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-rw-r--r--demo/tbl2asn.c793
1 files changed, 600 insertions, 193 deletions
diff --git a/demo/tbl2asn.c b/demo/tbl2asn.c
index ceae97b3..11c2f827 100644
--- a/demo/tbl2asn.c
+++ b/demo/tbl2asn.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 5/5/00
*
-* $Revision: 6.297 $
+* $Revision: 6.327 $
*
* File Description:
*
@@ -73,7 +73,7 @@ static char *date_of_compilation = __DATE__;
#include <objmacro.h>
#include <macroapi.h>
-#define TBL2ASN_APP_VER "14.3"
+#define TBL2ASN_APP_VER "15.4"
CharPtr TBL2ASN_APPLICATION = TBL2ASN_APP_VER;
@@ -83,6 +83,7 @@ typedef struct cleanupargs {
Boolean add_notes_to_overlapping_cds_without_abc;
Boolean extend_partial_features_to_gaps_or_ends;
Boolean add_exception_to_nonextendable_partials;
+ Boolean add_exception_to_short_introns;
FILE * cleanup_log;
} CleanupArgsData, PNTR CleanupArgsPtr;
@@ -96,6 +97,7 @@ typedef struct tblargs {
Boolean alignset;
Boolean gapped;
Boolean phrapace;
+ Boolean ftable;
Boolean genprodset;
Boolean linkbyoverlap;
Boolean linkbyproduct;
@@ -108,6 +110,7 @@ typedef struct tblargs {
Boolean dopublookup;
CharPtr accn;
CharPtr center;
+ Int4 project_version;
CharPtr organism;
CharPtr srcquals;
CharPtr comment;
@@ -1031,6 +1034,8 @@ static void PrintOneGeneLine (
SeqIdPtr sip;
CharPtr str;
TextSeqIdPtr tsip;
+ RnaRefPtr rrp;
+ RNAGenPtr rgp;
if (fp == NULL) return;
@@ -1142,6 +1147,13 @@ static void PrintOneGeneLine (
rna_type = gbq->val;
}
}
+ if (rna->data.choice == SEQFEAT_RNA
+ && (rrp = (RnaRefPtr) rna->data.value.ptrvalue) != NULL
+ && rrp->ext.choice == 3
+ && (rgp = (RNAGenPtr) rrp->ext.value.ptrvalue) != NULL
+ && StringDoesHaveText (rgp->_class)) {
+ rna_type = rgp->_class;
+ }
break;
case FEATDEF_tmRNA :
rna_type = "tmRNA";
@@ -1295,7 +1307,7 @@ static void GeneReportOneBsp (
SeqMgrFeatContext fcontext;
GmcDataPtr gdp, head;
GeneRefPtr grp;
- Int2 i, j, k, numgene, numcds, numrna, total;
+ Int2 i, j = 1, k, numgene, numcds, numrna, total;
SeqFeatPtr matchsfp, sfp, tmp;
SeqFeatXrefPtr xref;
@@ -1331,7 +1343,6 @@ static void GeneReportOneBsp (
if (head == NULL) return;
gdp = head;
- total = 0;
sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &fcontext);
while (sfp != NULL) {
if (sfp->data.choice == SEQFEAT_CDREGION || sfp->data.choice == SEQFEAT_RNA) {
@@ -1348,11 +1359,9 @@ static void GeneReportOneBsp (
}
}
gdp++;
- total++;
} else if (sfp->data.choice == SEQFEAT_GENE) {
gdp->gene = sfp;
gdp++;
- total++;
}
sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &fcontext);
}
@@ -1647,7 +1656,7 @@ static void EnhanceOneRna (
StringCat (nwstr, tmp);
if (nm_gbq != NULL) {
nm_gbq->val = (Pointer) nwstr;
- } else {
+ } else if (rrp != NULL) {
rrp->ext.value.ptrvalue = (Pointer) nwstr;
}
MemFree (name);
@@ -1667,7 +1676,7 @@ static void EnhanceOneRna (
StringCat (nwstr, str);
if (nm_gbq != NULL) {
nm_gbq->val = (Pointer) nwstr;
- } else {
+ } else if (rrp != NULL) {
rrp->ext.value.ptrvalue = (Pointer) nwstr;
}
MemFree (name);
@@ -2032,96 +2041,6 @@ static void GetFirstBiop (
*biopp = biop;
}
-static DatePtr DateParse (
- CharPtr str
-)
-
-{
- Int4 day = -1, month = -1, year = -1;
- DatePtr dp;
- CharPtr ptr;
- Char tmp [64];
- long int val;
-
- if (StringHasNoText (str)) return NULL;
-
- StringNCpy_0 (tmp, str, sizeof (tmp));
- ptr = StringChr (tmp, '/');
- if (ptr == NULL) {
- ptr = StringChr (tmp, '-');
- }
- if (ptr != NULL) {
- *ptr = '\0';
- ptr++;
- if (sscanf (tmp, "%ld", &val) == 1) {
- month = (Int4) val;
- }
- str = StringChr (ptr, '/');
- if (str == NULL) {
- str = StringChr (ptr, '-');
- }
- if (str != NULL) {
- *str = '\0';
- str++;
- if (sscanf (ptr, "%ld", &val) == 1) {
- day = (Int4) val;
- }
- if (sscanf (str, "%ld", &val) == 1) {
- year = (Int4) val;
- }
- }
- }
-
- if (month < 0 || day < 0 || year < 2000) return NULL;
- if (month > 12 || day > 31 || year > 2099) return NULL;
-
- dp = DateNew ();
