From cf811479f2fb00337652fb64c612a83c040c36ad Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Sun, 16 May 2021 14:51:33 +0200
Subject: [PATCH] fix datasets path in gga_get_data.py
---
gga_get_data.py | 20 ++++++++------------
utilities.py | 2 +-
2 files changed, 9 insertions(+), 13 deletions(-)
diff --git a/gga_get_data.py b/gga_get_data.py
index 9950a86..992e5c6 100755
--- a/gga_get_data.py
+++ b/gga_get_data.py
@@ -88,18 +88,14 @@ class GetData(speciesData.SpeciesData):
organism_annotation_dir = os.path.abspath("./src_data/annotation/{0}/OGS{1}".format(self.species_folder_name, self.ogs_version))
organism_genome_dir = os.path.abspath("./src_data/genome/{0}/v{1}".format(self.species_folder_name, self.genome_version))
- genome_datasets = [constants.ORG_PARAM_DATA_GENOME_PATH]
- annotation_datasets = [constants.ORG_PARAM_DATA_GFF_PATH,
- constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH,
- constants.ORG_PARAM_DATA_PROTEINS_PATH,
- constants.ORG_PARAM_DATA_INTERPRO_PATH,
- constants.ORG_PARAM_DATA_ORTHOFINDER_PATH,
- constants.ORG_PARAM_DATA_BLASTP_PATH,
- constants.ORG_PARAM_DATA_BLASTX_PATH]
- # Where to store blast results?
-
- # search_excluded_datasets = ["interpro_path", "orthofinder_path", "blastp_path", "blastx_path"]
- # These datasets will not be searched if missing in the input file
+ genome_datasets = {constants.ORG_PARAM_DATA_GENOME_PATH: self.genome_path}
+ annotation_datasets = {constants.ORG_PARAM_DATA_GFF_PATH: self.gff_path,
+ constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH: self.transcripts_path,
+ constants.ORG_PARAM_DATA_PROTEINS_PATH: self.proteins_path,
+ constants.ORG_PARAM_DATA_INTERPRO_PATH: self.interpro_path,
+ constants.ORG_PARAM_DATA_ORTHOFINDER_PATH: self.orthofinder_path,
+ constants.ORG_PARAM_DATA_BLASTP_PATH: self.blastp_path,
+ constants.ORG_PARAM_DATA_BLASTX_PATH: self.blastx_path}
# Copy datasets in the organism src_data dir tree correct folder
for k, v in genome_datasets.items():
diff --git a/utilities.py b/utilities.py
index 3e23ef4..3d734f2 100755
--- a/utilities.py
+++ b/utilities.py
@@ -37,7 +37,7 @@ def parse_config(config_file):
config_dict = load_yaml(config_file)
if isinstance(config_dict, dict):
- logging.debug("Config dictionary: {0}".format(config_dict))
+ #logging.debug("Config dictionary: {0}".format(config_dict))
return config_dict
else:
logging.critical("Config yaml file is not a dictionary" % config_file)
--
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