diff --git a/bioframe/__init__.py b/bioframe/__init__.py index 1141d5e..74b67b2 100644 --- a/bioframe/__init__.py +++ b/bioframe/__init__.py @@ -9,7 +9,25 @@ __version__ = "unknown" __all__ = [ + "SCHEMAS", + "UCSCClient", "arrops", + "assemblies_available", + "assembly_info", + "assign_view", + "binnify", + "closest", + "cluster", + "complement", + "count_overlaps", + "coverage", + "digest", + "expand", + "fetch_centromeres", + "fetch_chromsizes", + "frac_gc", + "frac_gene_coverage", + "frac_mapped", "from_any", "from_dict", "from_list", @@ -24,27 +42,17 @@ "is_sorted", "is_tiling", "is_viewframe", + "load_fasta", + "make_chromarms", "make_viewframe", + "mark_runs", + "merge", + "merge_runs", + "overlap", + "pair_by_distance", "parse_region", "parse_region_string", - "sanitize_bedframe", - "to_ucsc_string", - "update_default_colnames", - "binnify", - "digest", - "frac_gc", - "frac_gene_coverage", - "frac_mapped", - "make_chromarms", - "pair_by_distance", - "seq_gc", - "SCHEMAS", - "UCSCClient", - "assemblies_available", - "assembly_info", - "fetch_centromeres", - "fetch_chromsizes", - "load_fasta", + "plot_intervals", "read_alignments", "read_bam", "read_bigbed", @@ -53,30 +61,22 @@ "read_pairix", "read_tabix", "read_table", - "to_bed", - "to_bigbed", - "to_bigwig", - "assign_view", - "closest", - "cluster", - "complement", - "count_overlaps", - "coverage", - "expand", - "merge", - "overlap", - "mark_runs", - "merge_runs", + "sanitize_bedframe", "select", "select_indices", "select_labels", "select_mask", + "seq_gc", "setdiff", "sort_bedframe", "subtract", - "trim", - "plot_intervals", + "to_bed", + "to_bigbed", + "to_bigwig", "to_ucsc_colorstring", + "to_ucsc_string", + "trim", + "update_default_colnames", ] from .core import ( diff --git a/bioframe/core/__init__.py b/bioframe/core/__init__.py index eb6f11b..2a66745 100644 --- a/bioframe/core/__init__.py +++ b/bioframe/core/__init__.py @@ -27,24 +27,24 @@ __all__ = [ "arrops", + "from_any", + "from_dict", + "from_list", + "from_series", "is_bedframe", "is_cataloged", + "is_chrom_dtype", + "is_complete_ucsc_string", "is_contained", "is_covering", "is_overlapping", "is_sorted", "is_tiling", "is_viewframe", - "from_any", - "from_dict", - "from_list", - "from_series", "make_viewframe", - "sanitize_bedframe", - "is_chrom_dtype", - "update_default_colnames", - "is_complete_ucsc_string", "parse_region", "parse_region_string", + "sanitize_bedframe", "to_ucsc_string", + "update_default_colnames", ] diff --git a/bioframe/core/checks.py b/bioframe/core/checks.py index 279cf20..ba00ddd 100644 --- a/bioframe/core/checks.py +++ b/bioframe/core/checks.py @@ -8,12 +8,12 @@ __all__ = [ "is_bedframe", "is_cataloged", - "is_overlapping", - "is_viewframe", "is_contained", "is_covering", - "is_tiling", + "is_overlapping", "is_sorted", + "is_tiling", + "is_viewframe", ] diff --git a/bioframe/core/construction.py b/bioframe/core/construction.py index be54ca6..b7363a5 100644 --- a/bioframe/core/construction.py +++ b/bioframe/core/construction.py @@ -6,10 +6,10 @@ from .stringops import is_complete_ucsc_string, parse_region_string, to_ucsc_string __all__ = [ + "from_any", "from_dict", - "from_series", "from_list", - "from_any", + "from_series", "make_viewframe", "sanitize_bedframe", ] diff --git