_exec, pre_exec_data, &spawned_pid, &error)))
{
status = FALSE;
err_msg = error->message;
}
else
- zMapLogMessage("Blixem process spawned successfully. PID = '%d'", spawned_pid);
+ {
+ zMapLogMessage("Blixem process spawned successfully. PID = '%d'", spawned_pid);
+ }
zMapThreadForkUnlock();
@@ -448,6 +470,44 @@ gboolean zmapViewCallBlixem(ZMapView view, ZMapFeature feature, GList *local_seq
+/* Returns a ZMapGuiNotebookChapter containing all user settable blixem resources. */
+ZMapGuiNotebookChapter zMapViewBlixemGetConfigChapter(ZMapGuiNotebook note_book_parent)
+{
+ ZMapGuiNotebookChapter chapter = NULL ;
+ gboolean status = TRUE ;
+
+
+ /* If the current configuration has not been set yet then read stuff from the config file. */
+ if (!blixem_config_curr_G.init)
+ {
+ status = getUserPrefs(&blixem_config_curr_G);
+ if (!status)
+ {
+ /* ensure data struct is safe
+ * -> if read fails then options are zero
+ * -> if option not configured likewise
+ * make the dialog even if options not set so that they can fix it
+ */
+
+ // null values for strings should be ok, they are programmed by low level cGUINotebook functions
+
+ }
+ }
+
+ chapter = makeChapter(note_book_parent) ; // mh17: this uses blixen_config_curr_G
+
+ return chapter ;
+}
+
+gboolean zMapViewBlixemGetConfigFunctions(ZMapView view, gpointer *edit_func,
+ gpointer *apply_func, gpointer save_func, gpointer *data)
+{
+
+ return TRUE;
+}
+
+
+
/*
* Internal routines.
@@ -467,6 +527,8 @@ static gboolean initBlixemData(ZMapView view, ZMapFeature feature, blixemData bl
zMapAssert(block) ;
blixem_data->block = block ;
+ blixem_data->file_format = BLX_FILE_FORMAT_EXBLX ;
+
if (!(zMapFeatureBlockDNA(block, NULL, NULL, NULL)))
{
status = FALSE;
@@ -493,12 +555,12 @@ static void freeBlixemData(blixemData blixem_data)
g_free(blixem_data->fastAFile);
g_free(blixem_data->exblxFile);
g_free(blixem_data->seqbl_file);
+ g_free(blixem_data->gff_file);
g_free(blixem_data->netid);
g_free(blixem_data->script);
g_free(blixem_data->config_file);
-
if (blixem_data->dna_sets)
g_list_free(blixem_data->dna_sets) ;
if (blixem_data->protein_sets)
@@ -533,9 +595,14 @@ static void setPrefs(BlixemConfigData curr_prefs, blixemData blixem_data)
blixem_data->scope = curr_prefs->scope ;
if (curr_prefs->homol_max > 0)
blixem_data->homol_max = curr_prefs->homol_max ;
+
blixem_data->keep_tmpfiles = curr_prefs->keep_tmpfiles ;
+
blixem_data->kill_on_exit = curr_prefs->kill_on_exit ;
+ if (curr_prefs->file_format)
+ blixem_data->file_format = curr_prefs->file_format ;
+
if (blixem_data->dna_sets)
g_list_free(blixem_data->dna_sets) ;
if (curr_prefs->dna_sets)
@@ -559,60 +626,74 @@ static gboolean getUserPrefs(BlixemConfigData prefs)
ZMapConfigIniContext context = NULL;
gboolean status = FALSE;
- if((context = zMapConfigIniContextProvide()))
+ if ((context = zMapConfigIniContextProvide()))
{
char *tmp_string = NULL;
int tmp_int;
gboolean tmp_bool;
- if(zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
+ if (zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_NETID, &tmp_string))
prefs->netid = tmp_string;
- if(zMapConfigIniContextGetInt(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
+ if (zMapConfigIniContextGetInt(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_PORT, &tmp_int))
prefs->port = tmp_int;
- if(zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
+ if (zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_SCRIPT, &tmp_string))
prefs->script = tmp_string;
- if(zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
+ if (zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_CONF_FILE, &tmp_string))
prefs->config_file = tmp_string;
- if(zMapConfigIniContextGetInt(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
+ if (zMapConfigIniContextGetInt(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_SCOPE, &tmp_int))
prefs->scope = tmp_int;
- if(zMapConfigIniContextGetInt(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
+ if (zMapConfigIniContextGetInt(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_MAX, &tmp_int))
prefs->homol_max = tmp_int;
- if(zMapConfigIniContextGetBoolean(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
+ if (zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
+ ZMAPSTANZA_BLIXEM_FILE_FORMAT, &tmp_string))
+ {
+ g_strstrip(tmp_string) ;
+
+ if (g_ascii_strcasecmp(tmp_string, "exblx") == 0)
+ prefs->file_format = BLX_FILE_FORMAT_EXBLX ;
+ else if (g_ascii_strcasecmp(tmp_string, "gffv3") == 0)
+ prefs->file_format = BLX_FILE_FORMAT_GFF ;
+
+ g_free(tmp_string) ;
+ }
+
+
+ if (zMapConfigIniContextGetBoolean(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_KEEP_TEMP, &tmp_bool))
prefs->keep_tmpfiles = tmp_bool;
- if(zMapConfigIniContextGetBoolean(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
+ if (zMapConfigIniContextGetBoolean(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_KILL_EXIT, &tmp_bool))
prefs->kill_on_exit = tmp_bool;
- if(zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
+ if (zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_DNA_FS, &tmp_string))
{
prefs->dna_sets = zMapConfigString2QuarkList(tmp_string);
g_free(tmp_string);
}
- if(zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
+ if (zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_PROT_FS, &tmp_string))
{
prefs->protein_sets = zMapConfigString2QuarkList(tmp_string);
g_free(tmp_string);
}
- if(zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
- ZMAPSTANZA_BLIXEM_TRANS_FS, &tmp_string))
