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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,171 @@ | ||
| import pyranges as pr | ||
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| p1 = pr.PyRanges( | ||
| { | ||
| "Chromosome": [1, 1, 2, 2, 2, 2, 2, 3], | ||
| "Strand": ["+", "+", "-", "-", "+", "+", "+", "+"], | ||
| "Start": [1, 40, 10, 70, 85, 110, 150, 140], | ||
| "End": [11, 60, 25, 80, 100, 115, 180, 152], | ||
| "transcript_id": ["t1", "t1", "t2", "t2", "t3", "t3", "t3", "t4"], | ||
| "feature1": ["a", "a", "b", "b", "c", "c", "c", "d"], | ||
| "feature2": ["A", "A", "B", "B", "C", "C", "C", "D"], | ||
| } | ||
| ) | ||
|
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| p2 = pr.PyRanges( | ||
| { | ||
| "Chromosome": [1, 1, 2, 2, 2, 2, 2, 3, 4, 4, 4, 4, 4, 4], | ||
| "Strand": [ | ||
| "+", | ||
| "+", | ||
| "-", | ||
| "-", | ||
| "+", | ||
| "+", | ||
| "+", | ||
| "+", | ||
| "-", | ||
| "-", | ||
| "-", | ||
| "-", | ||
| "+", | ||
| "+", | ||
| ], | ||
| "Start": [ | ||
| 1, | ||
| 40, | ||
| 10, | ||
| 70, | ||
| 85, | ||
| 110, | ||
| 150, | ||
| 140, | ||
| 30100, | ||
| 30150, | ||
| 30500, | ||
| 30647, | ||
| 29850, | ||
| 29970, | ||
| ], | ||
| "End": [ | ||
| 11, | ||
| 60, | ||
| 25, | ||
| 80, | ||
| 100, | ||
| 115, | ||
| 180, | ||
| 152, | ||
| 30300, | ||
| 30300, | ||
| 30700, | ||
| 30700, | ||
| 29900, | ||
| 30000, | ||
| ], | ||
| "transcript_id": [ | ||
| "t1", | ||
| "t1", | ||
| "t2", | ||
| "t2", | ||
| "t3", | ||
| "t3", | ||
| "t3", | ||
| "t4", | ||
| "t5", | ||
| "t5", | ||
| "t5", | ||
| "t5", | ||
| "t6", | ||
| "t6", | ||
| ], | ||
| "feature1": [ | ||
| "1", | ||
| "1", | ||
| "1", | ||
| "1", | ||
| "1", | ||
| "2", | ||
| "2", | ||
| "2", | ||
| "2", | ||
| "2", | ||
| "2", | ||
| "2", | ||
| "2", | ||
| "2", | ||
| ], | ||
| "feature2": [ | ||
| "A", | ||
| "A", | ||
| "B", | ||
| "B", | ||
| "C", | ||
| "C", | ||
| "C", | ||
| "D", | ||
| "E", | ||
| "E", | ||
| "E", | ||
| "E", | ||
| "F", | ||
| "F", | ||
| ], | ||
| "Feature": [ | ||
| "exon", | ||
| "exon", | ||
| "CDS", | ||
| "CDS", | ||
| "CDS", | ||
| "CDS", | ||
| "CDS", | ||
| "exon", | ||
| "exon", | ||
| "CDS", | ||
| "CDS", | ||
| "exon", | ||
| "CDS", | ||
| "CDS", | ||
| ], | ||
| } | ||
| ) | ||
|
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||
| p3 = pr.PyRanges( | ||
| { | ||
| "Chromosome": ["1"] * 10 + ["2"] * 10, | ||
| "Strand": ["+", "+", "+", "+", "-", "-", "-", "-", "+", "+"] | ||
| + ["+", "+", "+", "+", "-", "-", "-", "-", "+", "+"], | ||
| "Start": [90, 61, 104, 228, 9, 142, 52, 149, 218, 151] | ||
| + [6, 27, 37, 47, 1, 7, 42, 37, 60, 80], | ||
| "End": [92, 64, 113, 229, 12, 147, 57, 155, 224, 153] | ||
| + [8, 32, 40, 50, 5, 10, 46, 40, 70, 90], | ||
| "transcript_id": ["t1", "t1", "t1", "t1", "t2", "t2", "t2", "t2", "t3", "t3"] | ||
| + ["t4", "t4", "t4", "t4", "t5", "t5", "t5", "t5", "t6", "t6"], | ||
| } | ||
| ) | ||
|
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||
|
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| p_ala = pr.PyRanges( | ||
| { | ||
| "Start": [10, 50, 90] + [13, 60, 72, 120], | ||
| "End": [20, 75, 130] + [16, 63, 75, 123], | ||
| "Chromosome": [1] * 7, | ||
| "id": ["gene1"] * 7, | ||
| "trait1": ["exon"] * 3 + ["aa"] * 4, | ||
| "trait2": ["gene_1"] * 3 + ["Ala"] * 4, | ||
| "depth": [0] * 3 + [1] * 4, | ||
| } | ||
| ) | ||
|
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| p_cys = pr.PyRanges( | ||
| { | ||
| "Start": [10, 50, 90] + [15, 55, 62, 100, 110], | ||
| "End": [20, 75, 130] + [18, 58, 65, 103, 113], | ||
| "Chromosome": [1] * 8, | ||
| "id": ["gene1"] * 8, | ||
| "trait1": ["exon"] * 3 + ["aa"] * 5, | ||
| "trait2": ["gene_1"] * 3 + ["Cys"] * 5, | ||
| "depth": [0] * 3 + [1] * 5, | ||
| } | ||
| ) |