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fathom.c
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fathom.c
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/*****************************************************************************\
fathom.c
Annotation investigation utility
Copyright (C) Ian Korf 2002-2013.
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be included
in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
The MIT License (MIT) - opensource.org/licenses/MIT
\*****************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include "zoe.h"
/* globals */
char * DNA_file = NULL;
char * ANN_file = NULL;
char * PRE_file = NULL;
zoeFile DNA_stream;
zoeFile ANN_stream;
zoeFile PRE_stream;
zoeDNA DNA = NULL; /* the current DNA */
zoeDNA ANTI = NULL; /* reverse complement of DNA */
zoeFeatureTable ANN = NULL; /* the current annotation */
zoeFeatureTable PRE = NULL; /* the current predictions */
int PREDICTIONS = 0; /* flag to determine if predictions are present */
int ANTI_REQUIRED = 0; /* flag to determine if ANTI DNA is required */
struct score_s {
score_t plus_score;
score_t minus_score;
strand_t strand; /* +, -, =, 0 : 0 means pseudo-site on both strands */
};
typedef struct score_s score_s;
/* prototypes - showing relationships */
void help (void);
void anti (void);
void fuse (void);
void validate (void);
void reformat (void);
void genestats (void);
void split (void);
void exon_intron (void);
void extract ();
zoeFeatureVec extractAcceptor (void);
zoeFeatureVec extractDonor (void);
zoeFeatureVec extractStart (void);
zoeFeatureVec extractStop (void);
zoeFeatureVec extractPolyA (void);
zoeFeatureVec extractInter (void);
zoeFeatureVec extractIntron (void);
zoeFeatureVec extractUTR5 (void);
zoeFeatureVec extractUTR3 (void);
zoeFeatureVec extractExon (void);
zoeFeatureVec extractFeature (zoeLabel);
void export (void);
zoeHash kill_list (const zoeVec);
void categorize (void);
void export_feature (void);
void score_genes (void);
void filter_genes (void);
void compare_genes (void);
void ace_format (void);
void openData (void);
void closeData (void);
int getData (void);
static float gc_content (const zoeDNA dna) {
int i;
int count[5];
for (i = 0; i < 5; i++) count[i] = 0;
for (i = 0; i < dna->length; i++) count[(int)dna->s5[i]]++;
return (float)(count[1]+count[2]) / (float)(count[0]+count[1]+count[2]+count[3]);
}
static char usage[] = "\n\
FATHOM - sequence and annotation tool (version 2006-07-28)\n\n\
usage: fathom <ann> <dna> <commands>\n\
commands:\n\
-help report useful information\n\
-validate [-quiet]\n\
-gene-stats [-errors-ok -nucleotide -dinucleotide]\n\
-categorize <int>\n\
-export <int> [-plus -errors-ok]\n\
-extract <feature> -length <int> -offset <int>\n\
-exon-intron\n\
-split <-number <int> | -training <float> | -GC <float> | -repeat <float>>\n\
-ace-format <-gene-method <string> [-dna -extra <string>]>\n\
-compare-genes <predictions> [-details]\n\
-score-genes <hmm> [-errors-ok]\n\
-filter-genes <hmm> -min-score <float> -min-length <int>\n\
";
/*****************************************************************************\
Main Program
\*****************************************************************************/
int main (int argc, char **argv) {
/* command line */
