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/* File: das.c
* Author: Ed Griffiths (edgrif@sanger.ac.uk)
* Copyright (c) J Thierry-Mieg and R Durbin, 2003
*-------------------------------------------------------------------
* Acedb is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
* or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
*-------------------------------------------------------------------
* This file is part of the ACEDB genome database package, written by
* Richard Durbin (Sanger Centre, UK) rd@sanger.ac.uk, and
* Jean Thierry-Mieg (CRBM du CNRS, France) mieg@kaa.crbm.cnrs-mop.fr
*
* Description: Functions to output DAS format information, e.g. for
* DNA, Features (GFF basically) and other DAS stuff.
*
* Exported functions: See das.h
* HISTORY:
* Last edited: May 25 09:11 2005 (rnc)
* Created: Tue Jan 28 14:01:03 2003 (edgrif)
* CVS info: $Id: das.c,v 1.8 2005/05/25 08:30:39 rnc Exp $
*-------------------------------------------------------------------
*/
#include <glib.h>
#include <wh/regular.h>
#include <wh/aceio.h>
#include <wh/acedb.h>
#include <wh/lex.h>
#include <whooks/classes.h>
#include <w7/fmap_.h>
#include <wh/dna.h>
#include <wh/gff.h>
/* This is work in progress, I'm just going to lash up some routines to enable command line
* output of DAS to do testing */
/* Data passed to our callback routine when its called from the GFF dumping code to output
* a GFF feature. */
typedef struct
{
ACEOUT fo ;
int *level ;
STORE_HANDLE handle ;
GString *attributes ;
GString *value ;
} DasGFFDataStruct, *DasGFFData ;
static void indent(ACEOUT fo, int level) ;
static void makeTags(STORE_HANDLE handle, char *tag, char *attributes,
char **start_tag_out, char **end_tag_out) ;
static void dumpTagStart(ACEOUT fo, int *level, char *tag) ;
static void dumpTagEnd(ACEOUT fo, int *level, char *tag) ;
static char *getDASHeader(void) ;
static void writeDASFeature(void *app_data,
char *seqname, char *seqclass, char *method, BOOL is_structural,
char *source, char *feature, int start, int end,
float *score, char strand, char frame,
char *attributes, char *comments, int segType) ;
/*
* -------------------- EXTERNAL FUNCTIONS --------------------
*/
/* Called from gifcommand.c to do a dump of a virtual sequence in DASGFF format. */
void dasGFF(ACEIN command_in, ACEOUT result_out, FeatureMap look)
{
int x1, x2 ;
int version = 2 ;
char *word ;
STORE_HANDLE handle = handleCreate() ;
DICT *sourceSet = dictHandleCreate (16, handle) ;
DICT *featSet = dictHandleCreate (16, handle) ;
DICT *methodSet = dictHandleCreate (16, handle) ;
BOOL raw_methods = FALSE ;
BOOL include_source = FALSE;
BOOL include_feature = FALSE;
BOOL include_method = FALSE;
BOOL isList = FALSE ;
ACEOUT fo = NULL, dump_out = NULL ;
char *das_start, *das_end,
*gff_start, *gff_end, *gff_atts,
*seg_start, *seg_end, *seg_atts ;
int level ;
KEY refSeq = KEY_UNDEFINED, seqKey ;
BOOL reversed ;
int offset, key_start, key_end, feature_start, feature_end ;
BOOL result ;
DasGFFData cb_data ;
enum {DAS_BUFFER_INITLEN = 256} ; /* Vague guess at initial length. */
/* Bother, we need some common code to analyse all the method include style junk.... */
messAssert((command_in && result_out && verifyFeatureMap(look, dasFeatures))) ;
/* by default output goes to same place as normal command results */
dump_out = aceOutCopy (result_out, 0);