+ if (zMapConfigIniContextGetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
+ ZMAPSTANZA_BLIXEM_FS, &tmp_string))
{
prefs->transcript_sets = zMapConfigString2QuarkList(tmp_string);
g_free(tmp_string);
@@ -620,9 +701,7 @@ static gboolean getUserPrefs(BlixemConfigData prefs)
zMapConfigIniContextDestroy(context);
}
- if((prefs->script) &&
- ((prefs->config_file) ||
- (prefs->netid && prefs->port)))
+ if ((prefs->script) && ((prefs->config_file) || (prefs->netid && prefs->port)))
{
char *tmp;
tmp = prefs->script;
@@ -639,10 +718,12 @@ static gboolean getUserPrefs(BlixemConfigData prefs)
prefs->config_file) ;
}
else
- zMapShowMsg(ZMAP_MSG_WARNING, "Some or all of the compulsory blixem parameters "
- "(\"netid\", \"port\") or config_file or \"script\" are missing from your config file.");
+ {
+ zMapShowMsg(ZMAP_MSG_WARNING, "Some or all of the compulsory blixem parameters "
+ "(\"netid\", \"port\") or config_file or \"script\" are missing from your config file.");
+ }
- if(prefs->script && prefs->config_file)
+ if (prefs->script && prefs->config_file)
status = TRUE;
prefs->init = TRUE;
@@ -672,8 +753,10 @@ static gboolean addFeatureDetails(blixemData blixem_data)
blixem_data->max = x2 + (scope / 2) ;
if (blixem_data->min < 1)
blixem_data->min = 1 ;
+
// if (blixem_data->max > blixem_data->view->features->length)
// blixem_data->max = blixem_data->view->features->length ;
+
length = blixem_data->block->block_to_sequence.t2 - blixem_data->block->block_to_sequence.t1 + 1;
if (blixem_data->max > length)
blixem_data->max = length ;
@@ -768,20 +851,35 @@ static gboolean makeTmpfiles(blixemData blixem_data)
status = setTmpPerms(blixem_data->fastAFile, FALSE) ;
}
- /* Create the file to hold the features in exblx format. */
+ /* Create file(s) to hold features. */
if (status)
{
- if ((status = makeTmpfile(blixem_data->tmpDir, "exblx_x", &(blixem_data->exblxFile))))
- status = setTmpPerms(blixem_data->exblxFile, FALSE) ;
- }
+ if (blixem_data->file_format == BLX_FILE_FORMAT_EXBLX)
+ {
+ /* Create the file to hold the features in exblx format. */
+ if (status)
+ {
+ if ((status = makeTmpfile(blixem_data->tmpDir, "exblx_x", &(blixem_data->exblxFile))))
+ status = setTmpPerms(blixem_data->exblxFile, FALSE) ;
+ }
- /* Create the file to hold the features in seqbl format. */
- if (status)
- {
- if ((status = makeTmpfile(blixem_data->tmpDir, "seqbl_x", &(blixem_data->seqbl_file))))
- status = setTmpPerms(blixem_data->seqbl_file, FALSE) ;
+ /* Create the file to hold the features in seqbl format. */
+ if (status)
+ {
+ if ((status = makeTmpfile(blixem_data->tmpDir, "seqbl_x", &(blixem_data->seqbl_file))))
+ status = setTmpPerms(blixem_data->seqbl_file, FALSE) ;
+ }
+ }
+ else
+ {
+ {
+ if ((status = makeTmpfile(blixem_data->tmpDir, "gff", &(blixem_data->gff_file))))
+ status = setTmpPerms(blixem_data->gff_file, FALSE) ;
+ }
+ }
}
+
return status ;
}
@@ -834,7 +932,9 @@ static gboolean buildParamString(blixemData blixem_data, char **paramString)
paramString[BLX_ARGV_NETID_PORT] = g_strdup_printf("%s:%d", blixem_data->netid, blixem_data->port);
}
else
- missed += 2;
+ {
+ missed += 2;
+ }
/* For testing purposes remove the "-r" flag to leave the temporary files.
* (keep_tempfiles = true in blixem stanza of ZMap file) */
@@ -849,7 +949,9 @@ static gboolean buildParamString(blixemData blixem_data, char **paramString)
paramString[BLX_ARGV_START - missed] = g_strdup_printf("%d", start);
}
else
- missed += 2;
+ {
+ missed += 2;
+ }
if (blixem_data->offset)
{
@@ -857,7 +959,9 @@ static gboolean buildParamString(blixemData blixem_data, char **paramString)
paramString[BLX_ARGV_OFFSET - missed] = g_strdup_printf("%d", blixem_data->offset);
}
else
- missed += 2;
+ {
+ missed += 2;
+ }
if (blixem_data->opts)
{
@@ -865,75 +969,78 @@ static gboolean buildParamString(blixemData blixem_data, char **paramString)
paramString[BLX_ARGV_OPTIONS - missed] = g_strdup_printf("%s", blixem_data->opts);
}
else
- missed += 2;
+ {
+ missed += 2;
+ }
- if (blixem_data->seqbl_file)
+ if (blixem_data->file_format == BLX_FILE_FORMAT_EXBLX
+ && blixem_data->seqbl_file)
{
- paramString[BLX_ARGV_SEQBL_FLAG - missed] = g_strdup("-x");
+ paramString[BLX_ARGV_SEQBL_FLAG - missed] = g_strdup("-x");
paramString[BLX_ARGV_SEQBL - missed] = g_strdup_printf("%s", blixem_data->seqbl_file);
}
else
- missed += 2;
+ {
+ missed += 2;
+ }
paramString[BLX_ARGV_FASTA_FILE - missed] = g_strdup_printf("%s", blixem_data->fastAFile);
- paramString[BLX_ARGV_EXBLX_FILE - missed] = g_strdup_printf("%s", blixem_data->exblxFile);
+
+ if (blixem_data->file_format == BLX_FILE_FORMAT_EXBLX)
+ {
+ paramString[BLX_ARGV_EXBLX_FILE - missed] = g_strdup_printf("%s", blixem_data->exblxFile);
+ }
+ else
+ {
+ paramString[BLX_ARGV_EXBLX_FILE - missed] = g_strdup_printf("%s", blixem_data->gff_file) ;
+ }
}
return status ;
}
-static gboolean writeExblxSeqblFiles(blixemData blixem_data)
+static gboolean writeFeatureFiles(blixemData blixem_data)
{
- GError *channel_error = NULL ;
gboolean status = TRUE ;
+ GError *channel_error = NULL ;
gboolean seqbl_file = FALSE ;
+ char *header ;
- if (blixem_data->local_sequences)
- seqbl_file = TRUE ;
-
- /* We just use the one gstring as a reusable buffer to format all output. */
+ /* We just use the one gstring as a reusable buffer to format all output. */
blixem_data->line = g_string_new("") ;
- /* Open the exblx file, always needed. */
- if ((blixem_data->exblx_channel = g_io_channel_new_file(blixem_data->exblxFile, "w", &channel_error)))
