From 446c1e813692b935907e2379ab8a40459829c6d6 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Wed, 4 Nov 2020 12:59:52 +0100
Subject: [PATCH] Merge into a local branch
---
gga_load_data.py | 13 ++++++-------
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/gga_load_data.py b/gga_load_data.py
index c267b63..de7834f 100644
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -58,10 +58,10 @@ class LoadData(speciesData.SpeciesData):
def modify_fasta_headers(self):
"""
Change the fasta headers before integration, so that the indexing tool in galaxy interprets the headers
- correctly and not throw an error
+ correctly and doesn't throw an error
- The function will use the attribute "source_datasets", pointing to files in the galaxy
- library to find the fasta files that need changing in their headers
+ The function will use the class attribute "source_datasets", pointing to files in the galaxy
+ library to find the fasta files that need their headers formatted
:return:
"""
@@ -94,7 +94,8 @@ class LoadData(speciesData.SpeciesData):
# Transcriptome
logging.debug("Formatting fasta headers for " + self.source_files["transcripts_file"])
-
+ self.format_fasta_headers(infile=self.source_files["transcripts_file"],
+ outfile=str(self.source_files["transcripts_file"]))
# Rename outputs and cleaning script logs
if os.path.exists(annotation_dir + "outfile"):
@@ -193,9 +194,7 @@ class LoadData(speciesData.SpeciesData):
def set_get_history(self):
"""
- Create an history for the current organism
- Get the history and its ID for the current organism
- TODO: Set the current history to the current organism history
+ Create or set the working history to the organism's one
:return:
"""
--
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