Merge pull request #61 from databio/dev

Release 0.2.1

Author: khoroshevskyi

bedboss/_version.py

@@ -1 +1 @@
-__version__ = "0.2.0"
+__version__ = "0.2.1"

bedboss/bedboss.py

@@ -13,7 +13,6 @@
 from bbconf.bbagent import BedBaseAgent
 from bbconf.models.base_models import FileModel
 
-
 from bedboss.bedstat.bedstat import bedstat
 from bedboss.bedmaker.bedmaker import make_all
 from bedboss.bedbuncher import run_bedbuncher
@@ -231,6 +230,7 @@ def insert_pep(
     :param str output_folder: output statistics folder
     :param Union[str, peppy.Project] pep: path to the pep file or pephub registry path
     :param str bedset_id: bedset identifier
+    :param str bedset_name: bedset name
     :param str rfg_config: path to the genome config file (refgenie)
     :param bool create_bedset: whether to create bedset
     :param bool upload_qdrant: whether to upload bedfiles to qdrant
@@ -263,6 +263,7 @@ def insert_pep(
     validate_project(pep, BEDBOSS_PEP_SCHEMA_PATH)
 
     for i, pep_sample in enumerate(pep.samples):
+        m.print_success(f"Processing sample {i + 1}/{len(pep.samples)}")
         _LOGGER.info(f"Running bedboss pipeline for {pep_sample.sample_name}")
         if pep_sample.get("file_type"):
             if pep_sample.get("file_type").lower() == "narrowpeak":
@@ -276,6 +277,7 @@ def insert_pep(
                 input_file=pep_sample.input_file,
                 input_type=pep_sample.input_type,
                 genome=pep_sample.genome,
+                name=pep_sample.sample_name,
                 bedbase_config=bbagent,
                 narrowpeak=is_narrow_peak,
                 chrom_sizes=pep_sample.get("chrom_sizes"),
@@ -310,6 +312,7 @@ def insert_pep(
             upload_pephub=upload_pephub,
             upload_s3=upload_s3,
             no_fail=no_fail,
+            force_overwrite=force_overwrite,
         )
     else:
         _LOGGER.info(

bedboss/bedbuncher/bedbuncher.py

@@ -161,6 +161,7 @@ def run_bedbuncher(
         plots=plots.model_dump(exclude_none=True, exclude_unset=True),
         local_path=output_folder,
         no_fail=no_fail,
+        overwrite=force_overwrite,
     )
 
 

bedboss/bedmaker/bedmaker.py

@@ -70,13 +70,14 @@ def make_bigbed(
         pm_clean = False
     _LOGGER.info(f"Generating bigBed files for: {bed_path}")
 
-    if not os.path.exists(output_path):
-        os.makedirs(output_path)
+    bigbed_output_folder = os.path.join(output_path, BIGBED_FILE_NAME)
+    if not os.path.exists(bigbed_output_folder):
+        os.makedirs(bigbed_output_folder)
 
     bedfile_name = os.path.split(bed_path)[1]
     fileid = os.path.splitext(os.path.splitext(bedfile_name)[0])[0]
     # Produce bigBed (big_narrow_peak) file from peak file
-    big_bed_path = os.path.join(output_path, BIGBED_FILE_NAME, fileid + ".bigBed")
+    big_bed_path = os.path.join(bigbed_output_folder, fileid + ".bigBed")
     if not chrom_sizes:
         try:
             chrom_sizes = get_chrom_sizes(genome=genome, rfg_config=rfg_config)
@@ -191,10 +192,13 @@ def make_bed(
 
     # creat cmd to run that convert non bed file to bed file
     if input_type == InputTypes.BED.value:
-        # If bed file was provided:
-        bbclient = BBClient()
-        bed_id = bbclient.add_bed_to_cache(input_file)
-        output_path = bbclient.seek(bed_id)
+        try:
+            # If bed file was provided:
+            bbclient = BBClient()
+            bed_id = bbclient.add_bed_to_cache(input_file)
+            output_path = bbclient.seek(bed_id)
+        except FileNotFoundError as e:
+            raise BedBossException(f"File not found: {input_file} Error: {e}")
 
     else:
         _LOGGER.info(f"Converting {input_file} to BED format")

bedboss/cli.py

@@ -414,6 +414,14 @@ def delete_bedset(
     print(f"BedSet {identifier} deleted from the bedbase database")
 
 
+@app.command(help="check installed R packages")
+def check_requirements():
+    from bedboss.bedboss import requirements_check
+
+    print("Checking piplines requirements...")
+    requirements_check()
+
+
 @app.callback()
 def common(
     ctx: typer.Context,

docs/changelog.md

@@ -2,6 +2,14 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+# [0.2.1] - 2024-04-09
+## Changed
+- small naming tweaks
+
+## Added
+- added requirement check to cli
+
+
 # [0.2.0] - 2024-04-08
 ## Changed
 - moved all uploading functionality to the `bbconf` package

requirements/requirements-all.txt

@@ -4,7 +4,7 @@ peppy>=0.40.1
 yacman>=0.8.4
 requests>=2.28.2
 piper>=v0.14.0
-bbconf>=0.5.0
+bbconf>=0.5.1
 # bbconf @ git+https://github.com/databio/bbconf.git@dev#egg=bbconf
 refgenconf>=0.12.2
 pandas>=1.5.3