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diff --git a/.dir-locals.el b/.dir-locals.el new file mode 100644 index 0000000..5fcdd95 --- /dev/null +++ b/.dir-locals.el @@ -0,0 +1,13 @@ +;;; Directory Local Variables +;;; For more information see (info "(emacs) Directory Variables") + +((nil + (indent-tabs-mode)) + (makefile-gmake-mode + (indent-tabs-mode t)) + (c-mode + (fill-column . 80)) + (python-mode + (fill-column . 80)) + (scheme-mode + (fill-column . 80))) diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..ed8ebf5 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +__pycache__ \ No newline at end of file diff --git a/.guix/domagi-package.scm b/.guix/domagi-package.scm new file mode 100644 index 0000000..2bbed06 --- /dev/null +++ b/.guix/domagi-package.scm @@ -0,0 +1,95 @@ +;;; domagi --- DuckDB-powered pangenome Swiss Army knife +;;; Copyright © 2026 Arun Isaac <arunisaac@systemreboot.net> +;;; +;;; This file is part of domagi. +;;; +;;; domagi is free software: you can redistribute it and/or modify it under the +;;; terms of the GNU General Public License as published by the Free Software +;;; Foundation, either version 3 of the License, or (at your option) any later +;;; version. +;;; +;;; domagi is distributed in the hope that it will be useful, but WITHOUT ANY +;;; WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +;;; FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +;;; details. +;;; +;;; You should have received a copy of the GNU General Public License along with +;;; domagi. If not, see <https://www.gnu.org/licenses/>. + +(define-module (domagi-package) + #:use-module ((gnu packages check) #:select (python-pytest)) + #:use-module ((gnu packages cmake) #:select (cmake)) + #:use-module ((gnu packages duckdb) #:select (duckdb python-duckdb)) + #:use-module ((gnu packages pkg-config) #:select (pkg-config)) + #:use-module ((gnu packages python-xyz) #:select (python-click python-meson)) + #:use-module (guix build-system copy) + #:use-module (guix build-system pyproject) + #:use-module (guix gexp) + #:use-module (guix git-download) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix utils)) + +(define-public verstable + (package + (name "verstable") + (version "2.2.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JacksonAllan/Verstable") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0lwh9kh0jl2vxcijd8606h5xvsjxxa051qaqlx82cl36nh0hkkxp")))) + (build-system copy-build-system) + (arguments + (list #:install-plan + #~'(("verstable.h" "include/verstable.h")))) + (home-page "https://github.com/JacksonAllan/Verstable") + (synopsis "Generic C hash table library") + (description "Verstable is a versatile generic hash table intended +to bring the speed and memory efficiency of state-of-the-art C++ hash +tables such as Abseil/Swiss, Boost, and Bytell to C. + +Its features include: +@begin itemize +@item Type safety +@item Customizable hash, comparison, and destructor functions +@item Single header +@item C99 compatibility +@item Generic API in C11 and later +@item High speed mostly impervious to load factor +@item Only two bytes of overhead per bucket +@item Tombstone-free deletion +@end itemize") + (license license:expat))) + +(define-public domagi + (package + (name "domagi") + (version "0.1.0") + (source (local-file ".." + "domagi-checkout" + #:recursive? #t + #:select? (or (git-predicate (dirname (current-source-directory))) + (const #t)))) + (build-system pyproject-build-system) + (inputs + (list duckdb + python-click + python-duckdb)) + (native-inputs + (list cmake + python-meson + pkg-config + python-pytest + verstable)) + (home-page "https://github.com/arunisaac/domagi") + (synopsis "DuckDB-powered pangenome Swiss Army knife") + (description "domagi is a DuckDB-powered clone of odgi, the pangenome +manipulation tool.") + (license license:gpl3+))) + +domagi diff --git a/.guix/odgi-package.scm b/.guix/odgi-package.scm new file mode 100644 index 0000000..5fa94d1 --- /dev/null +++ b/.guix/odgi-package.scm @@ -0,0 +1,72 @@ +;; This odgi package definition is from https://git.genenetwork.org/guix-bioinformatics/tree/gn/packages/pangenome.scm?id=e586976ac493d2f7480784f098d58c9fed065b02#n524 + +(define-module (odgi-package) + #:use-module ((gnu packages datastructures) + #:select (libdivsufsort sdsl-lite)) + #:use-module ((gnu packages jemalloc) #:select (jemalloc)) + #:use-module ((gnu packages mpi) #:select (openmpi)) + #:use-module ((gnu packages pkg-config) #:select (pkg-config)) + #:use-module ((gnu packages python) #:select (python)) + #:use-module ((gnu packages python-xyz) #:select (pybind11)) + #:use-module (guix build-system cmake) + #:use-module (guix download) + #:use-module (guix gexp) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages)) + +(define-public odgi + (package + (name "odgi") + (version "0.9.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/pangenome/odgi/releases" + "/download/v" version + "/odgi-v" version ".tar.gz")) + (sha256 + (base32 + "0brg0sz45v1wv4ld3p4jwiab10nyp2f691zfwpiva6g6f71q3cbk")) + (snippet + #~(begin + (use-modules (guix build utils)) + (substitute* "CMakeLists.txt" + (("-march=native") "") + (("-msse4\\.2") "")))))) + (build-system cmake-build-system) + (arguments + (list + #:tests? #f + #:parallel-build? #f ; parallel build uses too much memory + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'use-gnuinstalldirs-macros + (lambda _ + (substitute* "CMakeLists.txt" + (("project\\(odgi\\)" all) + (string-append all "\ninclude(GNUInstallDirs)")) + (("LIBRARY DESTINATION lib") + "LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}") + (("ARCHIVE DESTINATION lib") + "ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}")))) + (add-after 'unpack 'link-to-libodgi + (lambda _ + (substitute* "CMakeLists.txt" + (("^ \\$<TARGET_OBJECTS:odgi_objs>.*") "") + (("target_link_libraries\\(odgi " all) + (string-append all "libodgi_shared ")))))))) + (native-inputs (list pkg-config)) + (inputs + (list jemalloc + libdivsufsort + openmpi + pybind11 + python + sdsl-lite)) + (properties '((tunable? . #t))) + (home-page "https://github.com/vgteam/odgi") + (synopsis "Optimized Dynamic Genome/Graph Implementation") + (description "odgi provides an efficient and succinct dynamic DNA +sequence graph model, as well as algorithms for pangenome analysis.") + (license license:expat))) + +odgi diff --git a/COPYING b/COPYING new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/COPYING @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/> + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + <one line to give the program's name and a brief idea of what it does.> + Copyright (C) <year> <name of author> + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see <https://www.gnu.org/licenses/>. + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + <program> Copyright (C) <year> <name of author> + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +<https://www.gnu.org/licenses/>. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +<https://www.gnu.org/licenses/why-not-lgpl.html>. diff --git a/README.md b/README.md new file mode 100644 index 0000000..e69de29 --- /dev/null +++ b/README.md diff --git a/c/importgfa.c b/c/importgfa.c new file mode 100644 index 0000000..43cc948 --- /dev/null +++ b/c/importgfa.c @@ -0,0 +1,374 @@ +/// domagi --- DuckDB-powered pangenome Swiss Army knife +/// Copyright © 2026 Arun Isaac <arunisaac@systemreboot.net> +/// +/// This file is part of domagi. +/// +/// domagi is free software: you can redistribute it and/or modify it under the +/// terms of the GNU General Public License as published by the Free Software +/// Foundation, either version 3 of the License, or (at your option) any later +/// version. +/// +/// domagi is distributed in the hope that it will be useful, but WITHOUT ANY +/// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +/// FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +/// details. +/// +/// You should have received a copy of the GNU General Public License along with +/// domagi. If not, see <https://www.gnu.org/licenses/>. + +#include <assert.h> +#include <stdio.h> +#include <stdlib.h> +#include <string.h> + +#include <duckdb.h> + +#define NAME str_int_map +#define KEY_TY const char* +#define VAL_TY int +#include <verstable.h> + +void die(const char *message) +{ + fprintf(stderr, "%s\n", message); + exit(EXIT_FAILURE); +} + +static int ceildiv (int x, int y) +{ + return (x / y) + (x % y ? 1 : 0); +} + +static int hashtable_get (str_int_map *table, const char *key) +{ + // Look up key in hash table and return the corresponding key. The program is + // aborted if the key is not found. This is ok for our limited purposes since + // all keys we look up are guaranteed to be present. + str_int_map_itr itr = vt_get(table, key); + assert(!vt_is_end(itr)); + return itr.data->val; +} + +static uint8_t orientation2int (char c) +{ + return c == '+' ? 0 : 1; +} + +static void pass1_handle_s_line (char *line, str_int_map *segment_id_table, duckdb_appender *appender) +{ + static int segment_id = 0; + + // Split S line. + strsep(&line, "\t"); + char *segment_name = strsep(&line, "\t"); + char *sequence = strsep(&line, "\t\n"); + + // Map segment name to ID in table. + vt_insert(segment_id_table, strdup(segment_name), segment_id); + // Append to database. + duckdb_append_int32(*appender, segment_id); + duckdb_append_varchar(*appender, segment_name); + duckdb_append_varchar(*appender, sequence); + duckdb_appender_end_row(*appender); + // Increment segment ID for next segment. + segment_id++; +} + +static void pass1_handle_p_line (char *line, duckdb_appender *appender) +{ + static int path_id = 0; + + // Split P line. + strsep(&line, "\t"); + char *path_name = strsep(&line, "\t"); + + // Append to database. There are usually relatively few P lines. So, we're + // content with a simple row-wise appender. + duckdb_append_int32(*appender, path_id); + duckdb_append_varchar(*appender, path_name); + duckdb_appender_end_row(*appender); + // Increment path ID for next path. + path_id++; +} + +#define LINK_COLUMN_COUNT 4 +static void process_l_lines (char **lines, size_t line_count, str_int_map *segment_id_table, duckdb_database *db) +{ + idx_t vector_size = duckdb_vector_size(); + duckdb_logical_type int_type = duckdb_create_logical_type(DUCKDB_TYPE_INTEGER); + duckdb_logical_type orientation_type = duckdb_create_enum_type((const char *[]){"+", "-"}, 2); + duckdb_logical_type types[LINK_COLUMN_COUNT] + = {int_type, orientation_type, int_type, orientation_type}; +#pragma omp parallel + { + duckdb_connection con; + if (duckdb_connect(*db, &con) == DuckDBError) + die("Unable to connect to DuckDB database"); + duckdb_appender appender; + if (duckdb_appender_create(con, NULL, "link", &appender) == DuckDBError) + die("Unable to create appender for link table"); + duckdb_data_chunk chunk = duckdb_create_data_chunk(types, LINK_COLUMN_COUNT); + duckdb_data_chunk_set_size(chunk, vector_size); + int32_t *from_segment_data = duckdb_vector_get_data(duckdb_data_chunk_get_vector(chunk, 0)); + uint8_t *from_orientation_data = duckdb_vector_get_data(duckdb_data_chunk_get_vector(chunk, 1)); + int32_t *to_segment_data = duckdb_vector_get_data(duckdb_data_chunk_get_vector(chunk, 2)); + uint8_t *to_orientation_data = duckdb_vector_get_data(duckdb_data_chunk_get_vector(chunk, 3)); +#pragma omp for + for (size_t slice_index=0; slice_index<ceildiv(line_count, vector_size); slice_index++) { + size_t chunk_index, line_index; + for (chunk_index=0, line_index=slice_index*vector_size; + (chunk_index<vector_size) && (line_index<line_count); + chunk_index++, line_index++) { + char *original_line = lines[line_index]; + // Split L line and write results into data chunk. + strsep(&lines[line_index], "\t"); + from_segment_data[chunk_index] + = hashtable_get(segment_id_table, strsep(&lines[line_index], "\t")); + from_orientation_data[chunk_index] + = orientation2int(*strsep(&lines[line_index], "\t")); + to_segment_data[chunk_index] + = hashtable_get(segment_id_table, strsep(&lines[line_index], "\t")); + to_orientation_data[chunk_index] + = orientation2int(*strsep(&lines[line_index], "\t\n")); + free(original_line); + } + // Write chunk to database. + duckdb_data_chunk_set_size(chunk, chunk_index); + if (duckdb_append_data_chunk(appender, chunk) == DuckDBError) + die("Unable to append chunk to link table"); + } + duckdb_destroy_data_chunk(&chunk); + duckdb_appender_destroy(&appender); + duckdb_disconnect(&con); + } + duckdb_destroy_logical_type(&int_type); + duckdb_destroy_logical_type(&orientation_type); +} +#undef LINK_COLUMN_COUNT + +#define PATH_SEGMENT_COLUMN_COUNT 4 +#define SLICE_SIZE 65536 +static void process_p_line (char *line, size_t line_length, str_int_map *segment_id_table, int path_id, duckdb_database *db) +{ + // Split P line. + strsep(&line, "\t"); + char *path_name = strsep(&line, "\t"); + char *segment_names = strsep(&line, "\t\n"); + // segment_names is likely a very long string, and we want to avoid calling + // strlen on it. Hence, we compute its length in this roundabout way from the + // line length. + size_t segment_names_length = line_length + // This is the stuff before segment names. + - strlen("P\t") - strlen(path_name) - strlen("\t") + // And, this is the stuff after it. + - (line ? strlen(line) : 0); + + // Split segment_names string into slices. + // Allocate the slices array to an approximate upper bound; we need not bother + // with ceil. + char **slices = malloc((1+segment_names_length/SLICE_SIZE)*sizeof(char*)); + size_t slice_count; + { + slices[0] = segment_names; + int i = 1; + while (slices[i-1] + SLICE_SIZE < segment_names + segment_names_length) { + // Start the ith slice SLICE_SIZE bytes away from the beginning of the + // (i-1)th slice. + slices[i] = slices[i-1] + SLICE_SIZE; + // But, extend the (i-1)th slice a bit more so that its end lines up with + // a comma. + char *next_comma; + if ((next_comma = strchr(slices[i], ','))) { + *next_comma = '\0'; + slices[i] = next_comma + 1; + } + i++; + } + slice_count = i; + } + + // Count commas in each slice. + int *commas = calloc(slice_count, sizeof(int)); +#pragma omp parallel for + for (size_t i=0; i<slice_count; i++) { + char *slice = slices[i]; + char *comma; + while ((comma=strchr(slice, ','))) { + commas[i]++; + slice = comma + 1; + } + } + // Prefix-sum to get the number of commas in segment_names up to that slice. + for (size_t i=1; i<slice_count; i++) + commas[i] += commas[i-1]; + + // Split path segments