- if (dp == NULL) return NULL;
-
- dp->data [0] = 1;
- dp->data [1] = (Uint1) (year - 1900);
- dp->data [2] = (Uint1) month;
- dp->data [3] = (Uint1) day;
-
- return dp;
-}
-
-static void ParseTitleIntoSubmitBlock (
- SqnTagPtr stp,
- SubmitBlockPtr sbp
-)
-
-{
- DatePtr dp;
- CharPtr str;
-
- if (stp == NULL || sbp == NULL) return;
-
- str = SqnTagFind (stp, "hup");
- if (str != NULL) {
- sbp->hup = FALSE;
- sbp->reldate = DateFree (sbp->reldate);
- if (StringDoesHaveText (str)) {
- if (StringICmp (str, "y") == 0) {
- sbp->hup = TRUE;
- dp = DateCurr ();
- sbp->reldate = dp;
- if (dp != NULL) {
- if (dp->data [0] == 1) {
- (dp->data [1])++;
- }
- }
- } else {
- dp = DateParse (str);
- if (dp != NULL) {
- sbp->hup = TRUE;
- sbp->reldate = dp;
- }
- }
- }
- }
-}
-
static void ProcessOneNuc (
Uint2 entityID,
BioseqPtr bsp,
@@ -2396,7 +2315,7 @@ static void ProcessOneAnnot (
bsp = AttachSeqAnnotEntity (entityID, sap, tbl);
if (bsp == NULL) return;
- sep = GetTopSeqEntryForEntityID (entityID);
+ sep = GetTopSeqEntryForEntityID (entityID);
/* correct all idx parent pointers */
@@ -2827,6 +2746,25 @@ static void RnaProtTrailingCommaFix (SeqFeatPtr sfp, Pointer userdata)
}
}
+
+static Boolean FileHasMoreData (FILE *fp)
+{
+ Pointer dataptr;
+ Uint2 datatype;
+ Boolean rval = FALSE;
+
+ if (fp == NULL) {
+ return FALSE;
+ }
+ dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, TRUE, FALSE, TRUE, FALSE);
+ if (dataptr != NULL) {
+ rval = TRUE;
+ ObjMgrFree (datatype, dataptr);
+ }
+ return rval;
+}
+
+
static Uint2 ProcessOneAsn (
FILE* fp,
SubmitBlockPtr sbp,
@@ -2884,6 +2822,10 @@ static Uint2 ProcessOneAsn (
}
if (dataptr == NULL) return 0;
+ if (FileHasMoreData(fp)) {
+ Message (MSG_POSTERR, "File contains unexpected extra data");
+ }
+
sep = GetTopSeqEntryForEntityID (entityID);
bsp = FindNucBioseq (sep);
if (bsp == NULL) {
@@ -3677,7 +3619,7 @@ static Uint2 ProcessPhrapAce (
if (StringDoesHaveText (localname)) {
sip = MakeSeqID (localname);
- if (sip != NULL) {
+ if (sip != NULL && bsp != NULL) {
bsp->id = SeqIdSetFree (bsp->id);
bsp->id = sip;
SeqMgrReplaceInBioseqIndex (bsp);
@@ -3703,6 +3645,8 @@ static Uint2 ProcessBulkSet (
BioseqSetPtr bssp;
Uint2 entityID;
SeqEntryPtr lastsep, sep, topsep;
+ Raw2DeltData r;
+
/*
Pointer dataptr;
Uint2 datatype;
@@ -3771,7 +3715,16 @@ static Uint2 ProcessBulkSet (
}
lastsep = sep;
- ProcessOneNuc (entityID, bsp, sbp, src, tbl, template_molinfo);
+ if (tbl->raw2delt) {
+ r.entityID = entityID;
+ r.sbp = sbp;
+ r.src = src;
+ r.tbl = tbl;
+ r.template_molinfo = template_molinfo;
+ ProcessRaw2DeltCallback (bsp, &r);
+ } else {
+ ProcessOneNuc (entityID, bsp, sbp, src, tbl, template_molinfo);
+ }
}
SeqMgrLinkSeqEntry (topsep, 0, NULL);
@@ -4021,7 +3974,7 @@ static Uint2 ProcessDeltaSet (
if (StringDoesHaveText (localname)) {
sip = MakeSeqID (localname);
- if (sip != NULL) {
+ if (sip != NULL && bsp != NULL) {
bsp->id = SeqIdSetFree (bsp->id);
bsp->id = sip;
SeqMgrReplaceInBioseqIndex (bsp);
@@ -5596,75 +5549,290 @@ static void AddTemplateDescriptors (
}
}
+
+static Boolean UseProjectVersion (BioseqPtr bsp)
+{
+ SeqDescrPtr sdp;
+ SeqMgrDescContext context;
+ BioSourcePtr biop;
+ MolInfoPtr mip;
+
+ if (bsp == NULL) {
+ return FALSE;
+ }
+ if (ISA_aa (bsp->mol)) {
+ return FALSE;
+ }
+ if (bsp->repr != Seq_repr_delta) {
+ if (bsp->mol == Seq_mol_rna) {
+ /* suppress for mRNA */
+ sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &context);
+ if (sdp != NULL && (mip = (MolInfoPtr) sdp->data.ptrvalue) != NULL && mip->biomol == MOLECULE_TYPE_MRNA) {
+ return FALSE;
+ }
+ }
+ /* it's a contig */
+ return TRUE;
+ } else {
+ sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &context);
+ if (sdp != NULL && (biop = (BioSourcePtr) sdp->data.ptrvalue) != NULL && biop->genome == GENOME_chromosome) {
+ /* it's a chromosome */
+ return FALSE;
+ } else {
+ /* it's a scaffold */
+ return TRUE;