+ if (blixem_data->file_format == BLX_FILE_FORMAT_EXBLX)
{
- g_string_printf(blixem_data->line, "# exblx_x\n# blast%c\n", *blixem_data->opts) ;
- blixem_data->curr_channel = blixem_data->exblx_channel ;
- status = printLine(blixem_data, blixem_data->line->str) ;
- blixem_data->line = g_string_truncate(blixem_data->line, 0) ;
- }
- else
- {
- zMapShowMsg(ZMAP_MSG_WARNING, "Error: could not open exblx file: %s",
- channel_error->message) ;
- g_error_free(channel_error) ;
- channel_error = NULL;
- status = FALSE ;
- }
+ /* Open the exblx file, always needed. */
+ header = g_strdup_printf("# exblx_x\n# blast%c\n", *blixem_data->opts) ;
+ status = initFeatureFile(blixem_data->exblxFile, header, blixem_data->line,
+ &(blixem_data->exblx_channel), blixem_data) ;
+ g_free(header) ;
- /* Open the seqbl file, if needed. */
- if (status)
- {
- if (seqbl_file)
+ /* Open the seqbl file, if needed. */
+ if (status)
{
- if ((blixem_data->seqbl_channel = g_io_channel_new_file(blixem_data->seqbl_file, "w", &channel_error)))
- {
- g_string_printf(blixem_data->line, "# seqbl_x\n# blast%c\n", *blixem_data->opts) ;
- blixem_data->curr_channel = blixem_data->seqbl_channel ;
- status = printLine(blixem_data, blixem_data->line->str) ;
- blixem_data->line = g_string_truncate(blixem_data->line, 0) ;
- }
- else
+ if (blixem_data->local_sequences)
+ seqbl_file = TRUE ;
+
+ if (seqbl_file)
{
- zMapShowMsg(ZMAP_MSG_WARNING, "Error: could not open seqbl file: %s",
- channel_error->message) ;
- g_error_free(channel_error) ;
- channel_error = NULL;
- status = FALSE ;
+ header = g_strdup_printf("# seqbl_x\n# blast%c\n", *blixem_data->opts) ;
+ status = initFeatureFile(blixem_data->seqbl_file, header, blixem_data->line,
+ &(blixem_data->seqbl_channel), blixem_data) ;
+ g_free(header) ;
}
}
}
+ else
+ {
+ header = g_strdup_printf("##gff-version 3\n##sequence-region %s %d %d\n",
+ g_quark_to_string(blixem_data->block->original_id), blixem_data->min, blixem_data->max) ;
+ status = initFeatureFile(blixem_data->gff_file, header, blixem_data->line,
+ &(blixem_data->gff_channel), blixem_data) ;
+ g_free(header) ;
+ }
if (status)
{
@@ -1071,6 +1178,34 @@ static gboolean writeExblxSeqblFiles(blixemData blixem_data)
return status ;
}
+/* HACK...try to get rid of blixem_data param...needs curr_channel to go... */
+/* Open and initially format a feature file. */
+static gboolean initFeatureFile(char *filename, char *file_header, GString *buffer,
+ GIOChannel **gio_channel_out, blixemData blixem_data)
+{
+ gboolean status = TRUE ;
+ GError *channel_error = NULL ;
+
+ /* Open the exblx file, always needed. */
+ if ((*gio_channel_out = g_io_channel_new_file(filename, "w", &channel_error)))
+ {
+ g_string_printf(buffer, "%s", file_header) ;
+
+ status = printLine(*gio_channel_out, &(blixem_data->errorMsg), buffer->str) ;
+
+ buffer = g_string_truncate(buffer, 0) ;
+ }
+ else
+ {
+ zMapShowMsg(ZMAP_MSG_WARNING, "Error: could not open file: %s", channel_error->message) ;
+ g_error_free(channel_error) ;
+ status = FALSE ;
+ }
+
+ return status ;
+}
+
+
/* A GFunc() to step through the named feature sets and write them out for passing
* to blixem. */
@@ -1081,7 +1216,7 @@ static void processSetList(gpointer data, gpointer user_data)
blixemData blixem_data = (blixemData)user_data ;
ZMapFeatureSet feature_set ;
- canon_id = zMapFeatureSetCreateID(g_quark_to_string(set_id)) ;
+ canon_id = zMapFeatureSetCreateID((char *)g_quark_to_string(set_id)) ;
if (!(feature_set = g_hash_table_lookup(blixem_data->block->feature_sets, GINT_TO_POINTER(canon_id))))
{
@@ -1106,7 +1241,7 @@ static void writeHashEntry(gpointer key, gpointer data, gpointer user_data)
ZMapFeature feature = (ZMapFeature)data ;
blixemData blixem_data = (blixemData)user_data ;
- writeExblxSeqblLine(feature, blixem_data) ;
+ writeFeatureLine(feature, blixem_data) ;
return ;
}
@@ -1116,20 +1251,19 @@ static void writeListEntry(gpointer data, gpointer user_data)
ZMapFeature feature = (ZMapFeature)data ;
blixemData blixem_data = (blixemData)user_data ;
- writeExblxSeqblLine(feature, blixem_data) ;
+ writeFeatureLine(feature, blixem_data) ;
return ;
}
-
-static void writeExblxSeqblLine(ZMapFeature feature, blixemData blixem_data)
+static void writeFeatureLine(ZMapFeature feature, blixemData blixem_data)
{
/* There is no way to interrupt g_hash_table_foreach() so instead if errorMsg is set
* then it means there was an error in processing so we don't process any
* more records, displaying the error when we return. */
- if (!blixem_data->errorMsg)
+ if (!(blixem_data->errorMsg))
{
/* Only process features we want to dump. We then filter those features according to the
* following rules (inherited from acedb): alignment features must be wholly within the
@@ -1175,9 +1309,7 @@ static gboolean printAlignment(ZMapFeature feature, blixemData blixem_data)
{
gboolean status = TRUE ;
int min, max ;
- int score = 0 ;
int qstart, qend, sstart, send ;
- char qframe_strand, sframe_strand ;
int qframe = 0, sframe = 0 ;
GString *line ;
int x1, x2 ;
@@ -1209,12 +1341,10 @@ static gboolean printAlignment(ZMapFeature feature, blixemData blixem_data)
* bases if that distance is not a whole number of codons. */
if (feature->strand == ZMAPSTRAND_REVERSE)
{
- qframe_strand = '-' ;
qframe = 1 + (((max - min + 1) - qstart) % 3) ;
}
else
{
- qframe_strand = '+' ;
qframe = 1 + ((qstart - 1) % 3) ;
}
@@ -1224,15 +1354,11 @@ static gboolean printAlignment(ZMapFeature feature, blixemData blixem_data)