a/bioframe/core/specs.py b/bioframe/core/specs.py index 4d0b619..42fab2f 100644 --- a/bioframe/core/specs.py +++ b/bioframe/core/specs.py @@ -4,8 +4,8 @@ import pandas as pd __all__ = [ - "update_default_colnames", "is_chrom_dtype", + "update_default_colnames", ] _rc = {"colnames": {"chrom": "chrom", "start": "start", "end": "end"}} diff --git a/bioframe/core/stringops.py b/bioframe/core/stringops.py index 584152e..17611fc 100644 --- a/bioframe/core/stringops.py +++ b/bioframe/core/stringops.py @@ -4,9 +4,9 @@ import pandas as pd __all__ = [ + "is_complete_ucsc_string", "parse_region", "parse_region_string", - "is_complete_ucsc_string", "to_ucsc_string", ] diff --git a/bioframe/extras.py b/bioframe/extras.py index bcc9d76..d8cbe3b 100644 --- a/bioframe/extras.py +++ b/bioframe/extras.py @@ -7,16 +7,16 @@ from .core.specs import _get_default_colnames, _verify_columns __all__ = [ - "make_chromarms", "binnify", "digest", - "frac_mapped", "frac_gc", - "seq_gc", "frac_gene_coverage", - "pair_by_distance", + "frac_mapped", + "make_chromarms", "mark_runs", - "merge_runs" + "merge_runs", + "pair_by_distance", + "seq_gc" ] diff --git a/bioframe/io/__init__.py b/bioframe/io/__init__.py index f927e05..35b113f 100644 --- a/bioframe/io/__init__.py +++ b/bioframe/io/__init__.py @@ -17,22 +17,22 @@ from .schemas import SCHEMAS __all__ = [ + "SCHEMAS", + "UCSCClient", "assemblies_available", "assembly_info", - "read_table", - "read_chromsizes", - "read_tabix", - "read_pairix", - "read_bam", - "read_alignments", + "fetch_centromeres", + "fetch_chromsizes", "load_fasta", + "read_alignments", + "read_bam", + "read_bigbed", "read_bigwig", + "read_chromsizes", + "read_pairix", + "read_tabix", + "read_table", "to_bed", - "to_bigwig", - "read_bigbed", "to_bigbed", - "UCSCClient", - "fetch_centromeres", - "fetch_chromsizes", - "SCHEMAS", + "to_bigwig", ] diff --git a/bioframe/io/fileops.py b/bioframe/io/fileops.py index 1f4b35c..7d6cfcd 100644 --- a/bioframe/io/fileops.py +++ b/bioframe/io/fileops.py @@ -26,16 +26,16 @@ from .schemas import BAM_FIELDS, SCHEMAS __all__ = [ - "read_table", - "read_chromsizes", - "read_tabix", - "read_pairix", - "read_alignments", "load_fasta", - "read_bigwig", - "to_bigwig", + "read_alignments", "read_bigbed", + "read_bigwig", + "read_chromsizes", + "read_pairix", + "read_tabix", + "read_table", "to_bigbed", + "to_bigwig", ] diff --git a/bioframe/io/resources.py b/bioframe/io/resources.py index 95f88b0..60a5fee 100644 --- a/bioframe/io/resources.py +++ b/bioframe/io/resources.py @@ -11,9 +11,9 @@ from .schemas import SCHEMAS __all__ = [ - "fetch_chromsizes", - "fetch_centromeres", "UCSCClient", + "fetch_centromeres", + "fetch_chromsizes", ] diff --git a/bioframe/ops.py b/bioframe/ops.py index 2e3bfd1..dfc42d4 100644 --- a/bioframe/ops.py +++ b/bioframe/ops.py @@ -6,23 +6,23 @@ from .core.stringops import parse_region __all__ = [ + "assign_view", + "closest", + "cluster", + "complement", + "count_overlaps", + "coverage", + "expand", + "merge", + "overlap", "select", - "select_mask", "select_indices", "select_labels", - "expand", - "overlap", - "cluster", - "merge", - "coverage", - "closest", - "subtract", + "select_mask", "setdiff", - "count_overlaps", - "trim", - "complement", "sort_bedframe", - "assign_view", + "subtract", + "trim", ]