/* Decide which of these to support....... */
while (aceInCheck (command_in, "w"))
{
word = aceInWord (command_in) ;
if (strcmp (word, "-coords") == 0
&& aceInInt (command_in, &x1)
&& aceInInt (command_in, &x2)
&& (x2 != x1))
{
;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
setZoneUserCoords (look, x1, x2) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
}
else if (strcmp (word, "-file") == 0
&& aceInCheck (command_in, "w")
&& (fo = aceOutCreateToFile (aceInPath (command_in), "w", 0)))
{
/* replace default output with file output */
aceOutDestroy (dump_out);
dump_out = fo;
}
else if (strcmp (word, "-refseq") == 0
&& aceInCheck (command_in, "w")
&& (lexword2key (aceInWord (command_in), &refSeq, _VSequence)))
{ ; }
else if (strcmp (word, "-rawmethods") == 0)
{
raw_methods = TRUE ;
}
else if (strcmp (word, "-version") == 0
&& aceInInt (command_in, &version))
{ ; }
else if (strcmp (word, "-list") == 0)
{
isList = TRUE ;
}
else if (strcmp (word, "-source") == 0
&& aceInCheck (command_in, "w"))
{
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
addToSet (command_in, sourceSet) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
;
}
else if (strcmp (word, "-feature") == 0
&& aceInCheck (command_in, "w"))
{
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
addToSet (command_in, featSet) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
;
}
else
goto usage ;
}
aceOutPrint(dump_out, "%s\n", getDASHeader()) ;
level = -1 ;
makeTags(handle, "DASGFF", NULL, &das_start, &das_end) ;
dumpTagStart(dump_out, &level, das_start) ;
gff_atts = hprintf(handle, "version=\"%s\" href=\"%s\"", "1.0", "url") ;
makeTags(handle, "GFF", gff_atts, &gff_start, &gff_end) ;
dumpTagStart(dump_out, &level, gff_start) ;
GFFRefSeqPos(look, version,
&refSeq, &seqKey, &reversed,
&offset, &key_start, &key_end,
&feature_start, &feature_end) ;
level-- ; /* dump stuff is same level as GFF tag. */
seg_atts = hprintf(handle, "id=\"%s\" start=\"%d\" stop=\"%d\" version=\"%s\" \" label=\"%s\"",
nameWithClass(seqKey), key_start, key_end,
timeShow(timeParse("today")), name(seqKey)) ;
makeTags(handle, "SEGMENT", seg_atts, &seg_start, &seg_end) ;
dumpTagStart(dump_out, &level, seg_start) ;
/* Set up data/structs that writeDASFeature() will need, note we use GStrings
* because they are appendable and reusable which should help with performance. */
cb_data = messalloc(sizeof(DasGFFDataStruct)) ;
cb_data->fo = dump_out ;
cb_data->level = &level ;
cb_data->handle = handle ;
cb_data->attributes = g_string_sized_new(DAS_BUFFER_INITLEN) ;
cb_data->value = g_string_sized_new(DAS_BUFFER_INITLEN) ;
result = GFFDump(writeDASFeature, (void *)cb_data, look, version,
seqKey, offset, feature_start, feature_end,
GFF_LIST_NONE, NULL, raw_methods, NULL,
sourceSet, featSet, methodSet,
include_source, include_feature, include_method, FALSE) ;
g_string_free(cb_data->attributes, TRUE) ;
g_string_free(cb_data->value, TRUE) ;
messfree(cb_data) ;
dumpTagEnd(dump_out, &level, seg_end) ;
level++ ;
dumpTagEnd(dump_out, &level, gff_end) ;
dumpTagEnd(dump_out, &level, das_end) ;
aceOutDestroy (dump_out);
handleDestroy (handle) ;
if (result)
aceOutPrint(result_out, "// FMAP_FEATURES %s %d %d\n", freeprotect (name(refSeq)),
look->zoneMin+1+offset, look->zoneMax+offset) ;
return ;
usage:
aceOutDestroy (dump_out);
aceOutPrint (result_out, "// gif seqfeatures error: usage: SEQFEATURES [-coords x1 x2] ") ;