+ }
+ }
+}
+
+
+typedef struct genomizeseqid {
+ CharPtr center;
+ Int4 version;
+} GenomizeSeqIdData, PNTR GenomizeSeqIdPtr;
+
+
+static void UpdateGenomeId (SeqIdPtr sip, GenomizeSeqIdPtr gs)
+{
+ DbtagPtr db;
+ CharPtr fmt = "%s%02d";
+
+ if (sip == NULL || sip->choice != SEQID_GENERAL || gs == NULL || StringHasNoText (gs->center)) {
+ return;
+ }
+
+ db = (DbtagPtr) sip->data.ptrvalue;
+
+ db->db = MemFree (db->db);
+ if (gs->version < 1) {
+ db->db = StringSave (gs->center);
+ } else {
+ db->db = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (gs->center) + 15));
+ sprintf (db->db, fmt, gs->center, gs->version);
+ }
+}
+
+
+static void ReplaceLocalIdWithGenome (SeqIdPtr sip, GenomizeSeqIdPtr gs)
+{
+ ObjectIdPtr oip;
+ DbtagPtr db;
+ CharPtr fmt = "%s%02d";
+
+ if (sip == NULL || sip->choice != SEQID_LOCAL || gs == NULL || StringHasNoText (gs->center)) {
+ return;
+ }
+
+ oip = (ObjectIdPtr) sip->data.ptrvalue;
+
+ db = DbtagNew ();
+
+ if (gs->version < 1) {
+ db->db = StringSave (gs->center);
+ } else {
+ db->db = (CharPtr) MemNew (sizeof (Char) * (StringLen (fmt) + StringLen (gs->center) + 15));
+ sprintf (db->db, fmt, gs->center, gs->version);
+ }
+
+ db->tag = oip;
+ sip->choice = SEQID_GENERAL;
+ sip->data.ptrvalue = db;
+}
+
+
static void GenomizeSeqId (
SeqIdPtr sip,
Pointer userdata
)
{
- CharPtr accn = NULL;
- CharPtr center;
- DbtagPtr dbt;
- ObjectIdPtr oip;
+ GenomizeSeqIdPtr gs;
+ Int4 project_version;
+ BioseqPtr bsp;
+ SeqIdPtr cpy = NULL;
- if (sip == NULL || sip->choice != SEQID_LOCAL) return;
- center = (CharPtr) userdata;
- if (StringHasNoText (center)) return;
-
- oip = (ObjectIdPtr) sip->data.ptrvalue;
- if (oip == NULL) return;
- accn = oip->str;
- if (StringHasNoText (accn)) return;
+ if (sip == NULL || (gs = (GenomizeSeqIdPtr) userdata) == NULL) {
+ return;
+ }
+ if (sip->choice != SEQID_LOCAL && sip->choice != SEQID_GENERAL) {
+ return;
+ }
+
+ project_version = gs->version;
+ if (gs->version > 0) {
+ bsp = BioseqFind (sip);
+ if (bsp == NULL) {
+ cpy = SeqIdDup (sip);
+ if (cpy->choice == SEQID_LOCAL) {
+ ReplaceLocalIdWithGenome (cpy, gs);
+ } else if (cpy->choice == SEQID_GENERAL) {
+ UpdateGenomeId (cpy, gs);
+ }
+ bsp = BioseqFind (cpy);
+ if (bsp == NULL) {
+ gs->version = 0;
+ if (cpy->choice == SEQID_LOCAL) {
+ ReplaceLocalIdWithGenome (cpy, gs);
+ } else if (cpy->choice == SEQID_GENERAL) {
+ UpdateGenomeId (cpy, gs);
+ }
+ gs->version = project_version;
+ }
+ cpy = SeqIdFree (cpy);
+ }
+ if (bsp != NULL && !UseProjectVersion (bsp)) {
+ gs->version = 0;
+ }
+ }
- dbt = DbtagNew ();
- if (dbt == NULL) return;
- oip = ObjectIdNew ();
- if (oip == NULL) return;
- oip->str = StringSave (accn);
- dbt->db = StringSave (center);
- dbt->tag = oip;
+ if (sip->choice == SEQID_LOCAL) {
+ ReplaceLocalIdWithGenome (sip, gs);
+ } else if (sip->choice == SEQID_GENERAL) {
+ UpdateGenomeId (sip, gs);
+ }
- sip->data.ptrvalue = ObjectIdFree ((ObjectIdPtr) sip->data.ptrvalue);
- sip->data.ptrvalue = (Pointer) dbt;
- sip->choice = SEQID_GENERAL;
+ gs->version = project_version;
}
+
static void GenomizeFeatureSeqIds (
SeqFeatPtr sfp,
- Pointer userdata
+ GenomizeSeqIdPtr gs
)
{
- VisitSeqIdsInSeqLoc (sfp->location, userdata, GenomizeSeqId);
+ RnaRefPtr rrp;
+ tRNAPtr trp;
+ CodeBreakPtr cbp;
+ CdRegionPtr crp;
+ GBQualPtr gbq;
+ SeqIdPtr sip;
+ Char id_txt[500];
+ Int4 project_version;
+
+ /* replace ids in locations common to all features */
+ VisitSeqIdsInSeqLoc (sfp->location, gs, GenomizeSeqId);
+
+ project_version = gs->version;
+ if (sfp->data.choice == SEQFEAT_CDREGION) {
+ /* protein IDs don't use version */
+ gs->version = 0;
+ }
+ VisitSeqIdsInSeqLoc (sfp->product, gs, GenomizeSeqId);
+ gs->version = project_version;
+ for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) {
+ if (StringICmp (gbq->qual, "protein_id") == 0 || StringICmp (gbq->qual, "transcript_id") == 0) {