zoeSetProgramName(argv[0]);
/* dataset */
zoeSetOption("-help", 0);
zoeSetOption("-randseed", 1);
zoeSetOption("-lcfilter", 0);
zoeSetOption("-lcsmooth", 0);
zoeSetOption("-validate", 0);
zoeSetOption("-quiet", 0);
zoeSetOption("-gene-stats", 0);
zoeSetOption("-nucleotide", 0);
zoeSetOption("-dinucleotide", 0);
zoeSetOption("-reformat", 0);
zoeSetOption("-ace-format", 0);
zoeSetOption("-gene-method", 1);
zoeSetOption("-extra", 1);
zoeSetOption("-dna", 0);
zoeSetOption("-extract", 1);
zoeSetOption("-length", 1);
zoeSetOption("-offset", 1);
zoeSetOption("-export", 1);
zoeSetOption("-plus", 0);
zoeSetOption("-errors-ok", 0);
zoeSetOption("-exon-intron", 0);
zoeSetOption("-split", 0);
zoeSetOption("-number", 1);
zoeSetOption("-training", 1);
zoeSetOption("-GC", 1);
zoeSetOption("-repeat", 1);
zoeSetOption("-anti", 0);
zoeSetOption("-fuse", 1);
zoeSetOption("-categorize", 1);
zoeSetOption("-min-intron", 1);
zoeSetOption("-max-intron", 1);
zoeSetOption("-min-exon", 1);
zoeSetOption("-max-exon", 1);
zoeSetOption("-min-gene", 1);
zoeSetOption("-max-gene", 1);
zoeSetOption("-min-cds", 1);
zoeSetOption("-max-cds", 1);
/* scoring, comparison, filtering */
zoeSetOption("-compare-genes", 1);
zoeSetOption("-details", 0);
zoeSetOption("-score-genes", 1);
zoeSetOption("-filter-genes", 1);
zoeSetOption("-min-score", 1);
zoeSetOption("-min-length", 1);
/* begin */
zoeParseOptions(&argc, argv);
if (zoeOption("-help")) help();
if (argc != 3) {
zoeE("%s", usage);
exit(1);
}
ANN_file = argv[1];
DNA_file = argv[2];
if (zoeOption("-compare-genes")) {
PRE_file = zoeOption("-compare-genes");
PREDICTIONS = 1;
}
if (zoeOption("-score-genes")
|| zoeOption("-anti")
|| zoeOption("-fuse")
|| zoeOption("-filter-genes")
) ANTI_REQUIRED = 1;
if (zoeOption("-filter-genes")) {
if (!zoeOption("-min-score")) zoeExit("-min-score required");
if (!zoeOption("-min-length")) zoeExit("-min-length required");
}
if (zoeOption("-randseed")) srand(atoi(zoeOption("-randseed")));
else srand(time(NULL));
if (zoeOption("-min-intron")) zoeSetMinIntron(atoi(zoeOption("-min-intron")));
if (zoeOption("-max-intron")) zoeSetMaxIntron(atoi(zoeOption("-max-intron")));
if (zoeOption("-min-exon")) zoeSetMinExon(atoi(zoeOption("-min-exon")));
if (zoeOption("-max-exon")) zoeSetMaxExon(atoi(zoeOption("-max-exon")));
if (zoeOption("-min-gene")) zoeSetMinGene(atoi(zoeOption("-min-gene")));
if (zoeOption("-max-gene")) zoeSetMaxGene(atoi(zoeOption("-max-gene")));
if (zoeOption("-min-cds")) zoeSetMinCDS(atoi(zoeOption("-min-cds")));
if (zoeOption("-max-cds")) zoeSetMaxCDS(atoi(zoeOption("-max-cds")));
/* main control */
if (zoeOption("-validate")) validate();
else if (zoeOption("-gene-stats")) genestats();
else if (zoeOption("-reformat")) reformat();
else if (zoeOption("-categorize")) categorize();
else if (zoeOption("-export")) export();
else if (zoeOption("-exon-intron")) exon_intron();
else if (zoeOption("-anti")) anti();
else if (zoeOption("-fuse")) fuse();
else if (zoeOption("-score-genes")) score_genes();
else if (zoeOption("-filter-genes")) filter_genes();
else if (zoeOption("-compare-genes")) compare_genes();
else if (zoeOption("-split")) split();
else if (zoeOption("-ace-format")) ace_format();
else if (zoeOption("-extract")) extract();
return 0;
}
void anti (void) {
FILE *DNA_out, *ANN_out;