and append them to the database. + { + idx_t vector_size = duckdb_vector_size(); + duckdb_logical_type int_type = duckdb_create_logical_type(DUCKDB_TYPE_INTEGER); + duckdb_logical_type orientation_type = duckdb_create_enum_type((const char *[]){"+", "-"}, 2); + duckdb_logical_type types[PATH_SEGMENT_COLUMN_COUNT] + = {int_type, int_type, int_type, orientation_type}; +#pragma omp parallel + { + duckdb_connection con; + if (duckdb_connect(*db, &con) == DuckDBError) + die("Unable to connect to DuckDB database"); + duckdb_appender appender; + if (duckdb_appender_create(con, "internal", "path_segment", &appender) == DuckDBError) + die("Unable to create appender for path_segment table"); + duckdb_data_chunk chunk = duckdb_create_data_chunk(types, PATH_SEGMENT_COLUMN_COUNT); + int32_t *position_data = duckdb_vector_get_data(duckdb_data_chunk_get_vector(chunk, 0)); + int32_t *path_id_data = duckdb_vector_get_data(duckdb_data_chunk_get_vector(chunk, 1)); + int32_t *segment_id_data = duckdb_vector_get_data(duckdb_data_chunk_get_vector(chunk, 2)); + uint8_t *segment_orientation_data = duckdb_vector_get_data(duckdb_data_chunk_get_vector(chunk, 3)); +#pragma omp for + for (size_t i=0; i<slice_count; i++) { + char orientation; + int position = i ? commas[i-1] : 0; + char *comma; + do { + size_t chunk_index = 0; + do { + char *orientation_ptr; + if ((comma = strchr(slices[i], ','))) { + // Comma is found; pick up the orientation character and blot out + // the comma. + orientation_ptr = comma - 1; + *comma = '\0'; + } else + // Comma is not found; this must be the last segment—the character + // before the terminating null byte is the orientation character. + orientation_ptr = strchr(slices[i], '\0') - 1; + // Copy the orientation character and blot it out from the path + // segment name. + orientation = *orientation_ptr; + *orientation_ptr = '\0'; + // Look up segment ID in hash table. + int path_segment_id = hashtable_get(segment_id_table, slices[i]); + // Append to data chunk. + position_data[chunk_index] = position; + path_id_data[chunk_index] = path_id; + segment_id_data[chunk_index] = path_segment_id; + segment_orientation_data[chunk_index] = orientation2int(orientation); + // Prepare for the next iteration. + position++; + chunk_index++; + if (comma) + slices[i] = comma + 1; + } while (chunk_index<vector_size && comma); + duckdb_data_chunk_set_size(chunk, chunk_index); + if (duckdb_append_data_chunk(appender, chunk) == DuckDBError) + die("Unable to append chunk to path_segment table"); + } while (comma); + } + duckdb_destroy_data_chunk(&chunk); + duckdb_appender_destroy(&appender); + duckdb_disconnect(&con); + } + duckdb_destroy_logical_type(&int_type); + duckdb_destroy_logical_type(&orientation_type); + } + + free(commas); + free(slices); +} +#undef SLICE_SIZE +#undef PATH_SEGMENT_COLUMN_COUNT + +int import_gfa (const char *gfa_path, const char *duckdb_path) +{ + str_int_map segment_id_table; + vt_init(&segment_id_table); + + FILE *gfa_fp = fopen(gfa_path, "r"); + if (!gfa_fp) { + // TODO: Replace with die. + fprintf(stderr, "Unable to open GFA: %s\n", gfa_path); + exit(EXIT_FAILURE); + } + + duckdb_database db; + duckdb_connection con; + if (duckdb_open(duckdb_path, &db) == DuckDBError) { + // TODO: Replace with die. + fprintf(stderr, "Unable to open DuckDB database: %s\n", duckdb_path); + exit(EXIT_FAILURE); + } + if (duckdb_connect(db, &con) == DuckDBError) + die("Unable to connect to DuckDB database"); + + char *line = NULL; + size_t n; + ssize_t line_length; + size_t l_line_count = 0; + + // Pass 1 + { + duckdb_appender segment_appender, path_appender; + if (duckdb_appender_create(con, NULL, "segment", &segment_appender) == DuckDBError) + die("Unable to create appender for segment table"); + if (duckdb_appender_create(con, NULL, "path", &path_appender) == DuckDBError) + die("Unable to create appender for path table"); + while ((getline(&line, &n, gfa_fp)) > 0) { + switch (line[0]) { + case 'S': + pass1_handle_s_line(line, &segment_id_table, &segment_appender); + break; + case 'P': + pass1_handle_p_line(line, &path_appender); + break; + case 'L': + l_line_count++; + break; + default: + break; + } + } + if (duckdb_appender_destroy(&segment_appender) == DuckDBError) + die("Unable to destroy segment appender"); + if (duckdb_appender_destroy(&path_appender) == DuckDBError) + die("Unable to destroy path appender"); + } + rewind(gfa_fp); + // Pass 2 + { + char **l_lines = malloc(l_line_count*sizeof(char*)); + size_t l_line_index = 0, path_id = 0; + while ((line_length = getline(&line, &n, gfa_fp)) > 0) { + switch (line[0]) { + case 'L': + l_lines[l_line_index] = strdup(line); + l_line_index++; + break; + case 'P': + process_p_line(line, line_length, &segment_id_table, path_id, &db); + path_id++; + break; + default: + break; + } + } + process_l_lines(l_lines, l_line_count, &segment_id_table, &db); + free(l_lines); + } + + free(line); + fclose(gfa_fp); + duckdb_disconnect(&con); + duckdb_close(&db); + for (str_int_map_itr itr=vt_first(&segment_id_table); !vt_is_end(itr); itr=vt_next(itr)) + free((char*)itr.data->key); + vt_cleanup(&segment_id_table); + + return 0; +} + +int main (int argc, char *argv[]) +{ + if (argc != 3) { + fprintf(stderr, "Usage: %s <gfa_path> <duckdb_path>\n", argv[0]); + exit(EXIT_FAILURE); + } + return import_gfa(argv[1], argv[2]); +} diff --git a/domagi/__init__.py b/domagi/__init__.py new file mode 100644 index 0000000..e69de29 --- /dev/null +++ b/domagi/__init__.py diff --git a/domagi/bed-depth.sql b/domagi/bed-depth.sql new file mode 100644 index 0000000..b592b6a --- /dev/null +++ b/domagi/bed-depth.sql @@ -0,0 +1,39 @@ +-- Given a set of BED windows, compute the mean segment depth within +-- each window. The depth of each segment is weighted by the length of +-- the overlap between the segment and the window. +WITH bed_window AS ( + -- Read BED file windows and resolve path names to IDs. + SELECT row_number() OVER () AS id, + path.id AS path_id, + bed.start, bed.end + FROM read_csv(?, + columns={'path_name': 'VARCHAR', + 'start': 'INTEGER', + 'end': 'INTEGER'}) AS bed + INNER JOIN path ON path.name=bed.path_name), + window_segment AS ( + -- Many-to-many relation associating windows and segments that + -- intersect, combined with information about the length of + -- their overlap + SELECT id AS window_id, + segment_id, + (least(bed_window.end, ps.end) - greatest(bed_window.start, ps.start))::INTEGER AS overlap + FROM bed_window + INNER JOIN path_segment ps + ON bed_window.path_id=ps.path_id + AND ps.start<bed_window.end + AND ps.end>bed_window.start), + window_depth AS ( + -- Compute weighted average depth for each window. + SELECT window_id, + weighted_avg(depth, overlap) AS mean_depth + FROM segment_depth + INNER JOIN window_segment ON window_segment.segment_id=segment_depth.id + GROUP BY window_id) + -- Combine window path name and coordinate range with mean depth + -- for display. + SELECT path.name, bed_window.start, bed_window.end, mean_depth + FROM window_depth + INNER JOIN bed_window ON bed_window.id=window_depth.window_id + INNER JOIN path ON path.id=bed_window.path_id + ORDER BY window_id diff --git a/domagi/chop.sql b/domagi/chop.sql new file mode 100644 index 0000000..571a8ef --- /dev/null +++ b/domagi/chop.sql @@ -0,0 +1,12 @@ +WITH segment_chops AS ( + SELECT id, name, sequence, range(0, len(sequence), 3) AS starts + FROM segment), + segment_chop AS ( + SELECT id, name, sequence, 1 + unnest(starts) AS start, generate_subscripts(starts, 1)-1 AS chop_index + FROM segment_chops) + SELECT id, CASE WHEN chop_index=0 THEN name ELSE NULL END, array_slice(sequence, start, start + 3) + FROM segment_chop; + +-- chop index is computed as ceil(a/b) = (a+b-1)//b +-- SELECT id, name, unnest(range(0, len(sequence), 3)) AS starts, unnest(range(0, (len(sequence)+3-1)//3)) AS chop_index +-- FROM segment; diff --git a/domagi/domagi.py b/domagi/domagi.py new file mode 100644 index 0000000..a38581a --- /dev/null +++ b/domagi/domagi.py @@ -0,0 +1,339 @@ +### domagi --- DuckDB-powered pangenome Swiss Army knife +### Copyright © 2026 Arun Isaac <arunisaac@systemreboot.net> +### +### This file is part of domagi. +### +### domagi is free software: you can redistribute it and/or modify it under the +### terms of the GNU General Public License as published by the Free Software +### Foundation, either version 3 of the License, or (at your option) any later +### version. +### +### domagi is distributed in the hope that it will be useful, but WITHOUT ANY +### WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +### FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +### details. +### +### You should have received a copy of the GNU General Public License along with +### domagi. If not, see <https://www.gnu.org/licenses/>. + +from contextlib import contextmanager +import importlib.resources +import re +from pathlib import Path +import shutil +import subprocess +import sys +import tempfile + +import click +import duckdb + +common_options = click.option("-t", "--threads", "threads", + type=click.INT, + help="number of threads (default: number of CPUs)") + +class DuckDBParamType(click.ParamType): + name = "DB" + def __init__(self, read_only=True): + self.read_only = read_only + def convert(self, value, param, ctx): + # The click manual recommends checking for already valid + # values and passing them through. + if isinstance(value, duckdb.DuckDBPyConnection): + return value + try: + return ctx.with_resource(duckdb.connect(value, self.read_only)) + except duckdb.Error as err: + self.fail(str(err), param, ctx) + +def set_duckdb_threads(con, threads): + if threads: + con.execute(f"SET threads TO {threads}") + +@contextmanager +def connect_duckdb(path, threads): + with duckdb.connect(path) as con: + set_duckdb_threads(con, threads) + yield con + +def read_sql(filename): + # TODO: Move sql queries into their own directory and update this + # function once we move to python 3.13+. Only python 3.13+ + # supports multiple path names in read_text. + return importlib.resources.read_text(__package__, filename) + +@click.group(context_settings={"help_option_names": ["-h", "--help"]}) +def main(): + pass + +@main.command() +@click.option("-g", "--gfa", "gfa", + metavar="FILE", + required=True, + help="GFAv1 pangenome") +@click.option("-o", "--out", "db", + type=click.Path(), + required=True, + help="output pangenome duckdb database") +@common_options +def build(gfa, db, threads): + with connect_duckdb(db, threads) as con: + con.execute(read_sql("schema.sql")) + with connect_duckdb(db, threads) as con: + con.execute(read_sql("pre-import.sql")) + subprocess.run([shutil.which("domagi_importgfa"), gfa, db], + env={"OMP_NUM_THREADS": str(threads)} if threads else None) + with connect_duckdb(db, threads) as con: + con.execute(read_sql("post-import.sql")) + +@main.command() +@click.option("-i", "--db", "--idx", "con", + type=DuckDBParamType(), + required=True, + help="pangenome duckdb database") +@click.option("-o", "--out", "outfile", + type=click.Path(), + required=True, + help="path to output pangenome duckdb database") +@common_options +def crush(con, outfile, threads): + set_duckdb_threads(con, threads) + con.execute(f""" + ATTACH '{outfile}' AS output_db (READ_WRITE); + + CREATE TABLE output_db.segment AS + SELECT segment.id, name, regexp_replace(sequence, 'N+', 'N', 'g') AS sequence + FROM segment; + + CREATE TABLE output_db.link AS + SELECT * FROM link; + + CREATE TABLE output_db.path AS + SELECT * FROM path; + + CREATE TABLE output_db.path_segment AS + SELECT * FROM path_segment + ORDER BY path_id, start, "end" + """) + +@main.command() +@click.option("-i", "--db", "--idx", "con", + type=DuckDBParamType(), + required=True, + help="pangenome duckdb database") +@click.option("-d", "--graph-depth-table", + is_flag=True, + help="print depth and unique depth of every node") +@click.option("-r", "--path", "paths", + # We deviate a little from odgi and allow -r to be + # specified several times. + multiple=True, + help="only compute the depth of the given path") +@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): + set_duckdb_threads(con, threads) + # With the -d flag, print the depth and unique depth of every + # node. + if graph_depth_table: + print("\t".join(["#node.id", "depth", "depth.uniq"])) + for segment_name, depth, unique_depth in con.execute(""" + SELECT name, depth, unique_depth + FROM segment_depth + INNER JOIN segment ON segment.id=segment_depth.id + """).fetchall(): + print("\t".join([segment_name, str(depth), str(unique_depth)])) + elif bed_input: + print("\t".join(["#path", "start", "end", "mean.depth"])) + for path_name, start, end, mean_depth in con.execute( + read_sql("bed-depth.sql"), + [bed_input]).fetchall(): + print("\t".join([path_name, str(start), str(end), str(mean_depth)])) + # Else, print the mean node depth of each path. + else: + print("\t".join(["#path", "start", "end", "mean.depth"])) + for path_name, end, mean_depth in con.execute( + read_sql("path-depth.sql"), + [paths if paths else None]).fetchall(): + # The start is always 0. + print("\t".join([path_name, str(0), str(end), str(mean_depth)])) + +@main.command() +@click.option("-i", "--db", "--idx", "con", + type=DuckDBParamType(), + required=True, + help="input pangenome duckdb database") +@click.option("-o", "--out", "outfile", + type=click.Path(), + required=True, + help="path to output pangenome duckdb database") +@click.option("-n", "--node", "segment_name", + type=click.STRING, + help="segment name from which to begin the traversal") +@click.option("-r", "--path-range", "path_range", + type=click.STRING, + help="path range specifying segments from which to begin the traversal") +@click.option("-c", "--context-steps", "steps", + type=click.INT, + # TODO: Add default=0 + required=True, + help="number of traversal steps") +@common_options +def extract(con, outfile, segment_name, path_range, steps, threads): + set_duckdb_threads(con, threads) + with connect_duckdb(outfile, threads) as out_con: + out_con.execute(read_sql("schema.sql")) + if segment_name: + con.execute(""" + CREATE TEMPORARY TABLE initial_segment AS + SELECT id FROM segment WHERE segment.name=? + """, + [segment_name]) + elif path_range: + # TODO: We're assuming the interval is [start, end) rather + # than [start, end]. But check what odgi does. + con.execute(""" + CREATE TEMPORARY TABLE initial_segment AS + SELECT segment_id AS id + FROM path_segment + INNER JOIN path ON path.id=path_segment.path_id + WHERE path.name=? AND