+ sip = MakeSeqID (gbq->val);
+ if (sip != NULL) {
+ /* protein IDs and mRNA IDs don't use version */
+ gs->version = 0;
+ GenomizeSeqId (sip, gs);
+ gs->version = project_version;
+ SeqIdWrite (sip, id_txt, PRINTID_FASTA_SHORT, sizeof (id_txt) - 1);
+ if (StringICmp (gbq->val, id_txt) != 0) {
+ gbq->val = MemFree (gbq->val);
+ gbq->val = StringSave (id_txt);
+ }
+ }
+ }
+ }
+
+ /* specific feature data */
+ if (sfp->data.choice == SEQFEAT_RNA
+ && (rrp = (RnaRefPtr) sfp->data.value.ptrvalue) != NULL
+ && rrp->ext.choice == 2
+ && (trp = (tRNAPtr) rrp->ext.value.ptrvalue) != NULL
+ && trp->anticodon != NULL)
+ {
+ VisitSeqIdsInSeqLoc (trp->anticodon, gs, GenomizeSeqId);
+ }
+ else if (sfp->data.choice == SEQFEAT_CDREGION
+ && (crp = (CdRegionPtr) sfp->data.value.ptrvalue) != NULL)
+ {
+ for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) {
+ VisitSeqIdsInSeqLoc (cbp->loc, gs, GenomizeSeqId);
+ }
+ }
}
-static void GenomizeGraphSeqIds (
+
+static void GenomizeGraphIds (
SeqGraphPtr sgp,
- Pointer userdata
+ GenomizeSeqIdPtr gs
)
{
- VisitSeqIdsInSeqGraph (sgp, userdata, GenomizeSeqId);
+ if (sgp != NULL && gs != NULL) {
+ VisitSeqIdsInSeqLoc (sgp->loc, gs, GenomizeSeqId);
+ }
}
+
static void MakeGenomeCenterID (
BioseqPtr bsp,
Pointer userdata
)
{
- CharPtr center;
+ GenomizeSeqIdPtr gs;
+ SeqEntryPtr top_sep;
+ SeqIdPtr sip, sip_new, sip_local;
+ Int4 project_version;
if (bsp == NULL) return;
- center = (CharPtr) userdata;
- if (StringHasNoText (center)) return;
- VisitSeqIdsInBioseq (bsp, userdata, GenomizeSeqId);
- SeqMgrReplaceInBioseqIndex (bsp);
- VisitFeaturesOnBsp (bsp, userdata, GenomizeFeatureSeqIds);
- VisitGraphsOnBsp (bsp, userdata, GenomizeGraphSeqIds);
+ top_sep = GetTopSeqEntryForEntityID (bsp->idx.entityID);
+
+ gs = (GenomizeSeqIdPtr) userdata;
+ if (gs == NULL || StringHasNoText (gs->center)) return;
+
+ project_version = gs->version;
+ if (!UseProjectVersion(bsp)) {
+ gs->version = 0;
+ }
+
+ for (sip = bsp->id; sip != NULL; sip = sip->next) {
+ if (sip->choice == SEQID_LOCAL || sip->choice == SEQID_GENERAL) {
+ sip_local = SeqIdDup (sip);
+ sip_new = SeqIdDup (sip);
+ if (sip->choice == SEQID_LOCAL) {
+ ReplaceLocalIdWithGenome (sip_new, gs);
+ } else {
+ UpdateGenomeId (sip_new, gs);
+ }
+ ReplaceSeqIdWithSeqId (sip_local, sip_new, top_sep);
+ sip_local = SeqIdFree (sip_local);
+ sip_new = SeqIdFree (sip_new);
+ break;
+ }
+ }
+ gs->version = project_version;
+}
+
+
+static void GenomizeSeqAnnot (SeqAnnotPtr sap, GenomizeSeqIdPtr gs)
+{
+ SeqFeatPtr sfp;
+ SeqGraphPtr sgp;
+
+ if (gs == NULL || StringHasNoText (gs->center)) return;
+
+ switch (sap->type) {
+ case 1: /* feature table */
+ for (sfp = sap->data; sfp != NULL; sfp = sfp->next) {
+ GenomizeFeatureSeqIds (sfp, gs);
+ }
+ break;
+ case 3: /* graph */
+ for (sgp = sap->data; sgp != NULL; sgp = sgp->next) {
+ GenomizeGraphIds (sgp, gs);
+ }
+ break;
+ }
+
}
+
static void MakeAccessionID (
BioseqPtr bsp,
Pointer userdata
@@ -5941,7 +6109,7 @@ static ValNodePtr FindItemListForClickableItemCategory (ValNodePtr list, CharPtr
}
-static void Tbl2AsnFixBacterialExtendablePartials (ValNodePtr discrepancy_list, FILE *cleanup_log)
+static void Tbl2AsnFixExtendablePartials (ValNodePtr discrepancy_list, FILE *cleanup_log)
{
ValNodePtr vnp, vnp_c;
ClickableItemPtr cip;
@@ -5987,7 +6155,7 @@ static void Tbl2AsnFixBacterialExtendablePartials (ValNodePtr discrepancy_list,
}
orig_location = MemFree (orig_location);
}
- Tbl2AsnFixBacterialExtendablePartials (cip->subcategories, cleanup_log);
+ Tbl2AsnFixExtendablePartials (cip->subcategories, cleanup_log);
}
}
}
@@ -6043,6 +6211,56 @@ static void Tbl2AsnFixBacterialNonExtendablePartials (ValNodePtr discrepancy_lis
}
+static void RemoveTitleForShortIntronProtein (SeqFeatPtr sfp)
+{
+ BioseqPtr prot_bsp;
+ SeqDescrPtr sdp;
+ SeqMgrDescContext context;
+ CharPtr title;
+ ObjValNodePtr ovp;
+