DNA_out = fopen("anti.dna", "w");
ANN_out = fopen("anti.ann", "w");
openData();
while (getData()) {
zoeAntiFeatureTable(ANN, DNA->length);
zoeWriteTriteFeatureTable(ANN_out, ANN);
zoeWriteDNA(DNA_out, ANTI);
}
closeData();
fclose(DNA_out);
fclose(ANN_out);
}
void fuse (void) {
int i, j, group_size, group_num, offset;
float f;
FILE *DNA_out, *ANN_out;
DNA_out = fopen("fuse.dna", "w");
ANN_out = fopen("fuse.ann", "w");
group_size = atoi(zoeOption("-fuse"));
if (group_size < 1) zoeExit("-fuse must be >= 1");
group_num = 0;
openData();
while (getData()) {
offset = 0;
group_num++;
zoeS(DNA_out, ">fuse-%d\n", group_num);
zoeS(ANN_out, ">fuse-%d\n", group_num);
f = (float)rand()/(float)RAND_MAX;
if (f >= 0.5) {
zoeS(DNA_out, "%s\n", DNA->seq);
} else {
zoeS(DNA_out, "%s\n", ANTI->seq);
zoeAntiFeatureTable(ANN, DNA->length);
}
for (j = 0; j < ANN->vec->size; j++) {
ANN->vec->elem[j]->start += offset;
ANN->vec->elem[j]->end += offset;
zoeWriteTriteFeature(ANN_out, ANN->vec->elem[j]);
}
offset += DNA->length;
for (i = 1; i < group_size; i++) {
if (getData() == 0) break;
f = (float)rand()/(float)RAND_MAX;
if (f >= 0.5) {
zoeS(DNA_out, "%s\n", DNA->seq);
} else {
zoeS(DNA_out, "%s\n", ANTI->seq);
zoeAntiFeatureTable(ANN, DNA->length);
}
for (j = 0; j < ANN->vec->size; j++) {
ANN->vec->elem[j]->start += offset;
ANN->vec->elem[j]->end += offset;
zoeWriteTriteFeature(ANN_out, ANN->vec->elem[j]);
}
offset += DNA->length;
}
}
closeData();
fclose(DNA_out);
fclose(ANN_out);
}
/*****************************************************************************\
validate
\*****************************************************************************/
void validate (void) {
int i, tested = 0, OK = 0, warnings = 0, errors = 0;
zoeCDS cds;
zoeVec genes;
int quiet = zoeOption("-quiet") ? 1 : 0;
openData();
while (getData()) {
if (!quiet && strcmp(DNA->def, ANN->def) != 0) {
zoeWarn("DNA and annotation do not have the same def line!\n");
zoeWarn("%s\n%d\n", DNA->def, ANN->def);
}
genes = zoeGetGenes(ANN, DNA);
for (i = 0; i < genes->size; i++) {
tested++;
cds = genes->elem[i];
if (cds->errors->size) errors++;
if (cds->warnings->size) warnings++;
if (cds->OK) OK++;
zoeO("%s: ", DNA->def);
if (cds->errors->size || cds->warnings->size) {
zoeReportCDS(stdout, cds);
zoeWriteCDS(stdout, cds);
} else {
zoeO("%s OK\n", cds->name);
}
zoeDeleteCDS(cds);
}
zoeDeleteVec(genes);
}
closeData();
zoeE("%d genes, %d OK, %d warnings, %d errors\n", tested, OK, warnings, errors);
}
/*****************************************************************************\
reformat
\*****************************************************************************/
void reformat (void) {
int i;
zoeFeatureTable ft;
zoeCDS cds;
zoeVec genes;
openData();
while (getData()) {
genes = zoeGetGenes(ANN, DNA);
for (i = 0; i < genes->size; i++) {
cds = genes->elem[i];
if (cds->OK) {
if (zoeOption("-canonical") && cds->warnings->size) {
zoeE("%s skipped due to warnings");
} else {
ft = zoeNewFeatureTable(cds->name, cds->exons);
zoeWriteFeatureTable(stdout, ft);
zoeDeleteFeatureTable(ft);
}
} else {
zoeE("%s skipped due to errors\n", cds->name);
}
zoeDeleteCDS(cds);
}
zoeDeleteVec(genes);
}
closeData();
}
/*****************************************************************************\
gene stats
