-
Notifications
You must be signed in to change notification settings - Fork 8
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #29 from hillerlab/fixed_partitioning
Fixed partitioning
- Loading branch information
Showing
9 changed files
with
213 additions
and
37 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,120 @@ | ||
| #!/usr/bin/env python3 | ||
| """Intermediate layer to run LASTZ wrapper. | ||
| Needed to process the case if many little scaffolds are to be aligned | ||
| withing one cluster job.""" | ||
| import argparse | ||
| import subprocess | ||
| import sys | ||
| import json | ||
| from itertools import product | ||
|
|
||
|
|
||
| def read_chrom_sizes(chrom_sizes_path): | ||
| """Read chrom.sizes file""" | ||
| chrom_sizes = {} | ||
| f = open(chrom_sizes_path, "r") | ||
| for line in f: | ||
| line_data = line.rstrip().split("\t") | ||
| chrom = line_data[0] | ||
| chrom_size = int(line_data[1]) | ||
| chrom_sizes[chrom] = chrom_size | ||
| f.close() | ||
| return chrom_sizes | ||
|
|
||
|
|
||
| def read_json_file(file_path): | ||
| with open(file_path, 'r') as f: | ||
| return json.load(f) # TODO: move to commons | ||
|
|
||
|
|
||
| def parse_args(): | ||
| """Parse arguments. | ||
| Recapitulates run_lastz.py parameters.""" | ||
| app = argparse.ArgumentParser() | ||
| app.add_argument("target", help="Target: single sequence file or .lst") | ||
| app.add_argument("query", help="Query: single sequence file or .lst") | ||
| app.add_argument("params_json", help="pipeline configuration file") | ||
| app.add_argument("output", help="Output file location") | ||
| app.add_argument("run_lastz_script", help="Path to the run_lastz script") | ||
|
|
||
| app.add_argument("--output_format", choices=["psl", "axt"], help="Output format axt|psl") | ||
| app.add_argument("--temp_dir", | ||
| help="Temp directory to save intermediate fasta files (if needed)\n" | ||
| "/tmp/ is default, however, params_json key TMPDIR can provide a value" | ||
| "the command line argument has a higher priority than DEF file" | ||
| ) | ||
| app.add_argument("--verbose", | ||
| "-v", | ||
| action="store_true", | ||
| dest="verbose", | ||
| help="Show verbosity messages") | ||
| app.add_argument("--axt_to_psl", | ||
| default="axtToPsl", | ||
| help="If axtToPst is not in the path, use this" | ||
| "argument to provide path to this binary, if needed" | ||
| ) | ||
|
|
||
| if len(sys.argv) < 5: | ||
| app.print_help() | ||
| sys.exit(0) | ||
| args = app.parse_args() | ||
| return args | ||
|
|
||
|
|
||
| def get_intervals_list(to_ali_arg, chrom_sizes): | ||
| """For bulk partitions argument, create a list of chromosomes | ||
| to feed into the LASTZ wrapper command. | ||
| """ | ||
| ret = [] | ||
| if not to_ali_arg.startswith("BULK"): | ||
| return [to_ali_arg] | ||
| arg_split = to_ali_arg.split(":") | ||
| two_bit_path = arg_split[1] | ||
| chroms_to_be_aligned_in_bulk = arg_split[2:] | ||
| for chrom in chroms_to_be_aligned_in_bulk: | ||
| _start = 0 | ||
| _end = chrom_sizes[chrom] | ||
| upd_arg = f"{two_bit_path}:{chrom}:{_start}-{_end}" | ||
| ret.append(upd_arg) | ||
| return ret | ||
|
|
||
|
|
||
| def main(): | ||
| args = parse_args() | ||
| pipeline_params = read_json_file(args.params_json) | ||
| seq_1_sizes_path = pipeline_params["seq_1_len"] | ||
| seq_2_sizes_path = pipeline_params["seq_2_len"] | ||
| target_chrom_sizes = read_chrom_sizes(seq_1_sizes_path) | ||
| query_chrom_sizes = read_chrom_sizes(seq_2_sizes_path) | ||
| target_coordinates = get_intervals_list(args.target, target_chrom_sizes) | ||
| query_coordinates = get_intervals_list(args.query, query_chrom_sizes) | ||
|
|
||
| # for each combination of target and query partitions in this | ||
| # particular command, create and run the respective run_lastz.py command | ||
| # normally, it's just a single: | ||
| # reference chr 1 from 0 to 100000 vs query chr 2 1000000 to 3000000 | ||
| # but in case some little scaffolds were aggregated, it must be unfolded first. | ||
| for target_arg, query_arg in product(target_coordinates, query_coordinates): | ||
| lastz_cmd = [ | ||
| args.run_lastz_script, | ||
| target_arg, | ||
| query_arg, | ||
| args.params_json, | ||
| args.output, | ||
| "--output_format", | ||
| args.output_format, | ||
| ] | ||
| if args.temp_dir: | ||
| lastz_cmd.append(f"--temp_dir") | ||
| lastz_cmd.append(args.temp_dir) | ||
| if args.axt_to_psl: | ||
| lastz_cmd.append(f"--axt_to_psl") | ||
| lastz_cmd.append(args.axt_to_psl) | ||
| # print(" ".join(lastz_cmd)) | ||
| subprocess.call(lastz_cmd) | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| main() |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.