+ if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION || sfp->product == NULL
+ || (prot_bsp = BioseqFindFromSeqLoc (sfp->product)) == NULL) {
+ return;
+ }
+
+ for (sdp = SeqMgrGetNextDescriptor (prot_bsp, NULL, Seq_descr_title, &context);
+ sdp != NULL;
+ sdp = SeqMgrGetNextDescriptor (prot_bsp, sdp, Seq_descr_title, &context)) {
+ title = (CharPtr) sdp->data.ptrvalue;
+ if (StringNCmp (title, "LOW QUALITY PROTEIN:", 20) != 0
+ && sdp->extended != 0
+ && (ovp = (ObjValNodePtr) sdp) != NULL) {
+ ovp->idx.deleteme = TRUE;
+ }
+ }
+}
+
+
+static void Tbl2AsnAddExceptionsToShortIntrons (ValNodePtr discrepancy_list, FILE *cleanup_log)
+{
+ ValNodePtr vnp, vnp_c;
+ ClickableItemPtr cip;
+ LogInfoData lid;
+
+ MemSet (&lid, 0, sizeof (LogInfoData));
+ lid.data_in_log = FALSE;
+ lid.fp = cleanup_log;
+ for (vnp_c = discrepancy_list; vnp_c != NULL; vnp_c = vnp_c->next) {
+ cip = vnp_c->data.ptrvalue;
+ if (cip != NULL) {
+ AddExceptionsToShortIntrons (cip->item_list, NULL, &lid);
+ for (vnp = cip->item_list; vnp != NULL; vnp = vnp->next) {
+ if (vnp->choice == OBJ_SEQFEAT) {
+ RemoveTitleForShortIntronProtein (vnp->data.ptrvalue);
+ }
+ }
+ Tbl2AsnAddExceptionsToShortIntrons (cip->subcategories, cleanup_log);
+ }
+ }
+}
+
+
static void DoTbl2AsnCleanup (SeqEntryPtr sep, CleanupArgsPtr c)
{
ValNodePtr sep_list = NULL;
@@ -6084,12 +6302,12 @@ static void DoTbl2AsnCleanup (SeqEntryPtr sep, CleanupArgsPtr c)
SeqMgrIndexFeatures (entityID, NULL);
if (c->extend_partial_features_to_gaps_or_ends) {
- FindBacterialExtendablePartials (&discrepancy_list, sep_list);
+ FindExtendablePartials (&discrepancy_list, sep_list);
if (discrepancy_list != NULL) {
if (c->cleanup_log != NULL) {
fprintf (c->cleanup_log, "\nExtended Partial Features\n");
}
- Tbl2AsnFixBacterialExtendablePartials (discrepancy_list, c->cleanup_log);
+ Tbl2AsnFixExtendablePartials (discrepancy_list, c->cleanup_log);
SeqMgrClearFeatureIndexes (entityID, NULL);
SeqMgrIndexFeatures (entityID, NULL);
discrepancy_list = FreeClickableList (discrepancy_list);
@@ -6107,6 +6325,19 @@ static void DoTbl2AsnCleanup (SeqEntryPtr sep, CleanupArgsPtr c)
}
sep_list = ValNodeFree (sep_list);
}
+
+ if (c->add_exception_to_short_introns) {
+ ValNodeAddPointer (&sep_list, 0, sep);
+ entityID = ObjMgrGetEntityIDForChoice (sep);
+ SeqMgrIndexFeatures (entityID, NULL);
+ FindShortIntrons(&discrepancy_list, sep_list);
+ Tbl2AsnAddExceptionsToShortIntrons (discrepancy_list, c->cleanup_log);
+ discrepancy_list = FreeClickableList (discrepancy_list);
+ sep_list = ValNodeFree (sep_list);
+ DeleteMarkedObjects (entityID, 0, NULL);
+ InstantiateProteinTitles (entityID, NULL);
+ }
+
}
@@ -6156,6 +6387,65 @@ static Boolean SeqEntryHasConflictingIDs (SeqEntryPtr sep)
}
}
+static void ProcessFeatTable (
+ FILE *fp,
+ CharPtr directory,
+ CharPtr results,
+ CharPtr base,
+ TblArgsPtr tbl
+)
+
+{
+ AsnIoPtr aip;
+ Pointer dataptr;
+ Uint2 datatype;
+ Boolean failure = FALSE;
+ Int4 linenum = 0;
+ Char path [PATH_MAX];
+ SeqAnnotPtr sap;
+
+ if (fp == NULL || tbl == NULL) return;
+
+ if (StringHasNoText (results)) {
+ results = directory;
+ }
+
+ dataptr = ReadFeatureTableFile (fp, &datatype, NULL, &linenum, &failure);
+ if (failure) return;
+ if (datatype != OBJ_SEQANNOT) return;
+
+ sap = (SeqAnnotPtr) dataptr;
+ if (sap == NULL) return;
+
+ BasicSeqAnnotCleanup (sap);
+
+ StringNCpy_0 (path, results, sizeof (path));
+ FileBuildPath (path, NULL, base);
+ StringCat (path, ".sap");
+
+ aip = AsnIoOpen (path, "w");
+ if (aip == NULL) return;
+
+ SeqAnnotAsnWrite (sap, aip, NULL);
+
+ AsnIoFlush (aip);
+ AsnIoClose (aip);
+}
+
+
+static Boolean IsGenProdSet (SeqEntryPtr sep)
+{
+ BioseqSetPtr bssp;
+
+ if (sep == NULL || !IS_Bioseq_set (sep)
+ || (bssp = (BioseqSetPtr) sep->data.ptrvalue) == NULL
+ || bssp->_class != BioseqseqSet_class_gen_prod_set) {
+ return FALSE;
+ } else {
+ return TRUE;
+ }
+}
+
static void ProcessOneRecord (
SubmitBlockPtr sbp,