\*****************************************************************************/
float entropy (zoeDNA dna, zoeFeature exon) {
int i;
float f, h, H = 0;
int symbol[256];
zoeProtein pro = zoeTranslateFeature(">foo", dna, exon);
for (i = 0; i < 256; i++) symbol[i] = 0;
for (i = 0; i < pro->length; i++) symbol[(int)pro->seq[i]]++;
for (i = 0; i < 256; i++) {
if (symbol[i]) {
f = (float)symbol[i] / (float)pro->length;
h = f * log(f);
H -= h;
}
}
zoeDeleteProtein(pro);
return H;
}
void genestats (void) {
int i, j, length;
int gene_cnt = 0, max_gene = 0, min_gene = INT_MAX, plus = 0, minus = 0;
int Esngl = 0, multi = 0;
int exons = 0, exon_len = 0, max_exon = 0, min_exon = INT_MAX;
int introns = 0, intron_len = 0, max_intron = 0, min_intron = INT_MAX;
int dinuc[25];
int nuc[5];
zoeCDS gene;
zoeVec genes;
zoeFeature exon, intron;
int seq_count = 0;
float h, gc, min_gc = 1, max_gc = 0, gc_total = 0;
int H[50];
int index, total;
char * nt[5] = {"A", "C", "G", "T", "N"};
char * dd[25] = {
"AA", "AC", "AG", "AT", "AN",
"CA", "CC", "CG", "CT", "CN",
"GA", "GC", "GG", "GT", "GN",
"TA", "TC", "TG", "TT", "TN",
"NA", "NC", "NG", "NT", "NN"};
for (i = 0; i < 5; i++) nuc[i] = 0;
for (i = 0; i < 25; i++) dinuc[i] = 0;
for (i = 0; i < 50; i++) H[i] = 0;
openData();
while (getData()) {
if (zoeOption("-nucleotide")) {
for (i = 0; i < DNA->length; i++) {
nuc[(int)DNA->s5[i]]++;
}
}
if (zoeOption("-dinucleotide")) {
for (i = 1; i < DNA->length; i++) {
index = DNA->s5[i] + (5 * DNA->s5[i-1]);
dinuc[index]++;
}
}
gc = gc_content(DNA);
if (gc > max_gc) max_gc = gc;
if (gc < min_gc) min_gc = gc;
gc_total += gc;
seq_count++;
genes = zoeGetGenes(ANN, DNA);
for (i = 0; i < genes->size; i++) {
gene = genes->elem[i];
if (!gene->OK && !zoeOption("-errors-ok")) {
zoeE("%s skipped due to errors\n", gene->name);
continue;
} else if (zoeOption("-canonical") && gene->warnings->size) {
zoeE("%s skipped due to warnings\n", gene->name);
continue;
}
length = gene->end - gene->start + 1;
if (length < min_gene) min_gene = length;
if (length > max_gene) max_gene = length;
gene_cnt++;
if (gene->strand == '+') plus++;
else minus++;
if (gene->exons->size == 1) Esngl++;
else multi++;
exons += gene->exons->size;
introns += gene->introns->size;
for (j = 0; j < gene->exons->size; j++) {
exon = gene->exons->elem[j];
length = exon->end - exon->start + 1;
exon_len += length;
if (length < min_exon) min_exon = length;
if (length > max_exon) max_exon = length;
if (zoeOption("-entropy")) {
h = entropy(gene->dna, exon);
H[ (int)(h * 10) ]++;
}
}
for (j = 0; j < gene->introns->size; j++) {
intron = gene->introns->elem[j];
length = intron->end - intron->start +1;
intron_len += length;
if (length < min_intron) min_intron = length;
if (length > max_intron) max_intron = length;
}
}
for (i = 0; i < genes->size; i++) zoeDeleteCDS(genes->elem[i]);
zoeDeleteVec(genes);
}
closeData();
zoeO("%d sequences\n", seq_count);
zoeO("%f avg GC fraction (min=%f max=%f)\n", gc_total/(float)seq_count, min_gc, max_gc);
zoeO("%d genes (plus=%d minus=%d)\n", gene_cnt, plus, minus);
zoeO("%d (%f) single-exon\n", Esngl, (float)Esngl/(float)gene_cnt);
zoeO("%d (%f) multi-exon\n", multi, (float)multi/(float)gene_cnt);
zoeO("%f mean exon (min=%d max=%d)\n", (float)exon_len / (float)exons, min_exon, max_exon);
