Merge pull request #45 from gbouras13/dev

v1.5.1

HISTORY.md

@@ -1,5 +1,10 @@
 # History
 
+1.5.1 (2024-02-01)
+------------------
+
+* Fixes #44, where `--use_raven` was not working (Flye would be used instead). Thanks @[wanyuac](https://github.com/wanyuac).
+
 1.5.0 (2023-11-21)
 ------------------
 

docs/requirements.txt

@@ -1,4 +1,4 @@
 Pygments==2.15.0
 pymdown-extensions==10.0
-jinja2==3.0.3
+jinja2>=3.1.3
 Markdown==3.3.7

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "plassembler"
-version = "1.5.0" # change VERSION too
+version = "1.5.1" # change VERSION too
 description = "Quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates"
 authors = ["George Bouras <[email protected]>"]
 license = "MIT"

src/plassembler/__init__.py

@@ -400,6 +400,7 @@ def run(
     logger.info(f"--flye_assembly is {flye_assembly}")
     logger.info(f"--flye_info is {flye_info}")
     logger.info(f"--no_chromosome is {no_chromosome}")
+    logger.info(f"--use_raven is {use_raven}")
     logdir = Path(f"{outdir}/logs")
 
     # check deps
@@ -455,8 +456,12 @@ def run(
         skip_assembly = True
 
     if skip_assembly is False:
-        logger.info("Running Flye.")
-        run_flye(outdir, threads, raw_flag, pacbio_model, logdir)
+        if use_raven is False:
+            logger.info("Running Flye.")
+            run_flye(outdir, threads, raw_flag, pacbio_model, logdir)
+        else:
+            logger.info("Running Raven.")
+            run_raven(outdir, threads, logdir)
     else:
         if flye_directory != "nothing":
             logger.info(

src/plassembler/utils/CITATION

@@ -1,4 +1,3 @@
 Please cite plassembler in your paper using:
 
-Bouras, G., Sheppard A.E., Mallawaarachchi, V., Vreugde S. (2023) Plassembler https://github.com/gbouras13/plassembler.
-
+Bouras, G., Sheppard A.E., Mallawaarachchi, V., Vreugde S. (2023) Plassembler: an automated bacterial plasmid assembly tool, Bioinformatics, Volume 39, Issue 7, July 2023, btad409, https://doi.org/10.1093/bioinformatics/btad409

src/plassembler/utils/VERSION

@@ -1 +1 @@
-1.5.0
+1.5.1

tests/test_end_to_end.py

@@ -90,6 +90,17 @@ def test_plassembler_case_1(self):
         exec_command(cmd)
         remove_directory(outdir)
 
+    def test_plassembler_case_1_use_raven(self):
+        """test plassembler run - chromosome only assembled with Flye, no plasmids - plasmids recovered from the short reads"""
+        longreads: Path = f"{end_to_end}/case1.fastq.gz"
+        s1: Path = f"{end_to_end}/input_R1.fastq.gz"
+        s2: Path = f"{end_to_end}/input_R2.fastq.gz"
+        chromosome = 50000
+        outdir: Path = f"{end_to_end}/test_out"
+        cmd = f"plassembler run -l {longreads} -c {chromosome} -1 {s1} -2 {s2} -d {plassembler_db_dir} -o {outdir}  -t 8 -f"
+        exec_command(cmd)
+        remove_directory(outdir)
+
     def test_plassembler_case_2(self):
         with self.assertRaises(RuntimeError):
             """test plassembler run case 2 no chromosome assembled at all"""