Add to_bed as well as a few tests (#203)

* add test for reading some bed formats * renomae rgb to itemRgb * add to_bed and associated tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update tests/test_fileops.py --------- Co-authored-by: Felix Raimundo <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nezar Abdennur <[email protected]>
open2c · Apr 23, 2024 · d8788b1 · d8788b1
1 parent f3ed76c
commit d8788b1
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Showing 10 changed files with 1,031 additions and 2 deletions.
diff --git a/bioframe/__init__.py b/bioframe/__init__.py
@@ -52,6 +52,7 @@
     "read_pairix",
     "read_tabix",
     "read_table",
+    "to_bed",
     "to_bigbed",
     "to_bigwig",
     "assign_view",
@@ -123,6 +124,7 @@
     read_pairix,
     read_tabix,
     read_table,
+    to_bed,
     to_bigbed,
     to_bigwig,
 )

diff --git a/bioframe/io/__init__.py b/bioframe/io/__init__.py
@@ -1,4 +1,5 @@
 from .assembly import assemblies_available, assembly_info
+from .bed import to_bed
 from .fileops import (
     load_fasta,
     read_bam,
@@ -24,6 +25,7 @@
     "read_bam",
     "load_fasta",
     "read_bigwig",
+    "to_bed",
     "to_bigwig",
     "read_bigbed",
     "to_bigbed",