zoeO("%f mean intron (min=%d max=%d)\n", (float)intron_len / (float)introns, min_intron, max_intron);
if (zoeOption("-entropy")) {
zoeO("Exon entropy\n");
for (i = 0; i < 50; i++) {
if (H[i]) zoeO("%.1f %d\n", (float)i/10, H[i]);
}
}
if (zoeOption("-nucleotide")) {
total = 0;
for (i = 0; i < 5; i++) total += nuc[i];
for (i = 0; i < 5; i++) {
zoeO("%s\t%f\n", nt[i], (float)nuc[i] / (float)total);
}
}
if (zoeOption("-dinucleotide")) {
total = 0;
for (i = 0; i < 25; i++) total += dinuc[i];
for (i = 0; i < 25; i++) {
zoeO("%s\t%f\n", dd[i], (float)dinuc[i] / (float)total);
}
}
}
/*****************************************************************************\
exon-intron
\*****************************************************************************/
void exon_intron (void) {
int i, j;
zoeCDS cds;
zoeVec genes;
zoeDNA dna;
openData();
while (getData()) {
genes = zoeGetGenes(ANN, DNA);
if (genes->size != 1) {
zoeExit("fathom -exon-intron requires 1 gene per sequence");
}
cds = genes->elem[0];
zoeO(">%s\n", cds->name);
for (i = 0; i < cds->exons->size; i++) {
dna = zoeFeatureDNA("exon", cds->dna, cds->exons->elem[i]);
for (j = 0; j < dna->length; j++) {
if (dna->seq[j] > 'Z') dna->seq[j] -= 32;
}
zoeO("%s\n", dna->seq);
zoeDeleteDNA(dna);
if (cds->introns->size && i < cds->introns->size) {
dna = zoeFeatureDNA("intron", cds->dna, cds->introns->elem[i]);
for (j = 0; j < dna->length; j++) {
if (dna->seq[j] < 'a') dna->seq[j] += 32;
}
zoeO("%s\n", dna->seq);
zoeDeleteDNA(dna);
}
}
zoeO("\n");
zoeDeleteCDS(cds);
zoeDeleteVec(genes);
}
closeData();
}
/*****************************************************************************\
split functions
\*****************************************************************************/
float gc_frac (void) {
int i, c[5];
for (i = 0; i < 5; i++) c[i] = 0;
for (i = 0; i < DNA->length; i++) c[(int)DNA->s5[i]]++;
return (float)(c[1] + c[2]) / (float)(c[0] + c[1] + c[2] + c[3]);
}
void split_by_number (void) {
FILE *dna[20], *ann[20];
int split;
int i;
char filename[256];
int set;
split = atoi(zoeOption("-number"));
if (split < 2) {
zoeE("setting split -number to minimum value of 2\n");
split = 2;
} else if (split > 20) {
zoeE("setting split -number to maximum value of 20\n");
split = 20;
}
for (i = 0; i < split; i++) {
sprintf(filename, "%d.dna", i);
if ((dna[i] = fopen(filename, "w")) == NULL) zoeExit("error opening %s", filename);
sprintf(filename, "%d.ann", i);
if ((ann[i] = fopen(filename, "w")) == NULL) zoeExit("error opening %s", filename);
}
i = 0;
openData();
while (getData()) {
set = i % split;
zoeWriteDNA(dna[set], DNA);
zoeWriteFeatureTable(ann[set], ANN);
i++;
}
closeData();
for (i = 0; i < split; i++) {
fclose(dna[i]);
fclose(ann[i]);
}
}
void split (void) {
float f, cutoff;
FILE *train_dna, *train_ann, *test_dna, *test_ann;
FILE *hi_dna, *hi_ann, *lo_dna, *lo_ann;
train_dna = train_ann = test_dna = test_ann = hi_dna = hi_ann = lo_dna = lo_ann = NULL;
if (zoeOption("-number")) {
split_by_number();
return;
}
if (zoeOption("-training")) cutoff = atof(zoeOption("-training"));
else if (zoeOption("-GC")) cutoff = atof(zoeOption("-GC"));
else {
cutoff = 0; /* shush */
zoeExit("no data splitting method given, try -GC or -training");
}
if (cutoff <= 0 || cutoff >= 1) zoeExit("-split (%f) is out of range", cutoff);
/* open output files as "training" and "testing" */