if (feature->feature.homol.strand == ZMAPSTRAND_REVERSE)
{
- sframe_strand = '-' ;
-
if (feature->feature.homol.length)
sframe = (1 + ((feature->feature.homol.length) - sstart) % 3) ;
}
else
{
- sframe_strand = '+' ;
-
if (feature->feature.homol.length)
sframe = (1 + (sstart-1) % 3) ;
}
@@ -1253,186 +1379,696 @@ static gboolean printAlignment(ZMapFeature feature, blixemData blixem_data)
}
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ if (score)
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
- score = feature->score + 0.5 ; /* round up to integer ????????? */
-
- /* Is this test correct ? no I don't think so...test later.................. */
- if (score)
{
char *seq_str = NULL ;
char *description = NULL ; /* Unsupported currently. */
GList *list_ptr ;
+ char *match_name ;
+ char *source_name ;
+ GIOChannel *curr_channel ;
- if ((list_ptr = g_list_find_custom(blixem_data->local_sequences, feature, findFeature)))
- {
- ZMapSequence sequence = (ZMapSequence)list_ptr->data ;
+ match_name = (char *)g_quark_to_string(feature->original_id) ;
+ source_name = (char *)g_quark_to_string(feature->source_id) ;
- seq_str = sequence->sequence ;
- blixem_data->curr_channel = blixem_data->seqbl_channel ;
- }
- else
- {
- /* In theory we should be checking for a description for non-local sequences,
- * see acedb code in doShowAlign...don't know how important this is..... */
- seq_str = "" ;
- blixem_data->curr_channel = blixem_data->exblx_channel ;
- }
- g_string_printf(line, "%d\t(%c%d)\t%d\t%d\t(%c%d)\t%d\t%d\t%s",
- score,
- qframe_strand, qframe,
- qstart, qend,
- sframe_strand, sframe,
- sstart, send,
- g_quark_to_string(feature->original_id)) ;
+ /* Phase out stupid curr_channel */
- if (feature->feature.homol.align)
+ /* need to put this choice for seqbl into the exblx routine below... */
+ if (blixem_data->file_format == BLX_FILE_FORMAT_EXBLX)
{
- int k, index, incr ;
-
- g_string_append_printf(line, "%s", "\tGaps ") ;
-
-
- if (feature->strand == ZMAPSTRAND_REVERSE)
+ if ((list_ptr = g_list_find_custom(blixem_data->local_sequences, feature, findFeature)))
{
- index = feature->feature.homol.align->len - 1 ;
- incr = -1 ;
+ ZMapSequence sequence = (ZMapSequence)list_ptr->data ;
+
+ seq_str = sequence->sequence ;
+ curr_channel = blixem_data->seqbl_channel ;
}
else
{
- index = 0 ;
- incr = 1 ;
+ /* In theory we should be checking for a description for non-local sequences,
+ * see acedb code in doShowAlign...don't know how important this is..... */
+ seq_str = "" ;
+ curr_channel = blixem_data->exblx_channel ;
}
- for (k = 0 ; k < feature->feature.homol.align->len ; k++, index += incr)
- {
- ZMapAlignBlockStruct gap ;
-
- gap = g_array_index(feature->feature.homol.align, ZMapAlignBlockStruct, index) ;
-
- if (qstart > qend)
- zMapUtilsSwop(int, gap.t1, gap.t2) ;
+ status = formatAlignmentExbl(line,
+ min, max,
+ match_name,
+ qstart, qend, feature->strand, qframe,
+ sstart, send, feature->feature.homol.strand, sframe,
+ feature->score, feature->feature.homol.align, seq_str, description) ;
+ }
+ else
+ {
+ int tmp ;
- g_string_append_printf(line, " %d %d %d %d", gap.q1, gap.q2,
- (gap.t1 - min + 1), (gap.t2 - min + 1)) ;
- }
+ if (feature->strand == ZMAPSTRAND_REVERSE)
+ tmp = qstart, qstart = qend, qend = tmp ;
- g_string_append_printf(line, "%s", " ;") ;
- }
+ curr_channel = blixem_data->gff_channel ;
- /* In theory we should be outputting description for some files.... */
- if ((seq_str && *seq_str) || (description && *description))
- {
- char *tag, *text ;
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ /* DUH...WHAT IS THIS.... */
+ sstart = sstart - feature->feature.homol.length + 1 ;
+ send = sstart - feature->feature.homol.length + 1 ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
- if (seq_str)
- {
- tag = "Sequence" ;
- text = seq_str ;
- }
- else
- {
- tag = "Description" ;
- text = description ;
- }
- g_string_append_printf(line, "\t%s %s ;", tag, text) ;
+ status = formatAlignmentGFF(blixem_data->format_data, line,
+ min, max,
+ (char *)g_quark_to_string(blixem_data->block->original_id),
+ match_name, source_name, feature->feature.homol.type,
+ qstart, qend, feature->strand,
+ sstart, send, feature->feature.homol.strand,
+ feature->score, feature->feature.homol.align, seq_str, description) ;
}
- line = g_string_append(line, "\n") ;
+ if (status)
+ line = g_string_append(line, "\n") ;
- status = printLine(blixem_data, line->str) ;
+ status = printLine(curr_channel, &(blixem_data->errorMsg), line->str) ;
}
return status ;
}
-
-static gboolean printTranscript(ZMapFeature feature, blixemData blixem_data)
+static gboolean formatAlignmentExbl(GString *line,
+ int min_range, int max_range,
+ char *match_name,
+ int qstart, int qend, ZMapStrand q_strand, int qframe,
+ int sstart, int send, ZMapStrand s_strand, int sframe,
+ float score, GArray *gaps, char *sequence, char *description)
{
- gboolean status = TRUE;
- int min, max ;
- int cds_start, cds_end ;
- int score = 0, qstart, qend, sstart, send;
- ZMapSpan span = NULL;
- char *qframe, *sframe ;
- gboolean cds_only = TRUE ;
+ gboolean status = TRUE ;
+ char qframe_strand, sframe_strand ;
+ int score_int ;
+ if (q_strand == ZMAPSTRAND_REVERSE)
+ qframe_strand = '-' ;
+ else
+ qframe_strand = '+' ;
- /* For nucleotide alignments we do all transcripts, for proteins we only do those with a cds. */
- if (blixem_data->align_type == ZMAPHOMOL_N_HOMOL)
- cds_only = FALSE ;
+ if (s_strand == ZMAPSTRAND_REVERSE)