start>=? AND start<?; + """, + # TODO: Convert extracted strings to integers. + re.match(r"^([^:]*):(\d+)-(\d+)", path_range).groups()) + else: + raise ValueError("Neither --node and --path-range specified") + con.execute(""" + CREATE TEMPORARY TABLE reachable_segment AS + WITH RECURSIVE cte (id, distance) AS ( + SELECT id, 0 FROM initial_segment + UNION ALL + SELECT DISTINCT to_segment, distance+1 FROM cte + INNER JOIN link ON from_segment=id + WHERE distance<? + ) + SELECT id FROM cte; + """, + [steps]) + con.execute(f""" + ATTACH '{outfile}' AS subset_db (READ_WRITE); + + INSERT INTO subset_db.segment + SELECT segment.id, name, sequence FROM reachable_segment + INNER JOIN segment ON segment.id=reachable_segment.id; + + INSERT INTO subset_db.link + SELECT from_segment, from_orientation, to_segment, to_orientation + FROM reachable_segment + INNER JOIN link ON from_segment=reachable_segment.id; + + INSERT INTO subset_db.path_segment + SELECT path_id, segment_id, segment_orientation, start, "end" + FROM reachable_segment + INNER JOIN path_segment ON path_segment.segment_id=reachable_segment.id; + + INSERT INTO subset_db.path + SELECT id, ANY_VALUE(name) + FROM subset_db.path_segment + INNER JOIN path ON subset_db.path_segment.path_id=path.id + GROUP BY id; + + DROP TABLE reachable_segment; + DROP TABLE initial_segment; + """) + +# TODO: Add synopses for commands. +@main.command() +@click.option("-i", "--db", "--idx", "con", + type=DuckDBParamType(), + required=True, + help="pangenome duckdb database") +@common_options +def matrix(con, threads): + set_duckdb_threads(con, threads) + segment_count, = con.execute("SELECT COUNT() FROM segment").fetchone() + df = con.execute(read_sql("matrix.sql")).fetchdf() + print(segment_count, segment_count, df.shape[0]) + df.to_csv(sys.stdout, sep=" ", header=False, index=False) + +@main.command() +@click.option("-i", "--db", "--idx", "con", + type=DuckDBParamType(), + required=True, + help="pangenome duckdb database") +@click.option("-L", "--list-paths", + is_flag=True, + help="print path names") +@click.option("-f", "--fasta", "fasta", + is_flag=True, + help="print paths in FASTA format") +@common_options +def paths(con, list_paths, fasta, threads): + set_duckdb_threads(con, threads) + if list_paths: + for name, in con.execute("SELECT name FROM path").fetchall(): + print(name) + elif fasta: + for name, sequence in con.execute(""" + SELECT ANY_VALUE(path_name), + string_agg(sequence, '' ORDER BY position) + FROM path + INNER JOIN segment ON segment.id = path_segment.segment_id + GROUP BY path_id + """).fetchall(): + print(f">{name}") + print(sequence) + +@main.command() +@click.option("-i", "--db", "--idx", "con", + type=DuckDBParamType(), + required=True, + help="pangenome duckdb database") +# The --summarize flag seems to be a no-op in odgi. +@click.option("-S", "--summarize", + is_flag=True, + hidden=True) +@common_options +def stats(con, summarize, threads): + set_duckdb_threads(con, threads) + print("\t".join(["#length", "nodes", "edges", "paths", "steps"])) + length, = con.execute("SELECT sum(len(sequence)) FROM segment").fetchone() + nodes, = con.execute("SELECT COUNT() FROM segment").fetchone() + edges, = con.execute("SELECT COUNT() FROM link").fetchone() + paths, = con.execute("SELECT COUNT() FROM path").fetchone() + steps, = con.execute("SELECT COUNT() FROM path_segment").fetchone() + print("\t".join([str(length), str(nodes), str(edges), + str(paths), str(steps)])) + +@main.command() +@click.option("-i", "--db", "--idx", "con", + type=DuckDBParamType(), + required=True, + help="pangenome duckdb database") +@click.option("-g", "--to-gfa", + is_flag=True, + help="write the graph in GFAv1 format to stdout") +@common_options +def view(con, to_gfa, threads): + set_duckdb_threads(con, threads) + if to_gfa: + print("H\tVN:Z:1.0") + con.execute(""" + SELECT 'S', name, sequence FROM segment + """).fetchdf().to_csv(sys.stdout, sep="\t", header=False, index=False) + con.execute(""" + SELECT 'L', from_segment.name, from_orientation, to_segment.name, to_orientation FROM link + INNER JOIN segment AS from_segment ON from_segment.id=link.from_segment + INNER JOIN segment AS to_segment ON to_segment.id=link.to_segment + """).fetchdf().to_csv(sys.stdout, sep="\t", header=False, index=False) + con.execute(""" + SELECT 'P', ANY_VALUE(path.name), string_agg(segment.name || segment_orientation, ',' ORDER BY start) + FROM path + INNER JOIN path_segment ON path.id=path_segment.path_id + INNER JOIN segment ON segment.id=path_segment.segment_id + GROUP BY path.id; + """).fetchdf().to_csv(sys.stdout, sep="\t", header=False, index=False) + +if __name__ == "__main__": + main() diff --git a/domagi/matrix.sql b/domagi/matrix.sql new file mode 100644 index 0000000..df90cd5 --- /dev/null +++ b/domagi/matrix.sql @@ -0,0 +1,14 @@ +WITH segment_indices AS ( + SELECT id, dense_rank() OVER (ORDER BY id) AS index + FROM segment), + matrix AS ( + SELECT source.index AS source, destination.index AS destination + FROM link + INNER JOIN segment_indices source ON link.from_segment=source.id + INNER JOIN segment_indices destination ON link.to_segment=destination.id) + SELECT source, destination, 1 + FROM matrix + UNION ALL + SELECT destination, source, 1 + FROM matrix + diff --git a/domagi/path-depth.sql b/domagi/path-depth.sql new file mode 100644 index 0000000..081d015 --- /dev/null +++ b/domagi/path-depth.sql @@ -0,0 +1,26 @@ +-- Compute the mean segment depth for all paths, or a subset thereof. +-- The depth of each segment is weighted by its sequence length. +WITH path_depth AS ( + -- Compute weighted average segment depth of each path. + SELECT path_id, weighted_avg(depth, len(sequence)) AS mean_depth + FROM segment_depth + INNER JOIN segment ON segment.id=segment_depth.id + INNER JOIN path_segment ON path_segment.segment_id=segment_depth.id + INNER JOIN path ON path.id=path_segment.path_id + -- subset paths + WHERE ($1 IS NULL) OR (path.name IN (SELECT UNNEST($1))) + GROUP BY path_id), + path_length AS ( + -- Compute length of each path. + SELECT path_id, sum(len(sequence)) AS length + FROM path_segment + INNER JOIN segment ON segment_id=segment.id + INNER JOIN path ON path.id=path_segment.path_id + -- subset paths (same filter as above) + WHERE (($1 IS NULL) OR (path.name IN (SELECT UNNEST($1)))) + GROUP BY path_id) + -- Combine path name, length and mean depth for display. + SELECT name, length, mean_depth + FROM path_depth + INNER JOIN path_length ON path_depth.path_id=path_length.path_id + INNER JOIN path ON path.id=path_length.path_id diff --git a/domagi/post-import.sql b/domagi/post-import.sql new file mode 100644 index 0000000..3f28c1a --- /dev/null +++ b/domagi/post-import.sql @@ -0,0 +1,16 @@ +-- Convert internal.path_segment table with position information to +-- this path_segment table with [start, end) information. start and +-- end are zero-based coordinates. +INSERT INTO path_segment + SELECT path_id, + segment_id, + segment_orientation, + sum(len(sequence)) OVER (PARTITION BY path_id ORDER BY position) - len(sequence) AS start, + sum(len(sequence)) OVER (PARTITION BY path_id ORDER BY position) AS end + FROM internal.path_segment + INNER JOIN segment ON segment.id=path_segment.segment_id + ORDER BY path_id, start, "end"; + +-- Drop