if (zoeOption("-training")) {
if ((train_dna = fopen("train.dna", "w")) == NULL) zoeExit("can't open train.dna");
if ((train_ann = fopen("train.ann", "w")) == NULL) zoeExit("can't open train.ann");
if ((test_dna = fopen("test.dna", "w")) == NULL) zoeExit("can't open test.dna");
if ((test_ann = fopen("test.ann", "w")) == NULL) zoeExit("can't open test.ann");
} else {
if ((hi_dna = fopen("hi-gc.dna", "w")) == NULL) zoeExit("can't open hi-gc.dna");
if ((hi_ann = fopen("hi-gc.ann", "w")) == NULL) zoeExit("can't open hi-gc.ann");
if ((lo_dna = fopen("lo-gc.dna", "w")) == NULL) zoeExit("can't open lo-gc.dna");
if ((lo_ann = fopen("lo-gc.ann", "w")) == NULL) zoeExit("can't open lo-gc.ann");
}
/* repeat content not yet implemented */
openData();
while (getData()) {
if (zoeOption("-training")) f = (float)rand()/(float)RAND_MAX;
else if (zoeOption("-GC")) f = gc_frac();
else f = 0; /* shush */
if (f < cutoff) {
if (zoeOption("-training")) {
zoeWriteDNA(train_dna, DNA);
zoeWriteTriteFeatureTable(train_ann, ANN);
} else {
zoeWriteDNA(lo_dna, DNA);
zoeWriteTriteFeatureTable(lo_ann, ANN);
}
} else {
if (zoeOption("-training")) {
fflush(test_ann);
zoeWriteTriteFeatureTable(test_ann, ANN);
zoeWriteDNA(test_dna, DNA);
} else {
zoeWriteDNA(hi_dna, DNA);
zoeWriteTriteFeatureTable(hi_ann, ANN);
}
}
}
closeData();
if (zoeOption("-training")) {
fclose(train_dna);
fclose(train_ann);
fclose(test_dna);
fclose(test_ann);
} else {
fclose(hi_dna);
fclose(hi_ann);
fclose(lo_dna);
fclose(lo_ann);
}
}
/*****************************************************************************\
extract
\*****************************************************************************/
void extract (void) {
int i, length, offset, point_feature, id;
char * name, token[64];
zoeLabel label;
zoeFeatureVec vec = NULL;
zoeFeature f;
zoeDNA seq;
zoeVec genes;
zoeCDS gene;
name = zoeOption("-extract");
label = zoeText2Label(zoeOption("-extract"));
/* point features requires length and offset */
switch (label) {
case Acceptor: case Donor: case Start: case Stop:
if (! (zoeOption("-length") && zoeOption("-offset")))
zoeExit("extract requires -length and -offset for %s", name);
length = atoi(zoeOption("-length"));
offset = atoi(zoeOption("-offset"));
point_feature = 1;
break;
case Coding: case Intron: case Inter:
if (zoeOption("-length") || zoeOption("-offset"))
zoeWarn("ignoring -length and -offset for %s", name);
length = 0; offset = 0; point_feature = 0; /* shush */
break;
default:
length = 0; offset = 0; point_feature = 0; /* shush */
zoeExit("extract does not support %s yet", name);
}
/* main loop */
id = 0; /* index number for features */
openData();
while (getData()) {
switch (label) {
case Acceptor: vec = extractAcceptor(); break;
case Donor: vec = extractDonor(); break;
case Start: vec = extractStart(); break;
case Stop: vec = extractStop(); break;
case PolyA: vec = extractFeature(PolyA); break;
case Inter: vec = extractInter(); break;
case Intron: vec = extractIntron(); break;
case UTR5: vec = extractUTR5(); break;
case UTR3: vec = extractUTR3(); break;
case Coding:
genes = zoeGetGenes(ANN, DNA);
for (i = 0; i < genes->size; i++) {
gene = genes->elem[i];
zoeWriteDNA(stdout, gene->tx);
zoeDeleteCDS(gene);
}
zoeDeleteVec(genes);
continue; /* back to while */