+ sframe_strand = '-' ;
+ else
+ sframe_strand = '+' ;
+ score_int = (int)(score + 0.5) ;
- if (!cds_only || feature->feature.transcript.flags.cds)
+ g_string_printf(line, "%d\t(%c%d)\t%d\t%d\t(%c%d)\t%d\t%d\t%s",
+ score_int,
+ qframe_strand, qframe,
+ qstart, qend,
+ sframe_strand, sframe,
+ sstart, send,
+ match_name) ;
+
+ if (gaps)
{
- blixem_data->curr_channel = blixem_data->exblx_channel ;
+ int k, index, incr ;
- /* Do the exons... */
- status = processExons(blixem_data, feature, cds_only) ;
+ g_string_append_printf(line, "%s", "\tGaps ") ;
+ if (q_strand == ZMAPSTRAND_REVERSE)
+ {
+ index = gaps->len - 1 ;
+ incr = -1 ;
+ }
+ else
+ {
+ index = 0 ;
+ incr = 1 ;
+ }
- /* Do the introns... */
- if (status && feature->feature.transcript.introns)
+ for (k = 0 ; k < gaps->len ; k++, index += incr)
{
- int i ;
+ ZMapAlignBlockStruct gap ;
- cds_start = feature->feature.transcript.cds_start ;
- cds_end = feature->feature.transcript.cds_end ;
- min = blixem_data->min ;
- max = blixem_data->max ;
+ gap = g_array_index(gaps, ZMapAlignBlockStruct, index) ;
- for (i = 0; i < feature->feature.transcript.introns->len && status; i++)
- {
- span = &g_array_index(feature->feature.transcript.introns, ZMapSpanStruct, i);
+ if (qstart > qend)
+ zMapUtilsSwop(int, gap.t1, gap.t2) ;
- /* Only print introns that are within the cds section of the transcript and
- * within the blixem scope. */
- if ((span->x1 < min || span->x2 > max)
- || (cds_only && (span->x1 > cds_end || span->x2 < cds_start)))
- {
- continue ;
- }
+ g_string_append_printf(line, " %d %d %d %d", gap.q1, gap.q2,
+ (gap.t1 - min_range + 1), (gap.t2 - min_range + 1)) ;
+ }
+
+ g_string_append_printf(line, "%s", " ;") ;
+ }
+
+ /* In theory we should be outputting description for some files.... */
+ if ((sequence && *sequence) || (description && *description))
+ {
+ char *tag, *text ;
+
+ if (sequence)
+ {
+ tag = "Sequence" ;
+ text = sequence ;
+ }
+ else
+ {
+ tag = "Description" ;
+ text = description ;
+ }
+
+ g_string_append_printf(line, "\t%s %s ;", tag, text) ;
+ }
+
+
+
+
+ return status ;
+}
+
+
+static gboolean formatAlignmentGFF(GFFFormatData gff_data, GString *line,
+ int min_range, int max_range,
+ char *ref_name, char *match_name, char *source_name, ZMapHomolType homol_type,
+ int qstart, int qend, ZMapStrand q_strand,
+ int sstart, int send, ZMapStrand s_strand,
+ float score, GArray *gaps, char *sequence, char *description)
+{
+ gboolean status = TRUE ;
+ char *id_str = NULL ;
+
+ if (gff_data->maximise_ids)
+ {
+ gff_data->alignment_count++ ;
+
+ id_str = g_strdup_printf("ID=match%d;", gff_data->alignment_count) ;
+ }
+
+
+ /* ctg123 . cDNA_match 1050 1500 5.8e-42 + . ID=match00001;Target=cdna0123 12 462 */
+ g_string_printf(line, "%s\t%s\t%s\t%d\t%d\t%f\t%c\t.\t%sTarget=%s %d %d %c",
+ ref_name, source_name,
+ (homol_type == ZMAPHOMOL_N_HOMOL ? "nucleotide_match" : "protein_match"),
+ qstart, qend,
+ score,
+ (q_strand == ZMAPSTRAND_REVERSE ? '-' : '+'),
+ (id_str ? id_str : ""),
+ match_name,
+ sstart, send,
+ (s_strand == ZMAPSTRAND_REVERSE ? '-' : '+')) ;
+
+ if (gaps)
+ {
+ int k, index, incr ;
+ GString *align_str ;
+
+ align_str = g_string_sized_new(2000) ;
+
+ /* Gap=M8 D3 M6 I1 M6 */
+
+ /* correct, needed ?? */
+ if (q_strand == ZMAPSTRAND_REVERSE)
+ {
+ index = gaps->len - 1 ;
+ incr = -1 ;
+ }
+ else
+ {
+ index = 0 ;
+ incr = 1 ;
+ }
+
+ for (k = 0 ; k < gaps->len ; k++, index += incr)
+ {
+ ZMapAlignBlock gap ;
+
+ gap = &(g_array_index(gaps, ZMapAlignBlockStruct, index)) ;
+
+ g_string_append_printf(align_str, "M%d ", (gap->t2 - gap->t1) + 1) ;
+
+ if (k < gaps->len - 1)
+ {
+ ZMapAlignBlock next_gap ;
+ int curr_match, next_match, curr_ref, next_ref ;
+
+ next_gap = &(g_array_index(gaps, ZMapAlignBlockStruct, index + incr)) ;
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ if (gap->q_strand == ZMAPSTRAND_FORWARD && gap->t_strand == ZMAPSTRAND_FORWARD)
+ printf("forwards - forwards\n") ;
+ else if (gap->q_strand == ZMAPSTRAND_FORWARD && gap->t_strand == ZMAPSTRAND_REVERSE)
+ printf("forwards - backwards\n") ;
+ else if (gap->q_strand == ZMAPSTRAND_REVERSE && gap->t_strand == ZMAPSTRAND_FORWARD)
+ printf("backwards - forwards\n") ;
+ else if (gap->q_strand == ZMAPSTRAND_REVERSE && gap->t_strand == ZMAPSTRAND_REVERSE)
+ printf("backwards - backwards\n") ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
+ if (gap->q_strand == ZMAPSTRAND_FORWARD)
+ {
+ curr_match = gap->q2 ;
+ next_match = next_gap->q1 ;
+ }
else
{
- GString *line ;
+ curr_match = next_gap->q2 ;
+ next_match = gap->q1 ;
+ }
- line = blixem_data->line ;
+ if (gap->t_strand == ZMAPSTRAND_FORWARD)
+ {
+ curr_ref = gap->t2 ;
+ next_ref = next_gap->t1 ;
+ }
+ else
+ {
+ curr_ref = next_gap->t2 ;
+ next_ref = gap->t1 ;
+ }
- if (feature->strand == ZMAPSTRAND_REVERSE)
- {
- qstart = span->x2 - min + 1;
- qend = span->x1 - min + 1;
- }
- else
- {
- qstart = span->x1 - min + 1;
- qend = span->x2 - min + 1;
- }
+ if (next_match > curr_match + 1)
+ g_string_append_printf(align_str, "I%d ", (next_match - curr_match) - 1) ;
+ else if (next_ref > curr_ref + 1)
+ g_string_append_printf(align_str, "D%d ", (next_ref - curr_ref) - 1) ;
+ else
+ zMapLogWarning("Bad coords in GFFv3 writer: gap %d,%d -> %d, %d, next_gap %d, %d -> %d, %d",
+ gap->t1, gap->t2, gap->q1, gap->q2,
+ next_gap->t1, next_gap->t2, next_gap->q1, next_gap->q2) ;
+ }
+ }
+
+ g_string_append_printf(line, ";Gaps=%s", align_str->str) ;
+
+ g_string_free(align_str, TRUE) ;