internal tables and schema. +DROP TABLE internal.path_segment; +DROP SCHEMA internal; diff --git a/domagi/pre-import.sql b/domagi/pre-import.sql new file mode 100644 index 0000000..6eae40a --- /dev/null +++ b/domagi/pre-import.sql @@ -0,0 +1,11 @@ +CREATE schema internal; + +-- Internal table that gets inserted into when building the database, +-- but converted to the main.path_segment table and then dropped +-- during post-processing +CREATE TABLE internal.path_segment ( + position INTEGER, + path_id INTEGER, + segment_id INTEGER, + segment_orientation orientation +); diff --git a/domagi/schema.sql b/domagi/schema.sql new file mode 100644 index 0000000..29066f9 --- /dev/null +++ b/domagi/schema.sql @@ -0,0 +1,45 @@ +CREATE TYPE orientation as ENUM ('+', '-'); + +CREATE TABLE segment ( + id INTEGER, + name VARCHAR, + sequence VARCHAR +); + +CREATE TABLE link ( + from_segment INTEGER, + from_orientation orientation, + to_segment INTEGER, + to_orientation orientation +); + +CREATE TABLE path ( + id INTEGER, + name VARCHAR +); + +CREATE TABLE path_segment ( + path_id INTEGER, + segment_id INTEGER, + segment_orientation orientation, + -- Zero-based inclusive start coordinate of segment on the path + start INTEGER, + -- Zero-based exclusive end coordinate of segment on the path + "end" INTEGER, +); + +-- One-to-one relation mapping segment IDs to their depth +CREATE VIEW segment_depth AS + WITH segment_depth_nonzero_depths_only AS ( + SELECT segment_id AS id, + count()::INTEGER AS depth, + count(DISTINCT path_id)::INTEGER AS unique_depth + FROM path_segment + GROUP BY segment_id) + -- Segments that were not crossed by any paths will have a NULL + -- depth; we set their depth to 0. + SELECT segment.id, + ifnull(depth, 0) AS depth, + ifnull(unique_depth, 0) AS unique_depth + FROM segment + LEFT JOIN segment_depth_nonzero_depths_only nzdepth ON segment.id=nzdepth.id; diff --git a/manifest.scm b/manifest.scm new file mode 100644 index 0000000..a222533 --- /dev/null +++ b/manifest.scm @@ -0,0 +1,16 @@ +(use-modules ((gnu packages task-management) #:select (git-bug)) + ((domagi-package) #:select (domagi)) + ((odgi-package) #:select (odgi)) + (srfi srfi-1)) + +(define (manifest-cons* . args) + "ARGS is of the form (PACKAGES ... ONTO-MANIFEST). Return a manifest +with PACKAGES and all packages in ONTO-MANIFEST." + (let ((packages (drop-right args 1)) + (onto-manifest (last args))) + (manifest (append (map package->manifest-entry packages) + (manifest-entries onto-manifest))))) + +(manifest-cons* git-bug + odgi + (package->development-manifest domagi)) diff --git a/meson.build b/meson.build new file mode 100644 index 0000000..7d85388 --- /dev/null +++ b/meson.build @@ -0,0 +1,23 @@ +project('domagi', 'c') + +cc = meson.get_compiler('c') +cc.has_header('verstable.h', required: true) +duckdb = dependency('DuckDB') +omp = dependency('openmp') + +py = import('python').find_installation() +py.install_sources('domagi/domagi.py', + subdir: 'domagi') + +install_data('domagi/matrix.sql', + 'domagi/schema.sql', + 'domagi/bed-depth.sql', + 'domagi/path-depth.sql', + 'domagi/pre-import.sql', + 'domagi/post-import.sql', + install_dir: py.get_install_dir() / 'domagi') + +executable('domagi_importgfa', + 'c/importgfa.c', + dependencies: [duckdb, omp], + install: true) \ No newline at end of file diff --git a/pre-inst-env b/pre-inst-env new file mode 100755 index 0000000..e7a4f52 --- /dev/null +++ b/pre-inst-env @@ -0,0 +1,3 @@ +#!/bin/sh + +PATH=$(dirname $0)/builddir${PATH:+:}$PATH "$@" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..a862509 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,24 @@ +[build-system] +requires = ["meson-python"] +build-backend = "mesonpy" + +[project] +name = "domagi" +version = "0.1.0" +authors = [ + { name="Arun Isaac", email="arunisaac@systemreboot.net" } +] +description = "DuckDB Optimized Dynamic Graph Implementation" +readme = "README.md" +classifiers = [ + "Programming Language :: Python :: 3", + "Operating System :: OS Independent" +] +license = {file = "COPYING"} +dependencies = [ + "click", + "duckdb" +] + +[project.scripts] +domagi = "domagi.domagi:main" diff --git a/test-data/README.md b/test-data/README.md new file mode 100644 index 0000000..fdee295 --- /dev/null +++ b/test-data/README.md @@ -0,0 +1,4 @@ +# Data source + +test1.gfa: https://github.com/pangenome/odgi/blob/5e58a324057ff094a11690968b9cf4b14ba14232/test/k.gfa +test2.gfa: https://github.com/pangenome/odgi/blob/5e58a324057ff094a11690968b9cf4b14ba14232/test/note5.gfa diff --git a/test-data/expected-output/test-crush.gfa b/test-data/expected-output/test-crush.gfa new file mode 100644 index 0000000..9a86959 --- /dev/null +++ b/test-data/expected-output/test-crush.gfa @@ -0,0 +1,13 @@ +H VN:Z:1.0 +S 1 ANA +L 1 + 2 + 0M +L 1 + 3 + 0M +L 1 + 3 - 0M +S 2 A +L 2 + 4 + 0M +S 3 TC +L 3 - 4 + 0M +L 3 + 4 + 0M +S 4 TNCAGGN +P 5+ 1+,3+,4+ * +P 5- 1+,3-,4+ * diff --git a/test-data/expected-output/test1-depth b/test-data/expected-output/test1-depth new file mode 100644 index 0000000..3d5e7f5 --- /dev/null +++ b/test-data/expected-output/test1-depth @@ -0,0 +1,3 @@ +#path start end mean.depth +x 0 50 1.9 +y 0 50 1.9 diff --git a/test-data/expected-output/test1-depth-bed-windows b/test-data/expected-output/test1-depth-bed-windows new file mode 100644 index 0000000..6ed8582 --- /dev/null +++ b/test-data/expected-output/test1-depth-bed-windows @@ -0,0 +1,11 @@ +#path start end mean.depth +x 0 10 1.8 +x 10 20 1.9 +x 20 30 2 +x 30 40 1.8 +x 40 50 2 +y 0 10 1.8 +y 10 20 1.9 +y 20 30 2 +y 30 40 1.8 +y 40 50 2 diff --git a/test-data/expected-output/test1-depth-graph-depth b/test-data/expected-output/test1-depth-graph-depth new file mode 100644 index 0000000..04fd7d6 --- /dev/null +++ b/test-data/expected-output/test1-depth-graph-depth @@ -0,0 +1,16 @@ +#node.id depth depth.uniq +1 2 2 +2 1 1 +3 1 1 +4 1 1 +5 1 1 +6 2 2 +7 1 1 +8 1 1 +9 2 2 +10 1 1 +11 1 1 +12 2 2 +13 1 1 +14 1 1 +15 2 2 diff --git a/test-data/expected-output/test1-matrix b/test-data/expected-output/test1-matrix new file mode 100644 index 0000000..7839ceb --- /dev/null +++ b/test-data/expected-output/test1-matrix @@ -0,0 +1,41 @@ +15 15 40 +1 2 1 +2 1 1 +1 3 1 +3 1 1 +2 4 1 +4 2 1 +2 5 1 +5 2 1 +3 4 1 +4 3 1 +3 5 1 +5 3 1 +4 6 1 +6 4 1 +5 6 1 +6 5 1 +6 7 1 +7 6 1 +6 8 1 +8 6 1 +7 9 1 +9 7 1 +8 9 1 +9 8 1 +9 10 1 +10 9 1 +9 11 1 +11 9 1 +10 12 1 +12 10 1 +11 12 1 +12 11 1 +12 13 1 +13 12 1 +12 14 1 +14 12 1 +13 15 1 +15 13 1 +14 15 1 +15 14 1 diff --git a/test-data/expected-output/test1-paths b/test-data/expected-output/test1-paths new file mode 100644 index 0000000..b77b4eb --- /dev/null +++ b/test-data/expected-output/test1-paths @@ -0,0 +1,2 @@ +x +y diff --git a/test-data/expected-output/test1-stats b/test-data/expected-output/test1-stats new file mode 100644 index 0000000..a20d6a4 --- /dev/null +++ b/test-data/expected-output/test1-stats @@ -0,0 +1,2 @@ +#length nodes edges paths steps +55 15 20 2 20 diff --git a/test-data/expected-output/test2-depth b/test-data/expected-output/test2-depth new file mode 100644 index 0000000..d963e97 --- /dev/null +++ b/test-data/expected-output/test2-depth @@ -0,0 +1,3 @@ +#path start end mean.depth +5+ 0 13 2 +5- 0 13 2 diff --git a/test-data/expected-output/test2-depth-bed-windows