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Scrappie seqmappy and implementation of local penalty in mapping rout…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,241 @@ | ||
| #include <math.h> | ||
| #include <stdio.h> | ||
| //#include <string.h> | ||
| #include <strings.h> | ||
| #include <sys/types.h> | ||
| #include <unistd.h> | ||
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| #include "decode.h" | ||
| #include "fast5_interface.h" | ||
| #include "kseq.h" | ||
| #include "networks.h" | ||
| #include "scrappie_common.h" | ||
| #include "scrappie_licence.h" | ||
| #include "scrappie_seq_helpers.h" | ||
| #include "scrappie_stdlib.h" | ||
| #include "util.h" | ||
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| KSEQ_INIT(int, read) | ||
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| // Doesn't play nice with other headers, include last | ||
| #include <argp.h> | ||
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| extern const char *argp_program_version; | ||
| extern const char *argp_program_bug_address; | ||
| static char doc[] = "Scrappie seqmappy (local-global)"; | ||
| static char args_doc[] = "fasta fast5"; | ||
| static struct argp_option options[] = { | ||
| {"localpen", 'l', "float", 0, "Penalty for local matching"}, | ||
| {"min_prob", 'm', "probability", 0, "Minimum bound on probability of match"}, | ||
| {"output", 'o', "filename", 0, "Write to file rather than stdout"}, | ||
| {"prefix", 'p', "string", 0, "Prefix to append to name of read"}, | ||
| {"segmentation", 3, "chunk:percentile", 0, "Chunk size and percentile for variance based segmentation"}, | ||
| {"skip", 's', "penalty", 0, "Penalty for skipping a base"}, | ||
| {"stay", 'y', "penalty", 0, "Penalty for staying"}, | ||
| {"trim", 't', "start:end", 0, "Number of samples to trim, as start:end"}, | ||
| {"licence", 10, 0, 0, "Print licensing information"}, | ||
| {"license", 11, 0, OPTION_ALIAS, "Print licensing information"}, | ||
| {0} | ||
| }; | ||
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| typedef struct { | ||
| size_t n; | ||
| char * seq; | ||
| char * name; | ||
| } scrappie_seq_t; | ||
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| struct arguments { | ||
| float local_pen; | ||
| float min_prob; | ||
| float skip_pen; | ||
| float stay_pen; | ||
| FILE * output; | ||
| char * prefix; | ||
| int trim_start; | ||
| int trim_end; | ||
| int varseg_chunk; | ||
| float varseg_thresh; | ||
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| char * fasta_file; | ||
| char * fast5_file; | ||
| }; | ||
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| static struct arguments args = { | ||
| .local_pen = 4.0f, | ||
| .min_prob = 1e-5f, | ||
| .stay_pen = 0.0f, | ||
| .skip_pen = 0.0f, | ||
| .output = NULL, | ||
| .prefix = "", | ||
| .trim_start = 200, | ||
| .trim_end = 10, | ||
| .varseg_chunk = 100, | ||
| .varseg_thresh = 0.0f, | ||
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| .fasta_file = NULL, | ||
| .fast5_file = NULL | ||
| }; | ||
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| static error_t parse_arg(int key, char *arg, struct argp_state *state) { | ||
| switch (key) { | ||
| int ret = 0; | ||
| char * next_tok = NULL; | ||
| case 'l': | ||
| args.local_pen = atof(arg); | ||
| break; | ||
| case 'm': | ||
| args.min_prob = atof(arg); | ||
| break; | ||
| case 'o': | ||
| args.output = fopen(arg, "w"); | ||
| if(NULL == args.output){ | ||
| errx(EXIT_FAILURE, "Failed to open \"%s\" for output.", arg); | ||
| } | ||
| break; | ||
| case 'p': | ||
| args.prefix = arg; | ||
| break; | ||
| case 's': | ||
| args.skip_pen = atof(arg); | ||
| assert(isfinite(args.skip_pen)); | ||
| break; | ||
| case 't': | ||
| args.trim_start = atoi(strtok(arg, ":")); | ||
| next_tok = strtok(NULL, ":"); | ||
| if(NULL != next_tok){ | ||
| args.trim_end = atoi(next_tok); | ||
| } else { | ||
| args.trim_end = args.trim_start; | ||
| } | ||
| assert(args.trim_start >= 0); | ||
| assert(args.trim_end >= 0); | ||
| break; | ||
| case 'y': | ||
| args.stay_pen = atof(arg); | ||
| assert(isfinite(args.stay_pen)); | ||
| break; | ||
| case 3: | ||
| args.varseg_chunk = atoi(strtok(arg, ":")); | ||
| next_tok = strtok(NULL, ":"); | ||
| if(NULL == next_tok){ | ||
| errx(EXIT_FAILURE, "--segmentation should be of form chunk:percentile"); | ||
| } | ||
| args.varseg_thresh = atof(next_tok) / 100.0; | ||
| assert(args.varseg_chunk >= 0); | ||
| assert(args.varseg_thresh > 0.0 && args.varseg_thresh < 1.0); | ||
