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v1.1: mrcanavar-auto added for automated mapping & calling. Assumes t…
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,167 @@ | ||
| /* this is an autopilot for mrsfast mapping & mrcanavar calling. Intended for automated use in cloud. It works locally, but assumes a lot of things. */ | ||
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| #include <stdio.h> | ||
| #include <stdlib.h> | ||
| #include <string.h> | ||
| #include <getopt.h> | ||
| #include "utils.h" | ||
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| char *ref_genome; | ||
| char *input_files; | ||
| char *cnvr_conf; | ||
| char *gene_list; | ||
| int num_threads; | ||
| int skip_map; | ||
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| void print_help(void){ | ||
| fprintf(stderr, "Usage:\n\n"); | ||
| fprintf(stderr, "mrcanavar-auto\n\t--input [list]: comma-separated FASTQ(.gz) files.\n\t--ref [ref.fa]: repeat masked reference genome. mrsFAST index (ref.fa.index) should be in the same directory.\n"); | ||
| fprintf(stderr, "\t--conf [ref.cnvr]: mrCaNaVaR config file.\n\t--gene [genes.bed]: List of genes.\n\t--threads [int]: number of threads for mrsFAST.\n"); | ||
| fprintf(stderr, "\t--skip-mapping: Skip mrsFAST mapping. Use this only if you have the mapping output and rerunning mrCaNaVaR for some reason.\n\n"); | ||
| } | ||
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| int parse_command_line( int argc, char** argv) | ||
| { | ||
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| int o; | ||
| int index; | ||
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| ref_genome = NULL; input_files = NULL; cnvr_conf = NULL; gene_list = NULL; | ||
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| static struct option long_options[] = | ||
| { | ||
| {"input" , required_argument, 0, 'i'}, | ||
| {"ref" , required_argument, 0, 'f'}, | ||
| {"conf" , required_argument, 0, 'c'}, | ||
| {"gene" , required_argument, 0, 'g'}, | ||
| {"threads" , required_argument, 0, 't'}, | ||
| {"skip-mapping" , no_argument, &skip_map, 1}, | ||
| {0 , 0, 0, 0 } | ||
| }; | ||
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| if( argc == 1) | ||
| { | ||
| print_help(); | ||
| return -1; | ||
| } | ||
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| while( ( o = getopt_long( argc, argv, "i:f:c:g:t", long_options, &index)) != -1) | ||
| { | ||
| switch( o) | ||
| { | ||
| case 'i': | ||
| set_str(&input_files, optarg); | ||
| break; | ||
| case 'f': | ||
| set_str(&ref_genome, optarg); | ||
| break; | ||
| case 'g': | ||
| set_str(&gene_list, optarg); | ||
| break; | ||
| case 'c': | ||
| set_str(&cnvr_conf, optarg); | ||
| break; | ||
| case 't': | ||
| num_threads = atoi(optarg); | ||
| break; | ||
| } | ||
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| } | ||
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| if (input_files == NULL){ | ||
| fprintf (stderr, "Input files (FASTQ) are missing.\n"); | ||
| return -1; | ||
| } | ||
| if (ref_genome == NULL){ | ||
| fprintf (stderr, "Reference genome (repeatmasked FASTA) is missing.\n"); | ||
| return -1; | ||
| } | ||
| if (gene_list == NULL){ | ||
| fprintf (stderr, "Gene list (BED) is missing.\n"); | ||
| return -1; | ||
| } | ||
| if (cnvr_conf == NULL){ | ||
| fprintf (stderr, "Config file (CNVR) is missing.\n"); | ||
| return -1; | ||
| } | ||
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| return 0; | ||
| } | ||
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| int main (int argc, char **argv){ | ||
| int ret; | ||
| int i; | ||
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| int number_of_fastq = 0; | ||
| char **fastq_files; | ||
| char *safe_fastq_list = NULL; | ||
| char *token; | ||
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| char cmd_line[1048576]; | ||
| char tmp_line[1048576]; | ||
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| skip_map = 0; | ||
| num_threads = 4; | ||
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| ret = parse_command_line(argc, argv); | ||
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| if (ret == -1) | ||
| return ret; | ||
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| set_str(&safe_fastq_list, input_files); | ||
| token = strtok(safe_fastq_list, ","); | ||
| while (token != NULL){ | ||
| number_of_fastq++; | ||
| token = strtok(NULL, ","); | ||
| } | ||
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| fastq_files = (char **) getMem(sizeof(char *) * number_of_fastq); | ||
| memset(fastq_files, 0, sizeof(char *) * number_of_fastq); | ||
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| set_str(&safe_fastq_list, input_files); | ||
| token = strtok(safe_fastq_list, ","); | ||
| while(token != NULL){ | ||
| set_str(&(fastq_files[i++]), token); | ||
| token = strtok (NULL, ","); | ||
| } | ||
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| /* map */ | ||
| for (i=0; i<number_of_fastq; i++){ | ||
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| if (endswith (fastq_files[i], ".gz")) | ||
| sprintf(cmd_line, "mrsfast --search %s --seq %s --seqcomp --outcomp -t %d --mem 6 --crop 36 -e 2", ref_genome, fastq_files[i], num_threads); | ||
| else | ||
| sprintf(cmd_line, "mrsfast --search %s --seq %s --outcomp -t %d --mem 6 --crop 36 -e 2", ref_genome, fastq_files[i], num_threads); | ||
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| printf("[MAPPING] %s\n", cmd_line); | ||
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| if (!skip_map) | ||
| system(cmd_line); | ||
| } | ||
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| /* read */ | ||
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| if (number_of_fastq == 1){ | ||
| sprintf(cmd_line, "mrcanavar --read --gz -conf %s -samlist %s.sam.gz -depth %s.depth", cnvr_conf, fastq_files[0], fastq_files[0]); | ||
| } | ||
| else{ | ||
| tmp_line[0] = 0; | ||
| sprintf(tmp_line, "%s", fastq_files[0]); | ||
| for (i=1; i<number_of_fastq; i++){ | ||
| strcat(tmp_line, ".sam.gz,"); | ||
| strcat(tmp_line, fastq_files[i]); | ||
| } | ||
| strcat(tmp_line, ".sam.gz"); | ||
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| sprintf(cmd_line, "mrcanavar --read --gz -conf %s -samlist %s -depth %s.depth", cnvr_conf, tmp_line, fastq_files[0]); | ||
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| } | ||
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| printf("[READ SAM FILES] %s\n", cmd_line); | ||
| system(cmd_line); | ||
| /* call */ | ||
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| sprintf(cmd_line, "mrcanavar --call -conf %s -depth %s.depth -gene %s -o %s-out", cnvr_conf, fastq_files[0], gene_list, fastq_files[0]); | ||
| printf("[CALL COPY NUMBERS] %s\n", cmd_line); | ||
| system(cmd_line); | ||
| } |