default:
zoeExit("odd extract error");
}
for (i = 0; i < vec->size; i++) {
f = vec->elem[i];
if (f->start - offset < 0) continue;
id++;
sprintf(token, "%s-%d from sequence %s", name, id, DNA->def);
if (point_feature) seq = zoeSubseqDNA(token, DNA, f->start - offset, length);
else seq = zoeFeatureDNA(token, DNA, f);
zoeWriteDNA(stdout, seq);
zoeDeleteDNA(seq);
}
zoeDeleteFeatureVec(vec);
}
closeData();
}
zoeFeatureVec extractInter (void) {
int i, start, end;
zoeCDS gene, prev_gene, this_gene;
zoeFeature inter_p, inter_m;
zoeVec genes = zoeGetGenes(ANN, DNA);
zoeFeatureVec vec = zoeNewFeatureVec();
/* right now, this function ignores UTRs */
/* space before first gene */
gene = genes->elem[0];
start = 0;
end = gene->start -1;
if (end >= start) {
inter_p = zoeNewFeature(Inter, start, end, '+', MIN_SCORE, UNDEFINED_FRAME, UNDEFINED_FRAME, UNDEFINED_FRAME, "before"/*, NULL*/);
inter_m = zoeNewFeature(Inter, start, end, '-', MIN_SCORE, UNDEFINED_FRAME, UNDEFINED_FRAME, UNDEFINED_FRAME, "before"/*, NULL*/);
zoePushFeatureVec(vec, inter_p);
zoePushFeatureVec(vec, inter_m);
zoeDeleteFeature(inter_p);
zoeDeleteFeature(inter_m);
}
/* between genes */
for (i = 1; i < genes->size; i++) {
prev_gene = genes->elem[i-1];
this_gene = genes->elem[i];
start = prev_gene->end +1;
end = this_gene->start -1;
if (end >= start) {
inter_p = zoeNewFeature(Inter, start, end, '+', MIN_SCORE, UNDEFINED_FRAME, UNDEFINED_FRAME, UNDEFINED_FRAME, "between"/*, NULL*/);
inter_m = zoeNewFeature(Inter, start, end, '-', MIN_SCORE, UNDEFINED_FRAME, UNDEFINED_FRAME, UNDEFINED_FRAME, "between"/*, NULL*/);
zoePushFeatureVec(vec, inter_p);
zoePushFeatureVec(vec, inter_m);
zoeDeleteFeature(inter_p);
zoeDeleteFeature(inter_m);
}
}
/* space after genes */
gene = genes->elem[genes->size -1];
start = gene->end +1;
end = DNA->length -1;
if (end >= start) {
inter_p = zoeNewFeature(Inter, start, end, '+', MIN_SCORE, UNDEFINED_FRAME, UNDEFINED_FRAME, UNDEFINED_FRAME, "after"/*, NULL*/);
inter_m = zoeNewFeature(Inter, start, end, '-', MIN_SCORE, UNDEFINED_FRAME, UNDEFINED_FRAME, UNDEFINED_FRAME, "after"/*, NULL*/);
zoePushFeatureVec(vec, inter_p);
zoePushFeatureVec(vec, inter_m);
zoeDeleteFeature(inter_p);
zoeDeleteFeature(inter_m);
}
/* end */
for (i = 0; i < genes->size; i++) zoeDeleteCDS(genes->elem[i]);
zoeDeleteVec(genes);
return vec;
}
zoeFeatureVec extractUTR5 (void) {
int i, offset = 0, length = 0, start, end;
zoeCDS gene;
zoeFeature utr5;
zoeVec genes = zoeGetGenes(ANN, DNA);
zoeFeatureVec vec = zoeNewFeatureVec();
if (zoeOption("-offset")) offset = atoi(zoeOption("-offset"));
else zoeExit("you must supply -offset with UTR5/Upstream");
if (zoeOption("-length")) length = atoi(zoeOption("-length"));
else zoeExit("you must supply -length with UTR5/Upstream");
/* collect features */
for (i = 0; i < genes->size; i++) {
gene = genes->elem[i];
if (!gene->end_found) continue;
if (gene->strand == '+') {
end = gene->start -1 -offset;
start = end - length;
if (end < 0) continue; /* no UTR5 possible */
if (start < 0) start = 0;
} else {
start = gene->end +1 + offset;
end = start + length;
if (start > DNA->length -1) continue; /* no UTR5 possible */
if (end > DNA->length -1) end = DNA->length -1;
}
utr5 = zoeNewFeature(UTR5, start, end, gene->strand, MIN_SCORE, UNDEFINED_FRAME, UNDEFINED_FRAME, UNDEFINED_FRAME, NULL/*, NULL*/);
