diff options
| -rw-r--r-- | domagi/domagi.py | 17 | ||||
| -rw-r--r-- | test-data/expected-output/test1-extract-node-1.gfa | 4 | ||||
| -rw-r--r-- | test-data/expected-output/test1-extract-node-2.gfa | 4 | ||||
| -rw-r--r-- | test-data/expected-output/test1-extract-node-3.gfa | 4 | ||||
| -rw-r--r-- | test-data/expected-output/test1-extract-path-7-10.gfa | 4 | ||||
| -rw-r--r-- | test-data/expected-output/test1-extract-path-7-8.gfa | 4 | ||||
| -rw-r--r-- | test-data/expected-output/test1-extract-path-7-9.gfa | 4 | ||||
| -rw-r--r-- | test-data/expected-output/test1-extract-path-8-10.gfa | 2 | ||||
| -rw-r--r-- | test-data/expected-output/test1-extract-path-8-9.gfa | 2 |
9 files changed, 28 insertions, 17 deletions
diff --git a/domagi/domagi.py b/domagi/domagi.py index 20f5837..72f9d73 100644 --- a/domagi/domagi.py +++ b/domagi/domagi.py @@ -258,20 +258,31 @@ def extract(con, outfile, segment_name, path_range, steps, threads, progress): SELECT from_segment, from_orientation, to_segment, to_orientation FROM selected_segment INNER JOIN link ON from_segment=selected_segment.id; - + + CREATE TEMPORARY TABLE path_first_start AS + SELECT path_id, MIN(start) AS first_start + FROM selected_segment + INNER JOIN path_segment ON path_segment.segment_id=selected_segment.id + GROUP BY path_id; + INSERT INTO subset_db.path_segment - SELECT path_id, segment_id, segment_orientation, start, "end" + -- There are no gaps in the path segments. So, it's enough to subtract + -- first_start from the path segment coordinates. + SELECT path_segment.path_id, segment_id, segment_orientation, start-first_start, "end"-first_start FROM selected_segment INNER JOIN path_segment ON path_segment.segment_id=selected_segment.id + INNER JOIN path_first_start ON path_first_start.path_id=path_segment.path_id -- Re-order similar to post-import.sql for optimal access. ORDER BY path_id, start, "end"; INSERT INTO subset_db.path - SELECT id, ANY_VALUE(name) + SELECT id, ANY_VALUE(name) || ':' || MIN(start)+ANY_VALUE(first_start) || '-' || MAX("end")+ANY_VALUE(first_start) FROM subset_db.path_segment INNER JOIN path ON subset_db.path_segment.path_id=path.id + INNER JOIN path_first_start ON path_first_start.path_id=path.id GROUP BY id; + DROP TABLE path_first_start; DROP TABLE selected_segment; """) diff --git a/test-data/expected-output/test1-extract-node-1.gfa b/test-data/expected-output/test1-extract-node-1.gfa index 3beb269..9c2c36f 100644 --- a/test-data/expected-output/test1-extract-node-1.gfa +++ b/test-data/expected-output/test1-extract-node-1.gfa @@ -8,5 +8,5 @@ L 9 + 10 + 0M L 9 + 11 + 0M S 10 A S 11 T -P x 8+,9+,11+ * -P y 7+,9+,10+ * +P x:13-34 8+,9+,11+ * +P y:13-34 7+,9+,10+ * diff --git a/test-data/expected-output/test1-extract-node-2.gfa b/test-data/expected-output/test1-extract-node-2.gfa index 876dd44..9bcc91d 100644 --- a/test-data/expected-output/test1-extract-node-2.gfa +++ b/test-data/expected-output/test1-extract-node-2.gfa @@ -14,5 +14,5 @@ L 10 + 12 + 0M S 11 T L 11 + 12 + 0M S 12 ATAT -P x 6+,8+,9+,11+,12+ * -P y 6+,7+,9+,10+,12+ * +P x:10-38 6+,8+,9+,11+,12+ * +P y:10-38 6+,7+,9+,10+,12+ * diff --git a/test-data/expected-output/test1-extract-node-3.gfa b/test-data/expected-output/test1-extract-node-3.gfa index 0d58053..0a0113f 100644 --- a/test-data/expected-output/test1-extract-node-3.gfa +++ b/test-data/expected-output/test1-extract-node-3.gfa @@ -22,5 +22,5 @@ L 12 + 13 + 0M L 12 + 14 + 0M S 13 A S 14 T -P x 5+,6+,8+,9+,11+,12+,14+ * -P y 4+,6+,7+,9+,10+,12+,13+ * +P x:9-39 5+,6+,8+,9+,11+,12+,14+ * +P y:9-39 4+,6+,7+,9+,10+,12+,13+ * diff --git a/test-data/expected-output/test1-extract-path-7-10.gfa b/test-data/expected-output/test1-extract-path-7-10.gfa index 327c140..e01c715 100644 --- a/test-data/expected-output/test1-extract-path-7-10.gfa +++ b/test-data/expected-output/test1-extract-path-7-10.gfa @@ -4,5 +4,5 @@ L 1 + 3 + 0M S 3 G L 3 + 5 + 0M S 5 C -P x 1+,3+,5+ * -P y 1+ * +P x:0-10 1+,3+,5+ * +P y:0-8 1+ * diff --git a/test-data/expected-output/test1-extract-path-7-8.gfa b/test-data/expected-output/test1-extract-path-7-8.gfa index 6ac10e2..aea4b13 100644 --- a/test-data/expected-output/test1-extract-path-7-8.gfa +++ b/test-data/expected-output/test1-extract-path-7-8.gfa @@ -1,4 +1,4 @@ H VN:Z:1.0 S 1 CAAATAAG -P x 1+ * -P y 1+ * +P x:0-8 1+ * +P y:0-8 1+ * diff --git a/test-data/expected-output/test1-extract-path-7-9.gfa b/test-data/expected-output/test1-extract-path-7-9.gfa index d013efd..005ddaa 100644 --- a/test-data/expected-output/test1-extract-path-7-9.gfa +++ b/test-data/expected-output/test1-extract-path-7-9.gfa @@ -2,5 +2,5 @@ H VN:Z:1.0 S 1 CAAATAAG L 1 + 3 + 0M S 3 G -P x 1+,3+ * -P y 1+ * +P x:0-9 1+,3+ * +P y:0-8 1+ * diff --git a/test-data/expected-output/test1-extract-path-8-10.gfa b/test-data/expected-output/test1-extract-path-8-10.gfa index 703d856..a5d3421 100644 --- a/test-data/expected-output/test1-extract-path-8-10.gfa +++ b/test-data/expected-output/test1-extract-path-8-10.gfa @@ -2,4 +2,4 @@ H VN:Z:1.0 S 3 G L 3 + 5 + 0M S 5 C -P x 3+,5+ * +P x:8-10 3+,5+ * diff --git a/test-data/expected-output/test1-extract-path-8-9.gfa b/test-data/expected-output/test1-extract-path-8-9.gfa index 243a879..808e3fa 100644 --- a/test-data/expected-output/test1-extract-path-8-9.gfa +++ b/test-data/expected-output/test1-extract-path-8-9.gfa @@ -1,3 +1,3 @@ H VN:Z:1.0 S 3 G -P x 3+ * +P x:8-9 3+ * |