| |
| |
|
|
| import pytest |
|
|
| from motifbench_prosite.normalisation import ( |
| _parse_segment, |
| _format_segment, |
| remap_segments_with_residue_map, |
| remap_contig_string, |
| ) |
|
|
|
|
| def test_parse_segment_range(): |
| chain, start, end = _parse_segment("L24-43") |
| assert chain == "L" |
| assert start == 24 |
| assert end == 43 |
|
|
|
|
| def test_parse_segment_single(): |
| chain, start, end = _parse_segment("A5") |
| assert chain == "A" |
| assert start == end == 5 |
|
|
|
|
| def test_format_segment_range(): |
| assert _format_segment("A", 1, 10) == "A1-10" |
|
|
|
|
| def test_format_segment_single(): |
| assert _format_segment("B", 7, 7) == "B7" |
|
|
|
|
| def test_remap_segments_with_residue_map_simple(): |
| residue_map = { |
| ("L", 24): ("A", 1), |
| ("L", 25): ("A", 2), |
| ("L", 26): ("A", 3), |
| } |
| out = remap_segments_with_residue_map("L24-26", residue_map) |
| assert out == "A1-3" |
|
|
|
|
| def test_remap_segments_with_residue_map_split_chain_and_range_break(): |
| residue_map = { |
| ("L", 24): ("A", 1), |
| ("L", 25): ("A", 2), |
| ("L", 27): ("A", 4), |
| ("H", 10): ("B", 1), |
| } |
| out = remap_segments_with_residue_map("L24-27;H10-10", residue_map) |
| assert set(out.split(";")) == {"A1-2", "A4", "B1"} |
|
|
|
|
| def test_remap_segments_drops_unknown(): |
| residue_map = {("L", 24): ("A", 1)} |
| out = remap_segments_with_residue_map("L24-25;H10", residue_map) |
| assert out == "A1" |
|
|
|
|
| def test_remap_contig_string_motif_segments(): |
| segment_map = {"L24-43": "A1-20"} |
| contig = "0-100;L24-43;10-20" |
| out = remap_contig_string(contig, segment_map) |
| assert out == "0-100;A1-20;10-20" |
|
|
|
|
| def test_remap_contig_string_leaves_numeric_unchanged(): |
| out = remap_contig_string("0-100;10-20", {"L24-43": "A1-20"}) |
| assert out == "0-100;10-20" |
|
|