+ }
+
+
+ if (sequence)
+ {
+ g_string_append_printf(line, ";Sequence=%s", sequence) ;
+ }
+
+
+ if (id_str)
+ g_free(id_str) ;
+
+ return status ;
+}
+
+
+
+static gboolean printTranscript(ZMapFeature feature, blixemData blixem_data)
+{
+ gboolean status = TRUE;
+ gboolean cds_only = TRUE ;
+
+ if (blixem_data->align_type == ZMAPHOMOL_N_HOMOL)
+ cds_only = FALSE ;
+
+ if (!cds_only || feature->feature.transcript.flags.cds)
+ {
+ /* Do the exons... */
+ status = processExons(blixem_data, feature, cds_only) ;
+
+ /* Now do extra's for each file format. */
+ if (blixem_data->file_format == BLX_FILE_FORMAT_EXBLX)
+ {
+ printTranscriptExtrasExblx(feature, blixem_data, cds_only) ;
+ }
+ }
+
+ return status ;
+}
+
+
+/* Print out the exons taking account of the extent of the CDS within the transcript. */
+static gboolean processExons(blixemData blixem_data, ZMapFeature feature, gboolean cds_only)
+{
+ gboolean status = TRUE ;
+ GIOChannel *channel ;
+ int i ;
+ ZMapSpan span = NULL ;
+ int score = -1, qstart, qend, sstart, send ;
+ int min, max ;
+ int exon_base ;
+ int cds_start, cds_end ; /* Only used if cds_only == TRUE. */
+ GString *line ;
+ char *ref_name ;
+ char *transcript_name ;
+ char *source_name ;
- sstart = send = 0 ;
- score = -2 ;
- /* Note that sframe is meaningless so is set to an invalid value. */
+
+ if (blixem_data->file_format == BLX_FILE_FORMAT_EXBLX)
+ channel = blixem_data->exblx_channel ;
+ else
+ channel = blixem_data->gff_channel ;
+
+
+ line = blixem_data->line ;
+
+ min = blixem_data->min ;
+ max = blixem_data->max ;
+
+ ref_name = (char *)g_quark_to_string(blixem_data->block->original_id) ;
+ transcript_name = (char *)g_quark_to_string(feature->original_id) ;
+ source_name = (char *)g_quark_to_string(feature->source_id) ;
+
+ if (cds_only)
+ {
+ cds_start = feature->feature.transcript.cds_start ;
+ cds_end = feature->feature.transcript.cds_end ;
+ }
+
+ exon_base = 0 ;
+
+ /* We need to record how far we are along the exons in CDS relative coords, i.e. for the
+ * reverse strand we need to calculate from the other end of the transcript. */
+ if (feature->strand == ZMAPSTRAND_REVERSE)
+ {
+ for (i = 0 ; i < feature->feature.transcript.exons->len ; i++)
+ {
+ int start, end ;
+
+ span = &g_array_index(feature->feature.transcript.exons, ZMapSpanStruct, i) ;
+
+ if (cds_only && (span->x1 > cds_end || span->x2 < cds_start))
+ {
+ continue ;
+ }
+ else
+ {
+ start = span->x1 ;
+ end = span->x2 ;
+
+ /* Truncate to CDS start/end in transcript. */
+ if (cds_only)
+ {
+ if (cds_start >= span->x1 && cds_start <= span->x2)
+ start = cds_start ;
+ if (cds_end >= span->x1 && cds_end <= span->x2)
+ end = cds_end ;
+ }
+
+ exon_base += end - start + 1 ;
+ }
+ }
+ }
+
+
+ for (i = 0 ; i < feature->feature.transcript.exons->len ; i++)
+ {
+ span = &g_array_index(feature->feature.transcript.exons, ZMapSpanStruct, i) ;
+
+ /* We are only interested in the cds section of the transcript. */
+ if (cds_only && (span->x1 > cds_end || span->x2 < cds_start))
+ {
+ continue ;
+ }
+ else
+ {
+ int exon_start, exon_end ;
+
+ exon_start = span->x1 ;
+ exon_end = span->x2 ;
+
+ /* Truncate to CDS start/end in transcript. */
+ if (cds_only)
+ {
+ if (cds_start >= span->x1 && cds_start <= span->x2)
+ exon_start = cds_start ;
+ if (cds_end >= span->x1 && cds_end <= span->x2)
+ exon_end = cds_end ;
+ }
+
+ /* NEED TO REVISIT THIS FOR GFFv3... */
+ /* We only export exons that fit completely within the blixem scope. */
+ if (exon_start >= min && exon_end <= max)
+ {
+ /* Note that sframe is meaningless so is set to an invalid value. */
+ if (feature->strand == ZMAPSTRAND_REVERSE)
+ {
+ qstart = exon_end - min + 1;
+ qend = exon_start - min + 1;
+ sstart = ((exon_base - (exon_end - exon_start + 1)) + 3) / 3 ;
+ send = (exon_base - 1) / 3 ;
+ }
+ else
+ {
+ qstart = exon_start - min + 1;
+ qend = exon_end - min + 1;
+ sstart = (exon_base + 3) / 3 ;
+ send = (exon_base + (exon_end - exon_start)) / 3 ;
+ }
+
+ if (blixem_data->file_format == BLX_FILE_FORMAT_EXBLX)
+ {
+ formatTranscriptExblx(line, min, max,
+ transcript_name,
+ score,
+ exon_base, exon_start, exon_end,
+ qstart, qend, feature->strand,
+ sstart, send) ;
+ }
+ else
+ {
+ int tmp ;
+
if (feature->strand == ZMAPSTRAND_REVERSE)
- {
- qframe = "(-1)" ;
- sframe = "(-0)" ;
- }
- else
- {
- qframe = "(+1)" ;
- sframe = "(-1)" ;
- }
+ tmp = qstart, qstart = qend, qend = tmp ;
+
+ formatTranscriptGFF(blixem_data->format_data, line, min, max,
+ ref_name, source_name,
+ feature, transcript_name,
+ exon_start, exon_end,
+ qstart, qend, feature->strand,
+ sstart, send) ;
+ }
+
+
+ status = printLine(channel, &(blixem_data->errorMsg), line->str) ;
+
+ status = printLine(channel, &(blixem_data->errorMsg), "\n") ;
+
+ blixem_data->line = g_string_truncate(blixem_data->line, 0) ; /* Reset string buffer. */
+ }
+
+ if (feature->strand == ZMAPSTRAND_REVERSE)
+ {
+ exon_base -= (exon_end - exon_start + 1);
+ }
+ else
+ {
+ exon_base += (exon_end - exon_start + 1) ;
+ }
+ }
+ }
+
+
+ return status ;
+}
- g_string_printf(line, "%d\t%s\t%d\t%d\t%s\t%d\t%d\t%si\n",
- score,
- qframe, qstart, qend,
- sframe, sstart, send,
- g_quark_to_string(feature->original_id)) ;
- status = printLine(blixem_data, line->str) ;
+static gboolean formatTranscriptExblx(GString *line, int min, int max,
+ char *transcript_name,
+ float score_unused,
+ int exon_base, int exon_start, int exon_end,
+ int qstart, int qend, int qstrand,
+ int sstart, int send)
