new file: src/bed_flatten.c

	new file:   src/gtf2bed.c

src/bed_flatten.c

@@ -0,0 +1,68 @@
+#include "utils.h"
+#include "bed.h"
+#include "gtf.h"
+
+
+int bed_flatten_usage()
+{
+    fprintf(stderr, "# Convert overlapped bed to flattern bed.\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "\x1b[36m\x1b[1m$\x1b[0m \x1b[1mPISA\x1b[0m flatten -o merged.bed overlapped.bed\n");
+    fprintf(stderr, "\nOptions:\n");
+    fprintf(stderr, "-o    [FILE]    Output bed file.\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "For example:\n");
+    fprintf(stderr, "reg1 ===========\n");
+    fprintf(stderr, "reg2       ===========\n");
+    fprintf(stderr, "flattening of regions:\n");
+    fprintf(stderr, "reg1 ======\n");
+    fprintf(stderr, "reg2       =====\n");
+    fprintf(stderr, "reg3            ======\n");
+    return 1;
+}
+static struct args {
+    const char *input_fname;
+    const char *output_fname;
+} args = {
+    .input_fname = NULL,
+    .output_fname = NULL,
+};
+
+static int parse_args(int argc, char **argv)
+{
+    int i;
+    for (i = 1; i < argc;) {
+        const char *a = argv[i++];
+        const char **var = 0;
+
+        if (strcmp(a , "-o") == 0) var = &args.output_fname;
+
+        if (var != 0) {
+            if (i == argc) error("missing an argument after %s.", a);
+            *var = argv[i++];
+            continue;
+        }
+        if (a[0] == '-' && a[1] != '\0') error("unknown argument, %s", a);
+
+        if (args.input_fname == NULL) {
+            args.input_fname = a;
+            continue;
+        }
+        error("unknown argument, %s", a);
+    }
+
+    if (args.input_fname == NULL) return 1;   
+    return 0;
+}
+int bed_flatten(int argc, char **argv)
+{
+    if (parse_args(argc, argv)) return bed_flatten_usage();
+    struct bed_spec *B = bed_read(args.input_fname);
+    struct bed_spec *flatten = bed_spec_flatten(B);
+
+    bed_spec_write(flatten, args.output_fname, 0, 0);
+    bed_spec_destroy(B);
+    bed_spec_destroy(flatten);
+
+    return 0;
+}

src/gtf2bed.c

@@ -0,0 +1,98 @@
+#include "utils.h"
+#include "bed.h"
+#include "gtf.h"
+
+int gtf2bed_usage()
+{
+    fprintf(stderr, "# Convert GTF to BED.\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "\x1b[36m\x1b[1m$\x1b[0m \x1b[1mPISA\x1b[0m gtf2bed -o merged.bed in.gtf.gz\n");
+    fprintf(stderr, "\nOptions:\n");
+    fprintf(stderr, "  -o    [FILE]                          Output bed file.\n");
+    fprintf(stderr, "  -type [gene|transcript|exon]          Covert to bed.\n");
+    fprintf(stderr, "  -name [none|gene|transcript|exon]     Set name for bed.\n");
+    fprintf(stderr, "\n");
+    return 1;
+}
+
+static struct args {
+    const char *input_fname;
+    const char *output_fname;
+    // 1 for gene, 2 for transcript, 3 for exon
+    int type;
+
+    // 0 for none, 1 for gene, 2 for transcript, 3 for exon
+    int name_type;
+} args = {
+    .input_fname = NULL,
+    .output_fname = NULL,
+    .name_type = 0,
+    .type = 0
+};
+
+static int parse_args(int argc, char **argv)
+{
+    if (argc == 1) return gtf2bed_usage();
+
+    int i;
+    const char *name_type = NULL;
+    const char *type = NULL;
+
+    for (i = 1; i < argc;) {
+        const char *a = argv[i++];
+        const char **var = 0;
+
+        if (strcmp(a , "-o") == 0) var = &args.output_fname;
+        else if (strcmp(a, "-name") == 0) var = &name_type;
+        else if (strcmp(a, "-type") == 0) var = &type;
+
+        if (var != 0) {
+            if (i == argc) error("missing an argument after %s.", a);
+            *var = argv[i++];
+            continue;
+        }
+        if (a[0] == '-' && a[1] != '\0') error("unknown argument, %s", a);
+
+        if (args.input_fname == NULL) {
+            args.input_fname = a;
+            continue;
+        }
+        error("unknown argument, %s", a);
+    }
+
+    if (args.input_fname == NULL) error("No input specfied.");
+
+    if (type == NULL) error("No type specified, shoule be gene/transcript/exon.");
+
+    if (strcmp(type, "gene") == 0) args.type = 1;
+    else if (strcmp(type, "transcript") == 0) args.type = 2;
+    else if (strcmp(type, "exon") == 0) args.type = 3;
+    else {
+        error("unknown type, only support gene/transcript/exon");
+    }
+
+    if (name_type) {
+        if (strcmp(name_type, "none") == 0) args.name_type = 0;
+        else if (strcmp(name_type, "gene") == 0) args.name_type = 1;
+        else if (strcmp(name_type, "transcript") == 0) args.name_type = 2;
+        else if (strcmp(name_type, "exon") == 0) args.name_type = 3;
+        else {
+            error("unknown name type, only support none/gene/transcript/exon");
+        }
+    }
+    return 0;
+}
+int gtf2bed_main(int argc, char **argv)
+{
+    if (parse_args(argc, argv)) return gtf2bed_usage();
+
+    struct gtf_spec *G = gtf_read(args.input_fname, 0x3);
+    struct bed_spec *B = gtf2bed(G, args.type, args.name_type);
+
+    bed_spec_dedup(B, 1);
+    bed_spec_write(B, args.output_fname, 0, 0);
+
+    gtf_destroy(G);
+    bed_spec_destroy(B);
+    return 0;
+}