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11 files changed

+87
-87
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11 files changed

+87
-87
lines changed

‎bioframe/__init__.py‎

Lines changed: 34 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,25 @@
99
__version__ = "unknown"
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__all__ = [
12+
"SCHEMAS",
13+
"UCSCClient",
1214
"arrops",
15+
"assemblies_available",
16+
"assembly_info",
17+
"assign_view",
18+
"binnify",
19+
"closest",
20+
"cluster",
21+
"complement",
22+
"count_overlaps",
23+
"coverage",
24+
"digest",
25+
"expand",
26+
"fetch_centromeres",
27+
"fetch_chromsizes",
28+
"frac_gc",
29+
"frac_gene_coverage",
30+
"frac_mapped",
1331
"from_any",
1432
"from_dict",
1533
"from_list",
@@ -24,27 +42,17 @@
2442
"is_sorted",
2543
"is_tiling",
2644
"is_viewframe",
45+
"load_fasta",
46+
"make_chromarms",
2747
"make_viewframe",
48+
"mark_runs",
49+
"merge",
50+
"merge_runs",
51+
"overlap",
52+
"pair_by_distance",
2853
"parse_region",
2954
"parse_region_string",
30-
"sanitize_bedframe",
31-
"to_ucsc_string",
32-
"update_default_colnames",
33-
"binnify",
34-
"digest",
35-
"frac_gc",
36-
"frac_gene_coverage",
37-
"frac_mapped",
38-
"make_chromarms",
39-
"pair_by_distance",
40-
"seq_gc",
41-
"SCHEMAS",
42-
"UCSCClient",
43-
"assemblies_available",
44-
"assembly_info",
45-
"fetch_centromeres",
46-
"fetch_chromsizes",
47-
"load_fasta",
55+
"plot_intervals",
4856
"read_alignments",
4957
"read_bam",
5058
"read_bigbed",
@@ -53,30 +61,22 @@
5361
"read_pairix",
5462
"read_tabix",
5563
"read_table",
56-
"to_bed",
57-
"to_bigbed",
58-
"to_bigwig",
59-
"assign_view",
60-
"closest",
61-
"cluster",
62-
"complement",
63-
"count_overlaps",
64-
"coverage",
65-
"expand",
66-
"merge",
67-
"overlap",
68-
"mark_runs",
69-
"merge_runs",
64+
"sanitize_bedframe",
7065
"select",
7166
"select_indices",
7267
"select_labels",
7368
"select_mask",
69+
"seq_gc",
7470
"setdiff",
7571
"sort_bedframe",
7672
"subtract",
77-
"trim",
78-
"plot_intervals",
73+
"to_bed",
74+
"to_bigbed",
75+
"to_bigwig",
7976
"to_ucsc_colorstring",
77+
"to_ucsc_string",
78+
"trim",
79+
"update_default_colnames",
8080
]
8181

8282
from .core import (

‎bioframe/core/__init__.py‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -27,24 +27,24 @@
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__all__ = [
2929
"arrops",
30+
"from_any",
31+
"from_dict",
32+
"from_list",
33+
"from_series",
3034
"is_bedframe",
3135
"is_cataloged",
36+
"is_chrom_dtype",
37+
"is_complete_ucsc_string",
3238
"is_contained",
3339
"is_covering",
3440
"is_overlapping",
3541
"is_sorted",
3642
"is_tiling",
3743
"is_viewframe",
38-
"from_any",
39-
"from_dict",
40-
"from_list",
41-
"from_series",
4244
"make_viewframe",
43-
"sanitize_bedframe",
44-
"is_chrom_dtype",
45-
"update_default_colnames",
46-
"is_complete_ucsc_string",
4745
"parse_region",
4846
"parse_region_string",
47+
"sanitize_bedframe",
4948
"to_ucsc_string",
49+
"update_default_colnames",
5050
]