aceOutPrint (result_out, "[-file fname] [-refseq sequence] [-version 1|2] ") ;
aceOutPrint (result_out, "[-list] [-source source(s)] [-feature feature(s)]\n") ;
handleDestroy (handle) ;
return ;
}
/**************************************************************/
/* Write out sequence DNA in DAS format. */
void dasDNA (ACEIN command_in, ACEOUT result_out, FeatureMap look)
{
KEY key ;
int x1, x2 ;
ACEOUT fo = 0, dump_out = 0;
STORE_HANDLE handle = handleCreate() ;
char *word ;
char *dna_start, *dna_end,
*seq_start, *seq_end, *seq_atts,
*raw_start, *raw_end, *raw_atts ;
int level ;
messAssert((command_in && result_out && verifyFeatureMap(look, dasDNA))) ;
/* by default output goes to same place as normal command results */
dump_out = aceOutCopy (result_out, 0);
while (aceInCheck (command_in, "w"))
{
word = aceInWord (command_in) ;
if (strcmp (word, "-coords") == 0
&& aceInInt (command_in, &x1)
&& aceInInt (command_in, &x2)
&& (x2 != x1))
{
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
setZoneUserCoords (look, x1, x2) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
}
else if (strcmp (word, "-file") == 0
&& aceInCheck (command_in, "w")
&& (fo = aceOutCreateToFile (aceInPath (command_in), "w", 0)))
{
/* write to file instead of default output */
aceOutDestroy (dump_out);
dump_out = fo;
}
else
goto usage ;
}
key = look->seqKey ; x1 = look->start ; x2 = look->stop ;
/* If we extend this to do spliced and dna stuff then
* WE NEED TO CHECK OF look->seq is same as look->seqorig and if not, we should output
* look->seqorig for the spliced dna _only_.....*/
x1++, x2++ ; /* fMap keeps 0-based coords and we need to
report in 1-based coords. */
/* Needs to be removed in the end.... */
aceOutPrint (result_out, "// FMAP_DNA %s %d %d\n", freeprotect (name(key)), x1, x2) ;
/* Dump the dna in DAS format. */
aceOutPrint(dump_out, "%s\n", getDASHeader()) ;
level = -1 ;
makeTags(handle, "DASDNA", NULL, &dna_start, &dna_end) ;
dumpTagStart(dump_out, &level, dna_start) ;
seq_atts = hprintf(handle, "id=\"%s\" start=\"%d\" stop=\"%d\" version=\"%s\"",
name(key),
x1, x2, "X.XX") ;
makeTags(handle, "SEQUENCE", seq_atts, &seq_start, &seq_end) ;
dumpTagStart(dump_out, &level, seq_start) ;
raw_atts = hprintf(handle, "length=\"%d\"", (x2 - x1 + 1)) ;
makeTags(handle, "DNA", raw_atts, &raw_start, &raw_end) ;
dumpTagStart(dump_out, &level, raw_start) ;
/* Won't be indented at the moment..... */
dnaRawDump(look->dna, look->zoneMin, look->zoneMax-1, dump_out, TRUE) ;
dumpTagEnd(dump_out, &level, raw_end) ;
dumpTagEnd(dump_out, &level, seq_end) ;
dumpTagEnd(dump_out, &level, dna_end) ;
aceOutDestroy (dump_out);
handleDestroy(handle) ;
return;
usage:
aceOutDestroy (dump_out);
handleDestroy(handle) ;
aceOutPrint (result_out, "// dasdna error: usage: dasdna [-coords x1 x2] [-file fname]\n") ;
return;
}
/*
* -------------------- INTERNAL FUNCTIONS --------------------
*/
/* Makes the start and end xml format tags. */
static void makeTags(STORE_HANDLE handle,
char *tag, char *attributes, char **start_tag_out, char **end_tag_out)
{
if (start_tag_out)
{
*start_tag_out = hprintf(handle, "<%s%s%s>",
tag,
attributes ? " " : "",
attributes ? attributes: "") ;
}
if (end_tag_out)
{
*end_tag_out = hprintf(handle, "</%s>", tag) ;
}
return ;
}
/* Indenting only needed for human output really, should not do this for normal output. */
