From 7f1cf69f46d65666b20e2b49a62dba520e126233 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Wed, 4 Oct 2023 22:23:40 +0200
Subject: [PATCH] added docs + updated bbconf and pipestat

---
 bedboss/__init__.py               | 12 +++--
 bedboss/_version.py               |  2 +-
 bedboss/bedboss.py                |  8 +++-
 bedboss/bedstat/bedstat.py        |  2 +-
 bedboss/cli.py                    |  4 +-
 docs/how_run_script.md            | 77 +++++++++++++++++++++++++++++++
 requirements/requirements-all.txt |  7 ++-
 7 files changed, 99 insertions(+), 13 deletions(-)
 create mode 100644 docs/how_run_script.md

diff --git a/bedboss/__init__.py b/bedboss/__init__.py
index 22e102d..ba8f9e0 100644
--- a/bedboss/__init__.py
+++ b/bedboss/__init__.py
@@ -3,10 +3,12 @@
 import coloredlogs
 
 from bedboss import *
-from bedboss.bedqc import bedqc
-from bedboss.bedmaker import bedmaker
-from bedboss.bedstat import bedstat
+
+# from bedboss.bedqc.bedqc import bedqc
+# from bedboss.bedmaker.bedmaker import BedMaker
+# from bedboss.bedstat.bedstat import bedstat
 from bedboss._version import __version__
+from bedboss.bedboss import run_all, run_all_by_pep, bedqc, BedMaker, bedstat
 
 
 __package_name__ = "bedboss"
@@ -24,9 +26,13 @@
     "__version__",
     "__package_name__",
     "__author__",
+    "bedboss",
     "bedqc",
     "bedmaker",
+    "BedMaker",
     "bedstat",
+    "run_all",
+    "run_all_by_pep",
 ]
 
 _LOGGER = logmuse.init_logger("bedboss")
diff --git a/bedboss/_version.py b/bedboss/_version.py
index 1822f2d..b0548b6 100644
--- a/bedboss/_version.py
+++ b/bedboss/_version.py
@@ -1 +1 @@
-__version__ = "0.1.0a3"
+__version__ = "0.1.0a4"
diff --git a/bedboss/bedboss.py b/bedboss/bedboss.py
index f444f15..5b20030 100644
--- a/bedboss/bedboss.py
+++ b/bedboss/bedboss.py
@@ -28,7 +28,7 @@
     check_db_connection,
 )
 from bedboss.exceptions import OpenSignalMatrixException
-from bedboss import __version__
+from bedboss._version import __version__
 
 _LOGGER = logging.getLogger("bedboss")
 
@@ -57,7 +57,11 @@ def get_osm_path(genome: str) -> Union[str, None]:
     if not os.path.exists(osm_path):
         if not os.path.exists(OPEN_SIGNAL_FOLDER):
             os.makedirs(OPEN_SIGNAL_FOLDER)
-        download_file(url=f"{OPEN_SIGNAL_URL}{osm_name}", path=osm_path, no_fail=True,)
+        download_file(
+            url=f"{OPEN_SIGNAL_URL}{osm_name}",
+            path=osm_path,
+            no_fail=True,
+        )
     return osm_path
 
 
diff --git a/bedboss/bedstat/bedstat.py b/bedboss/bedstat/bedstat.py
index 0360235..ef14112 100755
--- a/bedboss/bedstat/bedstat.py
+++ b/bedboss/bedstat/bedstat.py
@@ -239,7 +239,7 @@ def bedstat(
             del plot["name"]
             data.update({plot_id: plot})
         bbc.bed.report(
-            sample_name=bed_digest,
+            record_identifier=bed_digest,
             values=data,
             force_overwrite=force_overwrite,
         )
diff --git a/bedboss/cli.py b/bedboss/cli.py
index ef97d3b..c566436 100644
--- a/bedboss/cli.py
+++ b/bedboss/cli.py
@@ -2,7 +2,7 @@
 from argparse import ArgumentParser
 import logmuse
 
-from bedboss import __version__, __package_name__
+from bedboss._version import __version__
 
 
 def build_argparser() -> ArgumentParser:
@@ -11,7 +11,7 @@ def build_argparser() -> ArgumentParser:
     :retrun: Tuple[pipeline, arguments]
     """
     parser = VersionInHelpParser(
-        prog=__package_name__,
+        prog="bedboss",
         description="Warehouse of pipelines for BED-like files: "
         "bedmaker, bedstat, and bedqc.",
         epilog="",
diff --git a/docs/how_run_script.md b/docs/how_run_script.md
new file mode 100644
index 0000000..c45c814
--- /dev/null
+++ b/docs/how_run_script.md
@@ -0,0 +1,77 @@
+# How to run bedboss as a Python API
+
+## Install bedboss
+
+```bash
+pip install bedboss
+```
+
+## Run bedboss all
+
+```python
+from bedboss import run_all
+
+run_all(
+    sample_name="example_sample_name",
+    input_file="example/path/to/input_file",
+    input_type="bed",
+    outfolder="example/path/to/outfolder",
+    genome="hg38",
+    bedbase_config="example/path/to/bedbase_config.yaml",
+    # + another optional arguments
+)
+
+
+```
+
+
+## Run bedboss all-pep
+
+```python
+from bedboss import run_all_by_pep
+
+run_all_by_pep(
+    pep="example/path/to/pep.yaml"
+)
+```
+
+## Run bedboss make
+
+```python
+from bedboss import BedMaker
+
+BedMaker(
+    input_file="example/path/to/input_file",
+    input_type="bed",
+    output_bed="example/path/to/output_bed",
+    output_bigbed="example/path/to/output_bigbed",
+    sample_name="example_sample_name",
+    genome="hg38",
+)
+
+```
+
+## Run bedboss stat
+
+```python
+from bedboss import bedstat
+
+bedstat( 
+    bedfile="example/path/to/bedfile.bed",
+    bedbase_config="example/path/to/bedbase_config.yaml",
+    genome="hg38",
+    outfolder="example/path/to/outfolder",
+)
+
+```
+
+## Run bedboss qc
+
+```python
+from bedboss import bedqc
+
+bedqc(
+    bedfile="example/path/to/bedfile.bed",
+    outfolder="example/path/to/outfolder",
+)
+```
\ No newline at end of file
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index 31c63db..d03f2b5 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -3,9 +3,8 @@ coloredlogs>=15.0.1
 peppy>=0.40.0a4
 yacman>=0.8.4
 requests>=2.28.2
-piper>=0.13.2
-bbconf>=0.4.0a1
+piper>=0.13.3a1
+bbconf>=0.4.0a3
 refgenconf>=0.12.2
 pandas>=1.5.3
-ubiquerg>=0.6.2
-# geniml
\ No newline at end of file
+ubiquerg>=0.6.2
\ No newline at end of file