integration of snakecdysis

.gitignore

@@ -41,11 +41,7 @@ clean.sh
 dag*
 
 # for dev
-#culebrONT/.mode.txt
-#CulebrONT_OUTPUT
-#Data-Xoo-sub
-#culebrONT/default_profile
-#culebrONT/containers/Singularity.culebront_tools.sif
-#culebrONT/containers/Singularity.report.sif
-#.tox
+frangiPANe/.mode.txt
+frangiPANe/default_profile
+frangiPANe/containers/frangiPANe_tools.sif
 frangiPANe/_version.py

frangiPANe/__init__.py

 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-from frangiPANe.global_variables import *
-from frangiPANe.module import frangiPANe
+#from frangiPANe.global_variables import *
+from .snakemake_scripts import generate_stats as gs
+from .module import FrangiPANe
 from pathlib import Path
 from .global_variables import GIT_URL, DOCS, DATATEST_URL_FILES, SINGULARITY_URL_FILES
 

frangiPANe/global_variables.py

@@ -3,13 +3,13 @@ from pathlib import Path
 DOCS = "https://frangiPANe.readthedocs.io/en/latest/"
 GIT_URL = "https://github.com/tranchant/frangiPANe"
 
-#SINGULARITY_URL_FILES = [('https://itrop.ird.fr/culebront_utilities/singularity_build/Singularity.culebront_tools.sif',
-#                          f'INSTALL_PATH/containers/Singularity.culebront_tools.sif'),
+SINGULARITY_URL_FILES = [('https://itrop.ird.fr/culebront_utilities/singularity_build/Singularity.culebront_tools.sif',
+                          f'INSTALL_PATH/containers/Singularity.culebront_tools.sif'),
 #                         ('https://itrop.ird.fr/culebront_utilities/singularity_build/Singularity.report.sif',
 #                          f'INSTALL_PATH/containers/Singularity.report.sif')
-#                         ]
+                         ]
 
-#DATATEST_URL_FILES = ("https://itrop.ird.fr/culebront_utilities/Data-Xoo-sub.zip", "Data-Xoo-sub.zip")
+DATATEST_URL_FILES = ("https://itrop.ird.fr/culebront_utilities/Data-Xoo-sub.zip", "Data-Xoo-sub.zip")
 
 
 #AVAIL_ASSEMBLY = ("CANU", "FLYE", "MINIASM", "RAVEN", "SMARTDENOVO", "SHASTA")

frangiPANe/install_files/config.yaml

+PROJECT:
+  Name: "ricenewwww"
+  outDir: "../../frangiPANe_snake/"
+  sampleDir: "/home/christine/Documents/Dev-test/data_test/fastq" 
+  groupFile: "../../../Dev-test/data_test/rice_group.txt"
+  #"/home/christine/Documents/Dev-test/data_test/rice_group.txt"
+  refFile: "/home/christine/Documents/Dev-test/data_test/reference/ref.fasta"
+  univecFile: "/home/christine/Documents/Dev-test/data_test/bank/UniVec_Core"
+
+RESOURCES:
+  cpuNumber: 6
+
+CONTIGS:
+  minLength: 300
+  anchoring_depth: 15
+
+PARAMS:
+  bwa_index: "-a is"
+  bwa_mem: "-M"
+  samtools_view: "-F 0x2"
+  abyss: "k=64"
+  assembly_stats: "-t"
+  assembly_stats2: "-s"
+  cd_hit: "-c 0.8 -s 0.95"
+
+
+#length minimum
\ No newline at end of file

frangiPANe/module.py

+# -*- coding: utf-8 -*-
+from pathlib import Path
+
+#from snakemake.logging import logger
+from snakemake.utils import validate
+#import re
+from .global_variables import *
+from snakecdysis import *
+
+
+class FrangiPANe(SnakEcdysis):
+    """
+    to read file config
+    """
+
+    def __init__(self, dico_tool, workflow, config):
+        super().__init__(**dico_tool, workflow=workflow, config=config)
+        # workflow is available only in __init__
+        # print("\n".join(list(workflow.__dict__.keys())))
+        # print(workflow.__dict__)
+
+        # Initialisation of PKGNAME attributes
+        self._check_dir_or_string('PROJECT','outDir', check_string=True)
\ No newline at end of file

frangiPANe/snakefiles/Snakefile

-from scripts import generate_stats as gs
-
+#from ..snakemake_scripts import generate_stats as gs
+from pprint import pp
 import glob
+from frangiPANe import FrangiPANe
+import frangiPANe
+
+frangiPane_obj = FrangiPANe(frangiPANe.dico_tool, workflow=workflow, config=config)
+tools_config = frangiPane_obj.tools_config
+cluster_config = frangiPane_obj.cluster_config
+
+#print(frangiPane_obj.export_use_yaml)
+#print for debug:
+pp(frangiPane_obj)
+exit()
+# print(tools_config)
+# exit()
 
 ##### setup report #####
-configfile: "../config/path.yaml"
+configfile: "../schemas/path.yaml"
 
 report: "report/workflow.rst"
 
@@ -35,9 +48,6 @@ include: "rules/fasta_stats2.smk"
 #print(workflow.global_resources)
 #print(";;;;;;;;;;;;;;;;;;; ", workflow._printshellcmds)
 #print(";;;;;;;;;;;;;;;;;;; ", workflow.overwrite_shellcmd)
-#print(config)
-#print(path_dico)
-# #include: "rules/report.smk"
 
 #print(SAMPLES)
 

frangiPANe/snakefiles/common.smk

@@ -32,7 +32,7 @@ with open('../config/path.yaml') as file:
 def check_config():
 
     frangiPANe.path_test(config['PROJECT']['outDir'] ,0)
-    config['PROJECT']['outDir'] = Path(config['PROJECT']['outDir']).absolute().resolve(strict=True)
+    config['PROJECT']['outDir'] = Path(config['PROJECT']['outDir']).absolute().resolve(strict=True) # TODEO seb 24 11 essayer avec resolve () seul (ou absolute)
 
     frangiPANe.path_test(config['PROJECT']['sampleDir'],0)
     config['PROJECT']['sampleDir'] = Path(config['PROJECT']['sampleDir']).absolute().resolve(strict=True)

pyproject.toml

@@ -29,7 +29,7 @@ maintainers = [
 dependencies = ["panel",
                 "biopython",
                 "pysam",
-                "snakemake.utils",
+                #"snakemake.utils",
                 "pandas",       #TODO: SEB 17/11 => actualiser avec packages python / rules etc.
                 "matplotlib",
                 "seaborn",