| break; | ||
| case 10: | ||
| case 11: | ||
| ret = fputs(scrappie_licence_text, stdout); | ||
| exit((EOF != ret) ? EXIT_SUCCESS : EXIT_FAILURE); | ||
| break; | ||
|
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| case ARGP_KEY_NO_ARGS: | ||
| argp_usage(state); | ||
| break; | ||
|
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| case ARGP_KEY_ARG: | ||
| args.fasta_file = state->argv[state->next - 1]; | ||
| if(NULL == state->argv[state->next]){ | ||
| errx(EXIT_FAILURE, "fast5 file is a required argument"); | ||
| } | ||
| args.fast5_file = state->argv[state->next]; | ||
| state->next = state->argc; | ||
| break; | ||
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| default: | ||
| return ARGP_ERR_UNKNOWN; | ||
| } | ||
| return 0; | ||
| } | ||
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| static struct argp argp = { options, parse_arg, args_doc, doc }; | ||
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| static scrappie_seq_t read_sequence_from_fasta(char const * filename){ | ||
| scrappie_seq_t seq = {0, NULL, NULL}; | ||
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| FILE * fh = fopen(filename, "r"); | ||
| if(NULL == fh){ | ||
| return seq; | ||
| } | ||
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| kseq_t * kseqer = kseq_init(fileno(fh)); | ||
| if(kseq_read(kseqer) >= 0){ | ||
| char * name = calloc(kseqer->name.l + 1, sizeof(char)); | ||
| char * base_seq = calloc(kseqer->seq.l, sizeof(char)); | ||
| if(NULL == base_seq || NULL == name){ | ||
| free(base_seq); | ||
| free(name); | ||
| } else { | ||
| seq.seq = strncpy(base_seq, kseqer->seq.s, kseqer->seq.l); | ||
| seq.name = strncpy(name, kseqer->name.s, kseqer->name.l); | ||
| seq.n = kseqer->seq.l; | ||
| } | ||
| } | ||
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| kseq_destroy(kseqer); | ||
| fclose(fh); | ||
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| return seq; | ||
| } | ||
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| int main_seqmappy(int argc, char *argv[]) { | ||
| argp_parse(&argp, argc, argv, 0, 0, NULL); | ||
| if(NULL == args.output){ | ||
| args.output = stdout; | ||
| } | ||
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| // Open sequence file | ||
| scrappie_seq_t seq = read_sequence_from_fasta(args.fasta_file); | ||
| if(NULL == seq.seq){ | ||
| warnx("Failed to open \"%s\" for input.\n", args.fasta_file); | ||
| return EXIT_FAILURE; | ||
| } | ||
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| const size_t state_len = 5; | ||
| int * states = encode_bases_to_integers(seq.seq, seq.n, state_len); | ||
| const size_t nstate = seq.n - state_len + 1; | ||
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| // Read raw signal and normalise | ||
| raw_table rt = read_raw(args.fast5_file, true); | ||
| rt = trim_and_segment_raw(rt, args.trim_start, args.trim_end, args.varseg_chunk, args.varseg_thresh); | ||
| if(NULL == rt.raw){ | ||
| warnx("Failed to open \"%s\" for input and trim signal.\n", args.fasta_file); | ||
| return EXIT_FAILURE; | ||
| } | ||
| medmad_normalise_array(rt.raw + rt.start, rt.end - rt.start); | ||
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| scrappie_matrix logpost = nanonet_rgrgr_r94_posterior(rt, args.min_prob, true); | ||
| if(NULL == logpost){ | ||
| warnx("Failed to calculate posterior for \"%s\" ", args.fasta_file); | ||
| return EXIT_SUCCESS; | ||
| } | ||
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| const size_t nblock = logpost->nc; | ||
| int * path = calloc(nblock, sizeof(int)); | ||
| if(NULL != path){ | ||
| float score = map_to_sequence_viterbi(logpost, args.stay_pen, args.skip_pen, args.local_pen, states, nstate, path); | ||
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| fprintf(args.output, "# %s to %s -- score %f over %zu blocks (%f per block)\n", args.fast5_file, args.fasta_file, -score, nblock, -score / nblock); | ||
| fprintf(args.output, "block\tpos\n"); | ||
| for(size_t i=0 ; i < nblock ; i++){ | ||
| const int32_t pos = path[i]; | ||
| fprintf(args.output, "%zu\t%d\n", i, pos); | ||
| } | ||
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| free(path); | ||
| } | ||
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| free(states); | ||
| logpost = free_scrappie_matrix(logpost); | ||
| free(seq.seq); | ||
| free(seq.name); | ||
|
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| return EXIT_SUCCESS; | ||
| } |
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