+{
+ gboolean status = TRUE;
+ char qframe_strand ;
+ int qframe ;
+ char *sframe_str ;
+
+
+ /* Note that sframe is meaningless so is set to an invalid value. */
+ if (qstrand == ZMAPSTRAND_REVERSE)
+ {
+ qframe_strand = '-' ;
+ qframe = ( (((max - min + 1) - qstart) - (exon_base - (exon_end - exon_start + 1))) % 3) + 1 ;
+
+ sframe_str = "(-0)" ;
+ }
+ else
+ {
+ qframe_strand = '+' ;
+ qframe = ((qstart - 1 - exon_base) % 3) + 1 ;
+
+ sframe_str = "(+0)" ;
+ }
+
+ g_string_printf(line, "-1\t(%c%d)\t%d\t%d\t%s\t%d\t%d\t%sx",
+ qframe_strand, qframe, qstart, qend,
+ sframe_str, sstart, send,
+ transcript_name) ;
+
+ return status ;
+}
+
+
+static gboolean formatTranscriptGFF(GFFFormatData gff_data, GString *line, int min, int max,
+ char *ref_name, char *source_name,
+ ZMapFeature feature, char *transcript_name,
+ int exon_start, int exon_end,
+ int qstart, int qend, int qstrand,
+ int sstart, int send)
+{
+ gboolean status = TRUE ;
+ static char *curr_transcript = NULL ;
+ char *SO_rna_id = "mRNA" ;
+ char *SO_exon_id = "exon" ;
+ char *SO_CDS_id = "CDS" ;
+ char *id_str = NULL ;
+
+ /* If it's a new transcript then write the transcript record with a new ID. */
+ if (!curr_transcript || strcmp(curr_transcript, transcript_name) != 0)
+ {
+ gff_data->transcript_count++ ;
+
+ /* ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Name=EDEN.1 */
+ g_string_printf(line, "%s\t%s\t%s\t%d\t%d\t.\t%c\t.\tID=transcript%d;Name=%s\n",
+ ref_name, source_name, SO_rna_id,
+ feature->x1, feature->x2,
+ (qstrand == ZMAPSTRAND_REVERSE ? '-' : '+'),
+ gff_data->transcript_count,
+ transcript_name) ;
+
+ curr_transcript = transcript_name ;
+ }
+
+ if (gff_data->maximise_ids)
+ {
+ gff_data->exon_count++ ;
+
+ id_str = g_strdup_printf("ID=exon%d;", gff_data->exon_count) ;
+ }
+
+
+ /* ctg123 . exon 1300 1500 . + . Parent=mRNA00003 */
+ g_string_append_printf(line, "%s\t%s\t%s\t%d\t%d\t.\t%c\t.\t%sParent=transcript%d",
+ ref_name, source_name, SO_exon_id,
+ qstart, qend,
+ (qstrand == ZMAPSTRAND_REVERSE ? '-' : '+'),
+ (id_str ? id_str : ""),
+ gff_data->transcript_count) ;
+
+
+ if (feature->feature.transcript.flags.cds)
+ {
+ int cds_start, cds_end ;
+
+ cds_start = feature->feature.transcript.cds_start ;
+ cds_end = feature->feature.transcript.cds_end ;
+
+ if (exon_start > cds_end || exon_end < cds_start)
+ {
+ ;
+ }
+ else
+ {
+ int tmp_cds1, tmp_cds2, phase ;
+
+ if (cds_start >= exon_start && cds_start <= exon_end)
+ qstart += cds_start - exon_start ;
+ if (cds_end >= qstart && cds_end <= qend)
+ qend -= exon_end - cds_end ;
+
+
+
+ /* ctg123 . CDS 1201 1500 . + 0 Parent=mRNA00001 */
+ if (zMapFeatureExon2CDS(feature,
+ exon_start, exon_end, &tmp_cds1, &tmp_cds2, &phase))
+ {
+ /* Only print if exon has cds section. */
+ g_string_append_printf(line, "\n%s\t%s\t%s\t%d\t%d\t.\t%c\t%d\t%sParent=transcript%d",
+ ref_name, source_name, SO_CDS_id,
+ qstart, qend,
+ (qstrand == ZMAPSTRAND_REVERSE ? '-' : '+'),
+ phase,
+ (id_str ? id_str : ""),
+ gff_data->transcript_count) ;
+ }
+ }
+ }
+
+ if (id_str)
+ g_free(id_str) ;
+
+ return status ;
+}
+
+
+
+static gboolean printTranscriptExtrasExblx(ZMapFeature feature, blixemData blixem_data, gboolean cds_only)
+{
+ gboolean status = TRUE;
+ int min, max ;
+ int cds_start, cds_end ;
+ int score = 0, qstart, qend, sstart, send;
+ ZMapSpan span = NULL;
+ char *qframe, *sframe ;
+
+
+ /* Do the introns... */
+ if (feature->feature.transcript.introns)
+ {
+ int i ;
+
+ cds_start = feature->feature.transcript.cds_start ;
+ cds_end = feature->feature.transcript.cds_end ;
+ min = blixem_data->min ;
+ max = blixem_data->max ;
+
+ for (i = 0; i < feature->feature.transcript.introns->len && status; i++)
+ {
+ span = &g_array_index(feature->feature.transcript.introns, ZMapSpanStruct, i);
+
+ /* Only print introns that are within the cds section of the transcript and
+ * within the blixem scope. */
+ if ((span->x1 < min || span->x2 > max)
+ || (cds_only && (span->x1 > cds_end || span->x2 < cds_start)))
+ {
+ continue ;
+ }
+ else
+ {
+ GString *line ;
+
+ line = blixem_data->line ;
+
+ if (feature->strand == ZMAPSTRAND_REVERSE)
+ {
+ qstart = span->x2 - min + 1;
+ qend = span->x1 - min + 1;
+ }
+ else
+ {
+ qstart = span->x1 - min + 1;
+ qend = span->x2 - min + 1;
}
+
+ sstart = send = 0 ;
+ score = -2 ;
+
+ /* Note that sframe is meaningless so is set to an invalid value. */
+ if (feature->strand == ZMAPSTRAND_REVERSE)
+ {
+ qframe = "(-1)" ;
+ sframe = "(-0)" ;
+ }
+ else
+ {
+ qframe = "(+1)" ;
+ sframe = "(-1)" ;
+ }
+
+ g_string_printf(line, "%d\t%s\t%d\t%d\t%s\t%d\t%d\t%si\n",
+ score,
+ qframe, qstart, qend,
+ sframe, sstart, send,
+ g_quark_to_string(feature->original_id)) ;
+
+ status = printLine(blixem_data->exblx_channel, &(blixem_data->errorMsg), line->str) ;
}
}
}
@@ -1441,19 +2077,21 @@ static gboolean printTranscript(ZMapFeature feature, blixemData blixem_data)
}
-static gboolean printLine(blixemData blixem_data, char *line)
+
+
+/* Output a line to file, returns FALSE if write fails and sets err_msg_out with
+ * the reason. */
+static gboolean printLine(GIOChannel *gio_channel, char **err_msg_out, char *line)
{
gboolean status = TRUE ;
GError *channel_error = NULL ;
gsize bytes_written ;
- if (g_io_channel_write_chars(blixem_data->curr_channel, line, -1,
+ if (g_io_channel_write_chars(gio_channel, line, -1,
&bytes_written, &channel_error) != G_IO_STATUS_NORMAL)
{
- /* don't display an error at this point, just write it to blixem_data for later.