static void indent(ACEOUT fo, int level)
{
int i ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
/* THIS BOMBS OUT IN THE GLIB STUFF SOMEWHERE....THIS ROUTINE IS A HACK TO COPE WITH THIS.... */
aceOutPrint(fo, "%*s", level * 3, " ") ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
for (i = 0 ; i < (level * 3) ; i++)
{
aceOutPrint(fo, "%s", " ") ;
}
return ;
}
/* routines to dump start, end or start & end tags. */
static void dumpTagStart(ACEOUT fo, int *level, char *tag)
{
(*level)++ ;
indent(fo, *level) ;
aceOutPrint(fo, "%s\n", tag) ;
return ;
}
static void dumpTagEnd(ACEOUT fo, int *level, char *tag)
{
indent(fo, *level) ;
aceOutPrint(fo, "%s\n", tag) ;
(*level)-- ;
return ;
}
static void dumpTagComplete(ACEOUT fo, int *level,
char *tag_name, char *tag_attributes, char *tag_value)
{
(*level)++ ;
indent(fo, *level) ;
aceOutPrint(fo, "<%s%s%s>%s</%s>\n",
tag_name,
tag_attributes ? " " : "",
tag_attributes ? tag_attributes : "",
tag_value,
tag_name) ;
(*level)-- ;
return ;
}
/* Return standard format DAS header. */
static char *getDASHeader(void)
{
char *header = "<?xml version=\"1.0\" standalone=\"no\"?>\n"
"<!DOCTYPE DASDNA SYSTEM \"http://www.biodas.org/dtd/dasdna.dtd\">" ;
return (header) ;
}
/* Callback routine (see wh/gff.h) which gets called from GFFDump() so we output
* GFF information in the format we like. NB segType added for debugging in
* WriteGFFLine which is the other callback routine. */
static void writeDASFeature(void *app_data,
char *seqname, char *seqclass, char *method, BOOL is_structural,
char *source, char *feature, int start, int end,
float *score, char strand, char frame,
char *attributes, char *comments, int segType)
{
DasGFFData cb_data = (DasGFFData)app_data ;
ACEOUT dump_out = cb_data->fo ;
STORE_HANDLE handle = cb_data->handle ;
int *level = cb_data->level ;
char *feature_start, *feature_end,
*type_start, *type_end,
*method_start, *method_end ;
GString *tag_attributes = cb_data->attributes ;
GString *tag_value = cb_data->value ;
g_string_sprintf(tag_attributes, "id=\"%s\" label=\"%s\"",
source, feature) ;
makeTags(handle, "FEATURE", tag_attributes->str, &feature_start, &feature_end) ;
dumpTagStart(dump_out, level, feature_start) ;
g_string_sprintf(tag_attributes, "id=\"%s:%s\" category=\"%s:%s\"%s",
method, source,
method, source,
is_structural ? " reference=\"yes\"" : "") ;
dumpTagComplete(dump_out, level, "TYPE", tag_attributes->str, source) ;
g_string_sprintf(tag_attributes, "id=\"%s\"", method) ;
dumpTagComplete(dump_out, level, "METHOD", tag_attributes->str, method) ;
g_string_sprintf(tag_value, "%d", start) ;
dumpTagComplete(dump_out, level, "START", NULL, tag_value->str) ;
g_string_sprintf(tag_value, "%d", end) ;
dumpTagComplete(dump_out, level, "END", NULL, tag_value->str) ;
g_string_sprintf(tag_value, "%f", score) ;
dumpTagComplete(dump_out, level, "SCORE", NULL, tag_value->str) ;
g_string_sprintf(tag_value, "%c", strand) ;
dumpTagComplete(dump_out, level, "ORIENTATION", NULL, tag_value->str) ;
g_string_sprintf(tag_value, "%c", frame) ;
dumpTagComplete(dump_out, level, "FRAME", NULL, tag_value->str) ;
dumpTagComplete(dump_out, level, "NOTE", NULL, attributes) ;
/* Need code to separate out homol stuff from attributes string..... */
dumpTagEnd(dump_out, level, feature_end) ;
return ;
}
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