b/test-data/expected-output/test2-depth-bed-windows new file mode 100644 index 0000000..45446de --- /dev/null +++ b/test-data/expected-output/test2-depth-bed-windows @@ -0,0 +1,5 @@ +#path start end mean.depth +5+ 0 10 2 +5+ 10 13 2 +5- 0 10 2 +5- 10 13 2 diff --git a/test-data/expected-output/test2-depth-graph-depth b/test-data/expected-output/test2-depth-graph-depth new file mode 100644 index 0000000..5769e3b --- /dev/null +++ b/test-data/expected-output/test2-depth-graph-depth @@ -0,0 +1,5 @@ +#node.id depth depth.uniq +1 2 2 +2 0 0 +3 2 2 +4 2 2 diff --git a/test-data/expected-output/test2-matrix b/test-data/expected-output/test2-matrix new file mode 100644 index 0000000..3a4001b --- /dev/null +++ b/test-data/expected-output/test2-matrix @@ -0,0 +1,13 @@ +4 4 12 +1 2 1 +2 1 1 +1 3 1 +3 1 1 +1 3 1 +3 1 1 +2 4 1 +4 2 1 +3 4 1 +4 3 1 +3 4 1 +4 3 1 diff --git a/test-data/expected-output/test2-paths b/test-data/expected-output/test2-paths new file mode 100644 index 0000000..2bc98a9 --- /dev/null +++ b/test-data/expected-output/test2-paths @@ -0,0 +1,2 @@ +5+ +5- diff --git a/test-data/expected-output/test2-stats b/test-data/expected-output/test2-stats new file mode 100644 index 0000000..ec05936 --- /dev/null +++ b/test-data/expected-output/test2-stats @@ -0,0 +1,2 @@ +#length nodes edges paths steps +14 4 6 2 6 diff --git a/test-data/expected-output/test3-depth b/test-data/expected-output/test3-depth new file mode 100644 index 0000000..44daf00 --- /dev/null +++ b/test-data/expected-output/test3-depth @@ -0,0 +1,3 @@ +#path start end mean.depth +5+ 0 20 2.7 +5- 0 13 2.53846 diff --git a/test-data/expected-output/test3-depth-bed-windows b/test-data/expected-output/test3-depth-bed-windows new file mode 100644 index 0000000..b78d410 --- /dev/null +++ b/test-data/expected-output/test3-depth-bed-windows @@ -0,0 +1,5 @@ +#path start end mean.depth +5+ 0 10 2.4 +5+ 10 20 3 +5- 0 10 2.4 +5- 10 13 3 diff --git a/test-data/expected-output/test3-depth-graph-depth b/test-data/expected-output/test3-depth-graph-depth new file mode 100644 index 0000000..1131a40 --- /dev/null +++ b/test-data/expected-output/test3-depth-graph-depth @@ -0,0 +1,5 @@ +#node.id depth depth.uniq +1 2 2 +2 0 0 +3 2 2 +4 3 2 diff --git a/test-data/expected-output/test3-matrix b/test-data/expected-output/test3-matrix new file mode 100644 index 0000000..3a4001b --- /dev/null +++ b/test-data/expected-output/test3-matrix @@ -0,0 +1,13 @@ +4 4 12 +1 2 1 +2 1 1 +1 3 1 +3 1 1 +1 3 1 +3 1 1 +2 4 1 +4 2 1 +3 4 1 +4 3 1 +3 4 1 +4 3 1 diff --git a/test-data/expected-output/test3-paths b/test-data/expected-output/test3-paths new file mode 100644 index 0000000..2bc98a9 --- /dev/null +++ b/test-data/expected-output/test3-paths @@ -0,0 +1,2 @@ +5+ +5- diff --git a/test-data/expected-output/test3-stats b/test-data/expected-output/test3-stats new file mode 100644 index 0000000..9f48a71 --- /dev/null +++ b/test-data/expected-output/test3-stats @@ -0,0 +1,2 @@ +#length nodes edges paths steps +14 4 6 2 7 diff --git a/test-data/test-crush.gfa b/test-data/test-crush.gfa new file mode 100644 index 0000000..e9c601b --- /dev/null +++ b/test-data/test-crush.gfa @@ -0,0 +1,13 @@ +H VN:Z:1.0 +S 1 ANNA +S 2 A +S 3 TC +S 4 TNNCAGGNNNN +P 5+ 1+,3+,4+ +P 5- 1+,3-,4+ +L 1 + 2 + +L 1 + 3 + +L 1 + 3 - +L 3 - 4 + +L 2 + 4 + +L 3 + 4 + diff --git a/test-data/test1-bed-windows b/test-data/test1-bed-windows new file mode 100644 index 0000000..48f9f6c --- /dev/null +++ b/test-data/test1-bed-windows @@ -0,0 +1,10 @@ +x 0 10 +x 10 20 +x 20 30 +x 30 40 +x 40 50 +y 0 10 +y 10 20 +y 20 30 +y 30 40 +y 40 50 diff --git a/test-data/test1.gfa b/test-data/test1.gfa new file mode 100644 index 0000000..b11f390 --- /dev/null +++ b/test-data/test1.gfa @@ -0,0 +1,38 @@ +H VN:Z:1.0 +S 1 CAAATAAG +S 2 A +S 3 G +S 4 T +S 5 C +S 6 TTG +S 7 A +S 8 G +S 9 AAATTTTCTGGAGTTCTAT +S 10 A +S 11 T +S 12 ATAT +S 13 A +S 14 T +S 15 CCAACTCTCTG +P x 1+,3+,5+,6+,8+,9+,11+,12+,14+,15+ 8M,1M,1M,3M,1M,19M,1M,4M,1M,11M +P y 1+,2+,4+,6+,7+,9+,10+,12+,13+,15+ 8M,1M,1M,3M,1M,19M,1M,4M,1M,11M +L 1 + 2 + 0M +L 1 + 3 + 0M +L 2 + 4 + 0M +L 2 + 5 + 0M +L 3 + 4 + 0M +L 3 + 5 + 0M +L 4 + 6 + 0M +L 5 + 6 + 0M +L 6 + 7 + 0M +L 6 + 8 + 0M +L 7 + 9 + 0M +L 8 + 9 + 0M +L 9 + 10 + 0M +L 9 + 11 + 0M +L 10 + 12 + 0M +L 11 + 12 + 0M +L 12 + 13 + 0M +L 12 + 14 + 0M +L 13 + 15 + 0M +L 14 + 15 + 0M diff --git a/test-data/test2-bed-windows b/test-data/test2-bed-windows new file mode 100644 index 0000000..8242604 --- /dev/null +++ b/test-data/test2-bed-windows @@ -0,0 +1,4 @@ +5+ 0 10 +5+ 10 13 +5- 0 10 +5- 10 13 diff --git a/test-data/test2.gfa b/test-data/test2.gfa new file mode 100644 index 0000000..f305609 --- /dev/null +++ b/test-data/test2.gfa @@ -0,0 +1,13 @@ +H VN:Z:1.0 +S 1 AGGA +S 2 A +S 3 TC +S 4 TCTCAGG +P 5+ 1+,3+,4+ 8M,1M,1M +P 5- 1+,3-,4+ 8M,1M,1M +L 1 + 2 + 0M +L 1 + 3 + 0M +L 1 + 3 - 0M +L 3 - 4 + 0M +L 2 + 4 + 0M +L 3 + 4 + 0M diff --git a/test-data/test3-bed-windows b/test-data/test3-bed-windows new file mode 100644 index 0000000..23cc623 --- /dev/null +++ b/test-data/test3-bed-windows @@ -0,0 +1,4 @@ +5+ 0 10 +5+ 10 20 +5- 0 10 +5- 10 13 diff --git a/test-data/test3.gfa b/test-data/test3.gfa new file mode 100644 index 0000000..1a28506 --- /dev/null +++ b/test-data/test3.gfa @@ -0,0 +1,13 @@ +H VN:Z:1.0 +S 1 AGGA +S 2 A +S 3 TC +S 4 TCTCAGG +P 5+ 1+,3+,4+,4+ 8M,1M,1M +P 5- 1+,3-,4+ 8M,1M,1M +L 1 + 2 + 0M +L 1 + 3 + 0M +L 1 + 3 - 0M +L 3 - 4 + 0M +L 2 + 4 + 0M +L 3 + 4 + 0M diff --git a/tests/test_domagi.py b/tests/test_domagi.py new file mode 100644 index 0000000..73897cf --- /dev/null +++ b/tests/test_domagi.py @@ -0,0 +1,248 @@ +### domagi --- DuckDB-powered pangenome Swiss Army knife +### Copyright © 2026 Arun Isaac <arunisaac@systemreboot.net> +### +### This file is part of domagi. +### +### domagi is free software: you can redistribute it and/or modify it under the +### terms of the GNU General Public License as published by the Free Software +### Foundation, either version 3 of the License, or (at your option) any later +### version. +### +### domagi is distributed in the hope that it will be useful, but WITHOUT ANY +### WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +### FOR A PARTICULAR PURPOSE. See the GNU General Public License for more +### details. +### +### You should have received a copy of the GNU General Public License along with +### domagi. If not, see <https://www.gnu.org/licenses/>. + +import io + +from click.testing import CliRunner +import pandas as pd +from pandas.testing import assert_frame_equal +from pathlib import Path +import pytest + +from domagi.domagi import main + +def assert_gfa_equal(expected, actual): + def process_gfa_line(line): + fields = line.split("\t") + if fields[0] == "L": + return fields[:5] + elif fields[0] == "P": + return fields[:3] + else: + return fields + + def read_gfa_file(file): + return sorted([process_gfa_line(line.rstrip()) + for line in file.readlines()]) + + assert read_gfa_file(expected) == read_gfa_file(actual) + +@pytest.mark.parametrize("test_data_file, expected_output", + [(Path("test-data/test-crush.gfa"), + Path("test-data/expected-output/test-crush.gfa"))]) +def test_domagi_crush(tmp_path, test_data_file, expected_output): + duckdb_path = tmp_path / f"{test_data_file.stem}.db" + crushed_duckdb_path = tmp_path / f"{test_data_file.stem}-crushed.db" + runner = CliRunner() + result = runner.invoke(main, ["build", + "--gfa", test_data_file, + "--out", duckdb_path]) + assert result.exit_code == 0 + result = runner.invoke(main, ["crush", + "--db", duckdb_path, + "--out", crushed_duckdb_path]) + assert result.exit_code == 0 + result = runner.invoke(main, ["view", + "--to-gfa", + "--db", crushed_duckdb_path]) + assert result.exit_code == 0 + with open(expected_output) as file: + assert_gfa_equal(file, io.StringIO(result.stdout)) + +@pytest.mark.parametrize("test_data_file, expected_output", + [(Path("test-data/test1.gfa"), + Path("test-data/expected-output/test1-depth")), + (Path("test-data/test2.gfa"), + Path("test-data/expected-output/test2-depth")), + (Path("test-data/test3.gfa"), + Path("test-data/expected-output/test3-depth"))]) +def test_domagi_depth(tmp_path, test_data_file, expected_output): + expected = (pd.read_csv(expected_output, sep="\t") + .sort_values(by=["#path"], ignore_index=True)) + duckdb_path = tmp_path / f"{test_data_file.stem}.db" + runner = CliRunner() + result = runner.invoke(main, ["build", + "--gfa", test_data_file, + "--out", duckdb_path]) + assert result.exit_code == 0 + result = runner.invoke(main, ["depth", + "--db", duckdb_path]) + assert result.exit_code == 0 + assert_frame_equal(expected, + pd.read_csv(io.StringIO(result.stdout), + sep="\t") + .sort_values(by=["#path"], + ignore_index=True), + check_dtype=False) + for _, row in expected.iterrows(): + per_path_expected = pd.DataFrame([row]).reset_index(drop=True) + path = row["#path"] + result = runner.invoke(main, ["depth", + "--db", duckdb_path, + "--path", path]) + assert result.exit_code == 0 + assert_frame_equal(per_path_expected, + pd.read_csv(io.StringIO(result.stdout), + sep="\t") + .sort_values(by=["#path"], + ignore_index=True), + check_dtype=False) + +@pytest.mark.parametrize("test_data_file, expected_output", + [(Path("test-data/test1.gfa"), + Path("test-data/expected-output/test1-depth-graph-depth")), + (Path("test-data/test2.gfa"), + Path("test-data/expected-output/test2-depth-graph-depth")), + (Path("test-data/test3.gfa"), + Path("test-data/expected-output/test3-depth-graph-depth"))]) +def test_domagi_depth_graph_depth(tmp_path, test_data_file, expected_output): + duckdb_path = tmp_path / f"{test_data_file.stem}.db" + runner = CliRunner() + result = runner.invoke(main, ["build", + "--gfa", test_data_file, + "--out", duckdb_path]) + assert result.exit_code == 0 + result = runner.invoke(main, ["depth", + "--graph-depth-table", + "--db", duckdb_path]) + assert result.exit_code == 0 + assert_frame_equal(pd.read_csv(expected_output, sep="\t") + .sort_values(by=["#node.id"], + ignore_index=True), + pd.read_csv(io.StringIO(result.stdout), + sep="\t") + .sort_values(by=["#node.id"], + ignore_index=True), + check_dtype=False) + +@pytest.mark.parametrize("test_data_file, bed_windows, expected_output", + [(Path("test-data/test1.gfa"), + Path("test-data/test1-bed-windows"), + Path("test-data/expected-output/test1-depth-bed-windows")), + (Path("test-data/test2.gfa"), + Path("test-data/test2-bed-windows"), + Path("test-data/expected-output/test2-depth-bed-windows")), + (Path("test-data/test3.gfa"), + Path("test-data/test3-bed-windows"), + Path("test-data/expected-output/test3-depth-bed-windows"))]) +def test_domagi_depth_bed_windows(tmp_path, test_data_file, bed_windows, expected_output): + duckdb_path = tmp_path / f"{test_data_file.stem}.db" + runner = CliRunner() + result = runner.invoke(main, ["build", + "--gfa", test_data_file, + "--out", duckdb_path]) + assert result.exit_code == 0 + result = runner.invoke(main, ["depth", + "--bed-input", bed_windows, + "--db", duckdb_path]) + assert result.exit_code == 0 + assert_frame_equal(pd.read_csv(expected_output, sep="\t"), + pd.read_csv(io.StringIO(result.stdout), sep="\t"), + check_dtype=False) + +@pytest.mark.parametrize("test_data_file, expected_output", + [(Path("test-data/test1.gfa"), + Path("test-data/expected-output/test1-matrix")), + (Path("test-data/test2.gfa"), + Path("test-data/expected-output/test2-matrix")), + (Path("test-data/test3.gfa"), + Path("test-data/expected-output/test3-matrix"))]) +def test_domagi_matrix(tmp_path, test_data_file, expected_output): + def read_matrix_file(file): + return (file.readline().rstrip(), + [line.rstrip() for line in sorted(file.readlines())]) + + duckdb_path = tmp_path / f"{test_data_file.stem}.db" + runner = CliRunner() + result = runner.invoke(main, ["build", + "--gfa", test_data_file, + "--out", duckdb_path]) + assert result.exit_code == 0 + result = runner.invoke(main, ["matrix", + "--db", duckdb_path]) + assert result.exit_code == 0 + with open(expected_output) as file: + expected_header, expected_lines = read_matrix_file(file) + with io.StringIO(result.stdout) as file: + actual_header, actual_lines = read_matrix_file(file) + assert expected_header == actual_header + assert expected_lines == actual_lines + +@pytest.mark.parametrize("test_data_file, expected_output", + [(Path("test-data/test1.gfa"), + Path("test-data/expected-output/test1-paths")), + (Path("test-data/test2.gfa"), + Path("test-data/expected-output/test2-paths")), + (Path("test-data/test3.gfa"), + Path("test-data/expected-output/test3-paths"))]) +def test_domagi_paths(tmp_path, test_data_file, expected_output): + duckdb_path = tmp_path / f"{test_data_file.stem}.db" + runner = CliRunner() + result = runner.invoke(main, ["build", + "--gfa", test_data_file, + "--out", duckdb_path]) + assert result.exit_code == 0 + result = runner.invoke(main, ["paths", + "--list-paths", + "--db", duckdb_path]) + assert result.exit_code == 0 + assert_frame_equal(pd.read_csv(expected_output, sep="\t", header=None), + pd.read_csv(io.StringIO(result.stdout), + sep="\t", + header=None), + check_dtype=False) + +@pytest.mark.parametrize("test_data_file, expected_output", + [(Path("test-data/test1.gfa"), + Path("test-data/expected-output/test1-stats")), + (Path("test-data/test2.gfa"), + Path("test-data/expected-output/test2-stats")), + (Path("test-data/test3.gfa"), + Path("test-data/expected-output/test3-stats"))]) +def test_domagi_stats(tmp_path, test_data_file, expected_output): + duckdb_path = tmp_path / f"{test_data_file.stem}.db" + runner = CliRunner() + result = runner.invoke(main, ["build", + "--gfa", test_data_file, + "--out", duckdb_path]) + assert result.exit_code == 0 + result = runner.invoke(main, ["stats", + "--db", duckdb_path]) + assert result.exit_code == 0 + assert_frame_equal(pd.read_csv(expected_output, sep="\t"), + pd.read_csv(io.StringIO(result.stdout), + sep="\t"), + check_dtype=False) + +@pytest.mark.parametrize("test_data_file", + [Path("test-data/test1.gfa"), + Path("test-data/test2.gfa"), + Path("test-data/test3.gfa")]) +def test_domagi_view(tmp_path, test_data_file): + duckdb_path = tmp_path / f"{test_data_file.stem}.db" + runner = CliRunner() + result = runner.invoke(main, ["build", + "--gfa", test_data_file, + "--out", duckdb_path]) + assert result.exit_code == 0 + result = runner.invoke(main, ["view", + "--to-gfa", + "--db", duckdb_path]) + assert result.exit_code == 0 + with open(test_data_file) as expected: + assert_gfa_equal(expected, io.StringIO(result.stdout)) |