- * Set and return status to prevent further processing. */
- blixem_data->errorMsg = g_strdup_printf("Error writing data to exblx file: %50s... : %s",
- line, channel_error->message) ;
+ *err_msg_out = g_strdup_printf("Could not write to file, error \"%s\" for line \"%50s...\"",
+ channel_error->message, line) ;
g_error_free(channel_error) ;
channel_error = NULL;
status = FALSE ;
@@ -1468,10 +2106,13 @@ static gboolean printLine(blixemData blixem_data, char *line)
static void getSetList(gpointer data, gpointer user_data)
{
GQuark set_id = GPOINTER_TO_UINT(data) ;
+ GQuark canon_id ;
blixemData blixem_data = (blixemData)user_data ;
ZMapFeatureSet feature_set ;
- if (!(feature_set = g_hash_table_lookup(blixem_data->block->feature_sets, GINT_TO_POINTER(set_id))))
+ canon_id = zMapFeatureSetCreateID((char *)g_quark_to_string(set_id)) ;
+
+ if (!(feature_set = g_hash_table_lookup(blixem_data->block->feature_sets, GINT_TO_POINTER(canon_id))))
{
zMapLogWarning("Could not find %s feature set \"%s\" in context feature sets.",
(blixem_data->required_feature_type == ZMAPSTYLE_MODE_ALIGNMENT
@@ -1667,151 +2308,6 @@ static gboolean writeFastAFile(blixemData blixem_data)
-/* Print out the exons taking account of the extent of the CDS within the transcript. */
-static gboolean processExons(blixemData blixem_data, ZMapFeature feature, gboolean cds_only)
-{
- gboolean status = TRUE ;
- int i ;
- ZMapSpan span = NULL ;
- int score = -1, qstart, qend, sstart, send ;
- int min, max ;
- int exon_base ;
- int cds_start, cds_end ; /* Only used if cds_only == TRUE. */
- GString *line ;
-
- line = blixem_data->line ;
-
- min = blixem_data->min ;
- max = blixem_data->max ;
-
- if (cds_only)
- {
- cds_start = feature->feature.transcript.cds_start ;
- cds_end = feature->feature.transcript.cds_end ;
- }
-
- exon_base = 0 ;
-
-
- /* We need to record how far we are along the exons in CDS relative coords, i.e. for the
- * reverse strand we need to calculate from the other end of the transcript. */
- if (feature->strand == ZMAPSTRAND_REVERSE)
- {
- for (i = 0 ; i < feature->feature.transcript.exons->len ; i++)
- {
- int start, end ;
-
- span = &g_array_index(feature->feature.transcript.exons, ZMapSpanStruct, i) ;
-
- if (cds_only && (span->x1 > cds_end || span->x2 < cds_start))
- {
- continue ;
- }
- else
- {
- start = span->x1 ;
- end = span->x2 ;
-
- /* Truncate to CDS start/end in transcript. */
- if (cds_only)
- {
- if (cds_start >= span->x1 && cds_start <= span->x2)
- start = cds_start ;
- if (cds_end >= span->x1 && cds_end <= span->x2)
- end = cds_end ;
- }
-
- exon_base += end - start + 1 ;
- }
- }
- }
-
-
- for (i = 0 ; i < feature->feature.transcript.exons->len ; i++)
- {
- span = &g_array_index(feature->feature.transcript.exons, ZMapSpanStruct, i) ;
-
- /* We are only interested in the cds section of the transcript. */
- if (cds_only && (span->x1 > cds_end || span->x2 < cds_start))
- {
- continue ;
- }
- else
- {
- char qframe_strand ;
- int qframe ;
- int start, end ;
-
- start = span->x1 ;
- end = span->x2 ;
-
- /* Truncate to CDS start/end in transcript. */
- if (cds_only)
- {
- if (cds_start >= span->x1 && cds_start <= span->x2)
- start = cds_start ;
- if (cds_end >= span->x1 && cds_end <= span->x2)
- end = cds_end ;
- }
-
- /* We only export exons that fit completely within the blixem scope. */
- if (start >= min && end <= max)
- {
- char *sframe ;
-
- /* Note that sframe is meaningless so is set to an invalid value. */
- if (feature->strand == ZMAPSTRAND_REVERSE)
- {
- qstart = end - min + 1;
- qend = start - min + 1;
-
- qframe_strand = '-' ;
- qframe = ( (((max - min + 1) - qstart) - (exon_base - (end - start + 1))) % 3) + 1 ;
-
- sframe = "(-0)" ;
- sstart = ((exon_base - (end - start + 1)) + 3) / 3 ;
- send = (exon_base - 1) / 3 ;
- }
- else
- {
- qstart = start - min + 1;
- qend = end - min + 1;
-
- qframe_strand = '+' ;
- qframe = ((qstart - 1 - exon_base) % 3) + 1 ;
-
- sframe = "(+0)" ;
- sstart = (exon_base + 3) / 3 ;
- send = (exon_base + (end - start)) / 3 ;
- }
-
- g_string_printf(line, "%d\t(%c%d)\t%d\t%d\t%s\t%d\t%d\t%sx\n",
- score,
- qframe_strand, qframe, qstart, qend,
- sframe, sstart, send,
- g_quark_to_string(feature->original_id)) ;
-
- status = printLine(blixem_data, line->str) ;
-
- blixem_data->line = g_string_truncate(blixem_data->line, 0) ; /* Reset string buffer. */
- }
-
- if (feature->strand == ZMAPSTRAND_REVERSE)
- {
- exon_base -= (end - start + 1);
- }
- else
- {
- exon_base += (end - start + 1) ;
- }
- }
- }
-
-
- return status ;
-}
-
-
gboolean makeTmpfile(char *tmp_dir, char *file_prefix, char **tmp_file_name_out)
{
gboolean status = FALSE ;
@@ -1933,27 +2429,27 @@ static gboolean check_edited_values(ZMapGuiNotebookAny note_any, const char *ent
char *text = (char *)entry_text;
gboolean allowed = TRUE;
- if(!text || (text && !*text))
+ if (!text || (text && !*text))
allowed = FALSE;
- else if(note_any->name == g_quark_from_string("Launch script"))
+ else if (note_any->name == g_quark_from_string("Launch script"))
{
- if(!(allowed = zMapFileAccess(text, "x")))
+ if (!(allowed = zMapFileAccess(text, "x")))
zMapWarning("%s is not executable.", text);
allowed = TRUE; /* just warn for now */
}
- else if(note_any->name == g_quark_from_string("Config File"))
+ else if (note_any->name == g_quark_from_string("Config File"))
{
- if(!(allowed = zMapFileAccess(text, "r")))
+ if (!(allowed = zMapFileAccess(text, "r")))
zMapWarning("%s is not readable.", text);
allowed = TRUE; /* just warn for now */
}
- else if(note_any->name == g_quark_from_string("Port"))
+ else if (note_any->name == g_quark_from_string("Port"))
{
int tmp = 0;
- if(zMapStr2Int(text, &tmp))
+ if (zMapStr2Int(text, &tmp))
{
int min = 1024, max = 65535;
- if(tmp < min || tmp > max)
+ if (tmp < min || tmp > max)
{
allowed = FALSE;
zMapWarning("Port should be in range of %d to %d", min, max);
@@ -2132,9 +2628,9 @@ static void saveUserPrefs(BlixemConfigData prefs)
{
ZMapConfigIniContext context = NULL;
- if((context = zMapConfigIniContextProvide()))
+ if ((context = zMapConfigIniContextProvide()))
{
- if(prefs->netid)
+ if (prefs->netid)
zMapConfigIniContextSetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_NETID, prefs->netid);
@@ -2153,27 +2649,27 @@ static void saveUserPrefs(BlixemConfigData prefs)
zMapConfigIniContextSetBoolean(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_KILL_EXIT, prefs->kill_on_exit);
- if(prefs->script)
+ if (prefs->script)
zMapConfigIniContextSetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_SCRIPT, prefs->script);
- if(prefs->config_file)
+ if (prefs->config_file)
zMapConfigIniContextSetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_CONF_FILE, prefs->config_file);
#ifdef RDS_DONT_INCLUDE
- if(prefs->dna_sets)
+ if (prefs->dna_sets)
zMapConfigIniContextSetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_DNA_FS, prefs->dna_sets);
- if(prefs->protein_sets)
+ if (prefs->protein_sets)
zMapConfigIniContextSetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
ZMAPSTANZA_BLIXEM_PROT_FS, prefs->protein_sets);
- if(prefs->transcript_sets)
+ if (prefs->transcript_sets)
zMapConfigIniContextSetString(context, ZMAPSTANZA_BLIXEM_CONFIG, ZMAPSTANZA_BLIXEM_CONFIG,
- ZMAPSTANZA_BLIXEM_TRANS_FS, prefs->transcript_sets);
+ ZMAPSTANZA_BLIXEM_FS, prefs->transcript_sets);
#endif
zMapConfigIniContextSave(context);
--
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