@@ -6175,8 +6465,7 @@ static void ProcessOneRecord (
{
AsnTypePtr atp_bssse;
BioSourcePtr biop;
- BioseqPtr bsp, feat_bsp;
- Boolean already_converted_ids = FALSE;
+ BioseqPtr bsp;
BioseqSetPtr bssp = NULL;
Char buf [256];
SeqMgrFeatContext context;
@@ -6220,6 +6509,16 @@ static void ProcessOneRecord (
SeqEntryPtr tmp;
MolInfoPtr template_molinfo = NULL;
ValNodePtr cmt_errors, vnp;
+ GenomizeSeqIdData gs;
+
+ if (tbl->ftable) {
+ fp = OpenOneFile (directory, base, ".tbl");
+ if (fp != NULL) {
+ ProcessFeatTable (fp, directory, results, base, tbl);
+ FileClose (fp);
+ }
+ return;
+ }
fp = OpenOneFile (directory, base, suffix);
if (fp == NULL) return;
@@ -6281,28 +6580,8 @@ static void ProcessOneRecord (
return;
}
- if (tbl->dotaxlookup) {
- sep = GetTopSeqEntryForEntityID (entityID);
- if (sep != NULL) {
-
- /* optionally do network taxonomy lookup - prior to instantiating mRNA and protein titles */
-
- Taxon3ReplaceOrgInSeqEntry (sep, FALSE);
- }
- }
-
- if (tbl->dopublookup) {
- sep = GetTopSeqEntryForEntityID (entityID);
- if (sep != NULL) {
-
- /* optionally do network publication lookup of just PMID references */
-
- VisitPubdescsInSep (sep, NULL, LookupPubdesc);
- }
- }
-
organism = NULL;
- if (tbl->genprodset) {
+ if (tbl->genprodset && bssp != NULL) {
descr = ExtractBioSourceAndPubs (bssp->seq_set);
for (sdp = descr; sdp != NULL; sdp = sdp->next) {
if (sdp->choice != Seq_descr_source) continue;
@@ -6317,6 +6596,17 @@ static void ProcessOneRecord (
ReplaceBioSourceAndPubs (gsep, descr);
}
+ gs.center = tbl->center;
+ /* get version from args later */
+ gs.version = tbl->project_version;
+ /* genomize the IDs */
+ if (!StringHasNoText (gs.center)) {
+ sep = GetTopSeqEntryForEntityID (entityID);
+ SeqMgrIndexFeatures (entityID, NULL);
+
+ VisitBioseqsInSep (sep, &gs, MakeGenomeCenterID);
+ }
+
/* read one or more feature tables from .tbl file */
if (StringDoesHaveText (tbl->tableFile)) {
@@ -6340,12 +6630,8 @@ static void ProcessOneRecord (
sap = (SeqAnnotPtr) dataptr;
- if (!StringHasNoText (tbl->center) && !already_converted_ids) {
- feat_bsp = GetBioseqReferencedByAnnot (sap, entityID);
- if (feat_bsp == NULL) {
- VisitBioseqsInSep (sep, tbl->center, MakeGenomeCenterID);
- already_converted_ids = TRUE;
- }
+ if (!StringHasNoText (gs.center)) {
+ GenomizeSeqAnnot (sap, &gs);
}
ProcessOneAnnot (sap, entityID, tbl);
@@ -6549,6 +6835,15 @@ static void ProcessOneRecord (
FileClose (fp);
}
+ /* re-genomize the IDs, in case a source descriptor was added that makes a sequence a chromosome (and therefore should not have the version) */
+ if (!StringHasNoText (gs.center) && gs.version > 0) {
+ sep = GetTopSeqEntryForEntityID (entityID);
+ SeqMgrIndexFeatures (entityID, NULL);
+
+ VisitBioseqsInSep (sep, &gs, MakeGenomeCenterID);
+ }
+
+
/* finish processing */
if (sbp == NULL) {
@@ -6576,7 +6871,7 @@ static void ProcessOneRecord (
sep = GetTopSeqEntryForEntityID (entityID);
}
- if (! tbl->genprodset) {
+ if (! tbl->genprodset && (!IsGenProdSet(sep) || tbl->gpstonps)) {
VisitFeaturesInSep (sep, NULL, RemoveGBQualIDs);
}
if (sdphead != NULL) {
@@ -6625,6 +6920,18 @@ static void ProcessOneRecord (
FileClose (fp);
}
+ if (tbl->dotaxlookup) {
+ /* optionally do network taxonomy lookup - prior to instantiating mRNA and protein titles */
+
+ Taxon3ReplaceOrgInSeqEntry (sep, FALSE);
+ }
+
+ if (tbl->dopublookup) {
+ /* optionally do network publication lookup of just PMID references */
+
+ VisitPubdescsInSep (sep, NULL, LookupPubdesc);
+ }
+
msev = ErrSetMessageLevel (SEV_MAX);
move_cds (sep);
@@ -6655,8 +6962,8 @@ static void ProcessOneRecord (
/* currently copying ncRNA feature onto product */
VisitFeaturesInSep (sep, NULL, CopyNcRna);
}
- if (! tbl->genprodset) {
- VisitFeaturesInSep (sep, NULL, ClearRnaProducts);
+ if (! tbl->genprodset && (!IsGenProdSet(sep) || tbl->gpstonps)) {
+ VisitFeaturesInSep (sep, NULL, ClearRnaProducts);
