diff options
| -rw-r--r-- | domagi/domagi.py | 28 |
1 files changed, 17 insertions, 11 deletions
diff --git a/domagi/domagi.py b/domagi/domagi.py index dca240d..e8e484a 100644 --- a/domagi/domagi.py +++ b/domagi/domagi.py @@ -28,9 +28,15 @@ import tempfile import click import duckdb -common_options = click.option("-t", "--threads", "threads", +threads_option = click.option("-t", "--threads", "threads", type=click.INT, help="number of threads (default: number of CPUs)") +# The -P, --progress flags are no-ops in domagi. But, we add them to remain +# compatible with odgi. +progress_option = click.option("-P", "--progress", is_flag=True, hidden=True) + +def common_options(func): + return threads_option(progress_option(func)) class DuckDBParamType(click.ParamType): name = "DB" @@ -86,7 +92,7 @@ def main(): required=True, help="output pangenome duckdb database") @common_options -def build(gfa, db, threads): +def build(gfa, db, threads, progress): with connect_duckdb(db, threads) as con: con.execute(read_sql("schema.sql")) with connect_duckdb(db, threads) as con: @@ -111,7 +117,7 @@ def build(gfa, db, threads): required=True, help="divide segments longer than N") @common_options -def chop(con, outfile, chop_to, threads): +def chop(con, outfile, chop_to, threads, progress): set_duckdb_threads(con, threads) with connect_duckdb(outfile, threads) as out_con: out_con.execute(read_sql("schema.sql")) @@ -136,7 +142,7 @@ def chop(con, outfile, chop_to, threads): required=True, help="path to output pangenome duckdb database") @common_options -def crush(con, outfile, threads): +def crush(con, outfile, threads, progress): set_duckdb_threads(con, threads) with connect_duckdb(outfile, threads) as out_con: out_con.execute(read_sql("schema.sql")) @@ -174,7 +180,7 @@ def crush(con, outfile, threads): @click.option("-b", "--bed-input", help="BED file of windows to compute depth over") @common_options -def depth(con, graph_depth_table, paths, bed_input, threads): +def depth(con, graph_depth_table, paths, bed_input, threads, progress): set_duckdb_threads(con, threads) assert_paths_exist(con, paths) # With the -d flag, print the depth and unique depth of every @@ -223,7 +229,7 @@ def depth(con, graph_depth_table, paths, bed_input, threads): required=True, help="number of traversal steps") @common_options -def extract(con, outfile, segment_name, path_range, steps, threads): +def extract(con, outfile, segment_name, path_range, steps, threads, progress): set_duckdb_threads(con, threads) with connect_duckdb(outfile, threads) as out_con: out_con.execute(read_sql("schema.sql")) @@ -292,7 +298,7 @@ def extract(con, outfile, segment_name, path_range, steps, threads): required=True, help="pangenome duckdb database") @common_options -def matrix(con, threads): +def matrix(con, threads, progress): set_duckdb_threads(con, threads) segment_count, = con.execute("SELECT COUNT() FROM segment").fetchone() df = con.execute(read_sql("matrix.sql")).fetchdf() @@ -315,7 +321,7 @@ def matrix(con, threads): metavar="FILE", help="find paths touched by paths listed in FILE") @common_options -def overlap(con, paths, paths_file, threads): +def overlap(con, paths, paths_file, threads, progress): set_duckdb_threads(con, threads) if paths_file: paths = [line.rstrip() for line in paths_file.readlines()] @@ -336,7 +342,7 @@ def overlap(con, paths, paths_file, threads): is_flag=True, help="print paths in FASTA format") @common_options -def paths(con, list_paths, fasta, threads): +def paths(con, list_paths, fasta, threads, progress): set_duckdb_threads(con, threads) if list_paths: for name, in con.execute("SELECT name FROM path").fetchall(): @@ -368,7 +374,7 @@ def paths(con, list_paths, fasta, threads): is_flag=True, hidden=True) @common_options -def stats(con, summarize, threads): +def stats(con, summarize, threads, progress): set_duckdb_threads(con, threads) print("\t".join(["#length", "nodes", "edges", "paths", "steps"])) length, = con.execute("SELECT sum(len(sequence)) FROM segment").fetchone() @@ -388,7 +394,7 @@ def stats(con, summarize, threads): is_flag=True, help="write the graph in GFAv1 format to stdout") @common_options -def view(con, to_gfa, threads): +def view(con, to_gfa, threads, progress): set_duckdb_threads(con, threads) if to_gfa: print("H\tVN:Z:1.0") |