zoePushFeatureVec(vec, utr5);
zoeDeleteFeature(utr5);
}
/* end */
for (i = 0; i < genes->size; i++) zoeDeleteCDS(genes->elem[i]);
zoeDeleteVec(genes);
return vec;
}
zoeFeatureVec extractUTR3 (void) {
int i, offset = 0, length = 0, start, end;
zoeCDS gene;
zoeFeature utr3;
zoeVec genes = zoeGetGenes(ANN, DNA);
zoeFeatureVec vec = zoeNewFeatureVec();
if (zoeOption("-offset")) offset = atoi(zoeOption("-offset"));
else zoeExit("you must supply -offset with UTR3/Downstream");
if (zoeOption("-length")) length = atoi(zoeOption("-length"));
else zoeExit("you must supply -length with UTR3/Downstream");
/* collect features */
for (i = 0; i < genes->size; i++) {
gene = genes->elem[i];
if (!gene->end_found) continue;
if (gene->strand == '+') {
start = gene->end +1 + offset;
end = start + length;
if (start > DNA->length -1) continue; /* no UTR3 possible */
if (end > DNA->length -1) end = DNA->length -1;
} else {
end = gene->start -1 -offset;
start = end - length;
if (end < 0) continue; /* no UTR3 possible */
if (start < 0) start = 0;
}
utr3 = zoeNewFeature(UTR3, start, end, gene->strand, MIN_SCORE, UNDEFINED_FRAME, UNDEFINED_FRAME, UNDEFINED_FRAME, NULL/*, NULL*/);
zoePushFeatureVec(vec, utr3);
zoeDeleteFeature(utr3);
}
/* end */
for (i = 0; i < genes->size; i++) zoeDeleteCDS(genes->elem[i]);
zoeDeleteVec(genes);
return vec;
}
zoeFeatureVec extractAcceptor (void) {
int i, j, coor;
zoeCDS gene;
zoeFeature acc, exon;
zoeVec genes = zoeGetGenes(ANN, DNA);
zoeFeatureVec vec = zoeNewFeatureVec();
/* collect features */
for (i = 0; i < genes->size; i++) {
gene = genes->elem[i];
for (j = 0; j < gene->exons->size; j++) {
exon = gene->exons->elem[j];
if ( !(exon->label == Exon || exon->label == Eterm) ) continue;
if (exon->strand == '+') coor = exon->start -1;
else coor = exon->end +1;
acc = zoeNewFeature(Acceptor, coor, coor, exon->strand, MIN_SCORE, UNDEFINED_FRAME, UNDEFINED_FRAME, UNDEFINED_FRAME, gene->name/*, NULL*/);
zoePushFeatureVec(vec, acc);
zoeDeleteFeature(acc);
}
}
/* end */
for (i = 0; i < genes->size; i++) zoeDeleteCDS(genes->elem[i]);
zoeDeleteVec(genes);
return vec;
}
zoeFeatureVec extractDonor (void) {
int i, j, coor;
zoeCDS gene;
zoeFeature donor, exon;
zoeVec genes = zoeGetGenes(ANN, DNA);
zoeFeatureVec vec = zoeNewFeatureVec();
/* collect features */
for (i = 0; i < genes->size; i++) {
gene = genes->elem[i];
for (j = 0; j < gene->exons->size; j++) {
exon = gene->exons->elem[j];
if ( !(exon->label == Exon || exon->label == Einit) ) continue;
if (exon->strand == '+') coor = exon->end +1;
else coor = exon->start -1;
donor = zoeNewFeature(Donor, coor, coor, exon->strand, MIN_SCORE, UNDEFINED_FRAME, UNDEFINED_FRAME, UNDEFINED_FRAME, gene->name/*, NULL*/);
zoePushFeatureVec(vec, donor);
zoeDeleteFeature(donor);
}
}
/* end */
for (i = 0; i < genes->size; i++) zoeDeleteCDS(genes->elem[i]);
zoeDeleteVec(genes);
return vec;
}
zoeFeatureVec extractStart (void) {
int i, j, coor;
zoeCDS gene;
zoeFeature start, exon;
zoeVec genes = zoeGetGenes(ANN, DNA);
zoeFeatureVec vec = zoeNewFeatureVec();
/* collect features */
for (i = 0; i < genes->size; i++) {
gene = genes->elem[i];
for (j = 0; j < gene->exons->size; j++) {
exon = gene->exons->elem[j];
if ( !(exon->label == Einit || exon->label == Esngl) ) continue;