}
if (tbl->removeunnecxref) {
@@ -6680,6 +6987,18 @@ static void ProcessOneRecord (
SeqMgrIndexFeatures (entityID, NULL);
bsp = FindNucBioseq (sep);
+ /* get organism name after any taxonomy lookup */
+ sdp = GetNextDescriptorUnindexed (bsp, Seq_descr_source, NULL);
+ if (sdp != NULL) {
+ biop = (BioSourcePtr) sdp->data.ptrvalue;
+ if (biop != NULL) {
+ orp = biop->org;
+ if (orp != NULL && StringDoesHaveText (orp->taxname)) {
+ organism = orp->taxname;
+ }
+ }
+ }
+
if (tbl->smarttitle) {
MakeSmartRnaTitles (bsp, organism);
} else {
@@ -6691,10 +7010,6 @@ static void ProcessOneRecord (
}
}
- if (StringDoesHaveText (tbl->center) && !already_converted_ids) {
- VisitBioseqsInSep (sep, tbl->center, MakeGenomeCenterID);
- }
-
if (StringDoesHaveText (tbl->accn)) {
bsp = FindNucBioseq (sep);
MakeAccessionID (bsp, tbl->accn);
@@ -7280,6 +7595,64 @@ static Boolean MoreThanYearOld (void)
return FALSE;
}
+
+static void AddStructuredCommentsFromTabFileToDescriptorList (CharPtr fname, ValNodePtr PNTR descr_list)
+{
+ ValNodePtr err_list = NULL;
+ ValNodePtr table, header, line, vnp_l, tmp;
+ UserObjectPtr uop;
+ SeqDescrPtr sdp;
+ FILE *fp;
+
+ if (StringHasNoText (fname) || descr_list == NULL) {
+ return;
+ }
+ fp = FileOpen (fname, "r");
+ if (fp == NULL) {
+ Message (MSG_POSTERR, "Unable to open structured comment file %s", fname);
+ return;
+ }
+
+ table = ReadTabTableFromFile (fp);
+ if (table == NULL || table->next == NULL || table->data.ptrvalue == NULL) {
+ ValNodeAddPointer (&err_list, 0, StringSave ("Unable to read table from file"));
+ } else {
+ tmp = FlipTabTableAxes (table);
+ table = FreeTabTable (table);
+ table = tmp;
+
+ header = table->data.ptrvalue;
+ header = table->data.ptrvalue;
+ if (header == NULL || header->data.ptrvalue == NULL || header->next == NULL) {
+ ValNodeAddPointer (&err_list, 0, StringSave ("Bad header line"));
+ } else {
+ line = table->next;
+
+ while (line != NULL) {
+ tmp = CreateStructuredCommentsFromRow (header, line->data.ptrvalue, NULL, &err_list);
+ for (vnp_l = tmp; vnp_l != NULL; vnp_l = vnp_l->next) {
+ uop = (UserObjectPtr) vnp_l->data.ptrvalue;
+ sdp = SeqDescrNew (*descr_list);
+ if (*descr_list == NULL) {
+ *descr_list = sdp;
+ }
+ sdp->choice = Seq_descr_user;
+ sdp->data.ptrvalue = uop;
+ }
+ tmp = ValNodeFree (tmp);
+ line = line->next;
+ }
+ }
+ }
+ table = FreeTabTable (table);
+ FileClose (fp);
+ for (tmp = err_list; tmp != NULL; tmp = tmp->next) {
+ Message (MSG_POSTERR, "Error processing structured comment file %s: %s", fname, tmp->data.ptrvalue);
+ }
+ err_list = ValNodeFreeData (err_list);
+}
+
+
/* Args structure contains command-line arguments */
#define p_argInputPath 0
@@ -7323,6 +7696,8 @@ static Boolean MoreThanYearOld (void)
#define c_argCleanupOptions 38
#define z_argCleanupLogFile 39
#define X_argExtraFlags 40
+#define N_argProjectVersion 41
+#define w_argStructuredCommentFile 42
Args myargs [] = {
@@ -7427,7 +7802,8 @@ Args myargs [] = {
" d Correct Collection Dates (assume month first)\n"
" D Correct Collection Dates (assume day first)\n"
" b Append note to coding regions that overlap other coding regions with similar product names and do not contain 'ABC'\n"
- " x Extend partial ends of features by one or two nucleotides to abut gaps or sequence ends",
+ " x Extend partial ends of features by one or two nucleotides to abut gaps or sequence ends\n"
+ " s Add exception to short introns",
NULL, NULL, NULL,
TRUE, 'c', ARG_STRING, 0.0, 0, NULL},
{"Cleanup Log File", NULL, NULL, NULL,
@@ -7435,6 +7811,10 @@ Args myargs [] = {
{"Extra Flags (combine any of the following letters)\n"
" C Apply comments in .cmt files to all sequences\n", NULL, NULL, NULL,
TRUE, 'X', ARG_STRING, 0.0, 0, NULL},
+ {"Project Version Number", "0", NULL, NULL,
+ TRUE, 'N', ARG_INT, 0.0, 0, NULL},
+ {"Single Structured Comment File", NULL, NULL, NULL,
+ TRUE, 'w', ARG_FILE_IN, 0.0, 0, NULL},
};
