diff --git a/gga_load_data.py b/gga_load_data.py index c267b636a51cf96c6d59db3b2e98883ae84736b7..de7834fa6aa2d922bc28561c10b4d17cf92b4307 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: """