‎bioframe/core/checks.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -8,12 +8,12 @@
88
__all__ = [
99
"is_bedframe",
1010
"is_cataloged",
11-
"is_overlapping",
12-
"is_viewframe",
1311
"is_contained",
1412
"is_covering",
15-
"is_tiling",
13+
"is_overlapping",
1614
"is_sorted",
15+
"is_tiling",
16+
"is_viewframe",
1717
]
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1919

‎bioframe/core/construction.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,10 +6,10 @@
66
from .stringops import is_complete_ucsc_string, parse_region_string, to_ucsc_string
77

88
__all__ = [
9+
"from_any",
910
"from_dict",
10-
"from_series",
1111
"from_list",
12-
"from_any",
12+
"from_series",
1313
"make_viewframe",
1414
"sanitize_bedframe",
1515
]

‎bioframe/core/specs.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@
44
import pandas as pd
55

66
__all__ = [
7-
"update_default_colnames",
87
"is_chrom_dtype",
8+
"update_default_colnames",
99
]
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1111
_rc = {"colnames": {"chrom": "chrom", "start": "start", "end": "end"}}

‎bioframe/core/stringops.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,9 +4,9 @@
44
import pandas as pd
55

66
__all__ = [
7+
"is_complete_ucsc_string",
78
"parse_region",
89
"parse_region_string",
9-
"is_complete_ucsc_string",
1010
"to_ucsc_string",
1111
]
1212

‎bioframe/extras.py‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -7,16 +7,16 @@
77
from .core.specs import _get_default_colnames, _verify_columns
88

99
__all__ = [
10-
"make_chromarms",
1110
"binnify",
1211
"digest",
13-
"frac_mapped",
1412
"frac_gc",
15-
"seq_gc",
1613
"frac_gene_coverage",
17-
"pair_by_distance",
14+
"frac_mapped",
15+
"make_chromarms",
1816
"mark_runs",
19-
"merge_runs"
17+
"merge_runs",
18+
"pair_by_distance",
19+
"seq_gc"
2020
]
2121

2222

‎bioframe/io/__init__.py‎

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -17,22 +17,22 @@
1717
from .schemas import SCHEMAS
1818

1919
__all__ = [
20+
"SCHEMAS",
21+
"UCSCClient",
2022
"assemblies_available",
2123
"assembly_info",
22-
"read_table",
23-
"read_chromsizes",
24-
"read_tabix",
25-
"read_pairix",
26-
"read_bam",
27-
"read_alignments",
24+
"fetch_centromeres",
25+
"fetch_chromsizes",
2826
"load_fasta",
27+
"read_alignments",
28+
"read_bam",
29+
"read_bigbed",
2930
"read_bigwig",
31+
"read_chromsizes",
32+
"read_pairix",
33+
"read_tabix",
34+
"read_table",
3035
"to_bed",
31-
"to_bigwig",
32-
"read_bigbed",
3336
"to_bigbed",
34-
"UCSCClient",
35-
"fetch_centromeres",
36-
"fetch_chromsizes",
37-
"SCHEMAS",
37+
"to_bigwig",
3838
]

‎bioframe/io/fileops.py‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -26,16 +26,16 @@
2626
from .schemas import BAM_FIELDS, SCHEMAS
2727

2828
__all__ = [
29-
"read_table",
30-
"read_chromsizes",
31-
"read_tabix",
32-
"read_pairix",
33-
"read_alignments",
3429
"load_fasta",
35-
"read_bigwig",
36-
"to_bigwig",
30+
"read_alignments",
3731
"read_bigbed",
32+
"read_bigwig",
33+
"read_chromsizes",
34+
"read_pairix",
35+
"read_tabix",
36+
"read_table",
3837
"to_bigbed",
38+
"to_bigwig",
3939
]
4040

4141

‎bioframe/io/resources.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -11,9 +11,9 @@
1111
from .schemas import SCHEMAS
1212

1313
__all__ = [
14-
"fetch_chromsizes",
15-
"fetch_centromeres",
1614
"UCSCClient",
15+
"fetch_centromeres",
16+
"fetch_chromsizes",
1717
]
1818

1919

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