Int2 Main (void)
@@ -7444,6 +7824,7 @@ Int2 Main (void)
Char app [64];
CharPtr base;
AsnTypePtr bssp_atp = NULL;
+ DatePtr cd;
CitSubPtr csp;
Pointer dataptr;
Uint2 datatype;
@@ -7551,39 +7932,46 @@ Int2 Main (void)
/* process new -a type argument */
ptr = myargs [a_argType].strvalue;
- if (StringICmp (ptr, "r20u") == 0) {
+ if (StringISearch (ptr, "r20u") != NULL) {
tbl.raw2delt = TRUE;
tbl.r2dmin = 20;
tbl.r2dunk100 = TRUE;
- } else if (StringICmp (ptr, "r20k") == 0) {
+ } else if (StringISearch (ptr, "r20k") != NULL) {
tbl.raw2delt = TRUE;
tbl.r2dmin = 20;
tbl.r2dunk100 = FALSE;
- } else if (StringICmp (ptr, "s") == 0) {
- tbl.fastaset = TRUE;
- } else if (StringICmp (ptr, "w1") == 0 || StringICmp (ptr, "s1") == 0) {
+ } else if (StringISearch (ptr, "di") != NULL) {
+ tbl.deltaset = TRUE;
+ tbl.implicitgaps = TRUE;
+ } else if (StringISearch (ptr, "d") != NULL) {
+ tbl.deltaset = TRUE;
+ }
+
+ if (StringISearch (ptr, "w1") != NULL || StringISearch (ptr, "s1") != NULL) {
tbl.fastaset = TRUE;
tbl.whichclass = 1;
- } else if (StringICmp (ptr, "w2") == 0 || StringICmp (ptr, "s2") == 0) {
+ } else if (StringISearch (ptr, "w2") != NULL || StringISearch (ptr, "s2") != NULL) {
tbl.fastaset = TRUE;
tbl.whichclass = 2;
- } else if (StringICmp (ptr, "w3") == 0 || StringICmp (ptr, "s3") == 0) {
+ } else if (StringISearch (ptr, "w3") != NULL || StringISearch (ptr, "s3") != NULL) {
tbl.fastaset = TRUE;
tbl.whichclass = 3;
- } else if (StringICmp (ptr, "w4") == 0 || StringICmp (ptr, "s4") == 0) {
+ } else if (StringISearch (ptr, "w4") != NULL || StringISearch (ptr, "s4") != NULL) {
tbl.fastaset = TRUE;
tbl.whichclass = 4;
- } else if (StringICmp (ptr, "d") == 0) {
- tbl.deltaset = TRUE;
- } else if (StringICmp (ptr, "di") == 0) {
- tbl.deltaset = TRUE;
- tbl.implicitgaps = TRUE;
- } else if (StringICmp (ptr, "l") == 0) {
+ } else if (StringISearch (ptr, "s") != NULL) {
+ tbl.fastaset = TRUE;
+ } else if (StringISearch (ptr, "l") != NULL) {
tbl.alignset = TRUE;
- } else if (StringICmp (ptr, "z") == 0) {
+ } else if (StringISearch (ptr, "z") != NULL) {
tbl.gapped = TRUE;
- } else if (StringICmp (ptr, "e") == 0) {
+ } else if (StringISearch (ptr, "e") != NULL) {
tbl.phrapace = TRUE;
+ /*
+ } else if (StringICmp (ptr, "t") == 0) {
+ tbl.ftable = TRUE;
+ suffix = ".tbl";
+ */
}
tbl.genprodset = (Boolean) myargs [g_argGenProdSet].intvalue;
@@ -7598,6 +7986,7 @@ Int2 Main (void)
tbl.gnltonote = (Boolean) myargs [h_argGnlToNote].intvalue;
tbl.accn = (CharPtr) myargs [A_argAccession].strvalue;
tbl.center = (CharPtr) myargs [C_argCenter].strvalue;
+ tbl.project_version = myargs[N_argProjectVersion].intvalue;
tbl.organism = (CharPtr) myargs [n_argOrgName].strvalue;
tbl.srcquals = (CharPtr) myargs [j_argSrcQuals].strvalue;
tbl.comment = (CharPtr) myargs [y_argComment].strvalue;
@@ -7771,6 +8160,10 @@ Int2 Main (void)
tbl.cleanup_args.add_exception_to_nonextendable_partials = TRUE;
}
+ if (StringChr (ptr, 's') != NULL) {
+ tbl.cleanup_args.add_exception_to_short_introns = TRUE;
+ }
+
ptr = (CharPtr) myargs [z_argCleanupLogFile].strvalue;
if (StringDoesHaveText (ptr)) {
tbl.cleanup_args.cleanup_log = FileOpen (ptr, "w");
@@ -7850,6 +8243,13 @@ Int2 Main (void)
if (dp != NULL) {
sbp->hup = TRUE;
sbp->reldate = dp;
+ cd = DateCurr ();
+ if (cd != NULL) {
+ if (DateMatch (dp, cd, FALSE) == -1) {
+ Message (MSG_POSTERR, "Record release date has already passed");
+ }
+ }
+ DateFree (cd);
}
}
}
@@ -7902,6 +8302,13 @@ Int2 Main (void)
}
}
+ /* if the user has specified a single file for structured comments, use it to create a descriptor
+ * to be added to all entries
+ */
+ AddStructuredCommentsFromTabFileToDescriptorList ((CharPtr) myargs [w_argStructuredCommentFile].strvalue,
+ &sdphead);
+
+
gotags = TextFsaNew ();
TextFsaAdd (gotags, "go_component");
TextFsaAdd (gotags, "go_function");
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-26 17:49:03 +0000