diff --git a/gga_get_data.py b/gga_get_data.py
index 5724b9b42c5a9073011831929c4dbdab4e08ac5f..f936657600ce098e1a9359ff524390e3467ffc70 100644
--- a/gga_get_data.py
+++ b/gga_get_data.py
@@ -53,71 +53,6 @@ class GetData(speciesData.SpeciesData):
return 1
- # def batch_modify_fasta_headers(self):
- # """
- # Change the fasta headers before integration, so that the indexing tool in galaxy interprets the headers
- # correctly and doesn't throw an error
-
- # 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:
- # """
-
- # proteins_file = None
- # proteins_outfile = None
- # annotation_dir = None
- # organism_annotation_dir = os.path.abspath("./src_data/annotation/{0}/OGS{1}".format(self.species_folder_name, self.ogs_version))
-
- # self.goto_species_dir()
-
- # for d in [i[0] for i in os.walk(os.getcwd() + "/src_data")]:
- # if "annotation" in d and self.species_folder_name in d and self.ogs_version in d:
- # for f in os.listdir(d):
- # if "proteins" in f:
- # proteins_file = os.path.join(d, f)
- # proteins_outfile = os.path.join(d, "outfile_proteins.fa")
- # annotation_dir = os.path.abspath(d)
- # # Formatting the headers
- # if proteins_file is not None:
- # self.format_fasta_headers(infile=proteins_file,
- # outfile=proteins_outfile,
- # pattern="^>mRNA",
- # repl=">protein")
- # if os.path.exists(annotation_dir + "/outfile_proteins.fa"):
- # subprocess.call(["mv", annotation_dir + "/outfile_proteins.fa", proteins_file],
- # stdout=subprocess.PIPE,
- # stderr=subprocess.PIPE,
- # cwd=annotation_dir)
- # subprocess.call(["rm", annotation_dir + "/outfile_proteins.fa"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=annotation_dir)
-
- # else:
- # logging.warning("Skipping proteins fasta headers formatting (FileNotFound)")
-
- # @staticmethod
- # def format_fasta_headers(infile, outfile, pattern, repl):
- # """
- # Format the fasta headers of a given file, given a matching pattern and a replacement string
-
- # :param infile:
- # :param outfile:
- # :param pattern:
- # :param repl:
- # :return:
- # """
-
- # infile = open(infile, 'r')
- # outfile = open(outfile, 'w')
-
- # lines = infile.readlines()
-
- # for line in lines:
- # line_out = re.sub(pattern, repl, line)
- # outfile.write(line_out)
-
- # infile.close()
- # outfile.close()
-
def get_source_data_files_from_path(self):
"""
Find source data files in the parent_directory
@@ -154,16 +89,6 @@ class GetData(speciesData.SpeciesData):
search_excluded_datasets = ["interpro_path", "orthofinder_path", "blastp_path", "blastx_path"]
# These datasets will not be searched if missing in the input file
- # Automatically find the "main" genome and annotation datasets (genome, transcripts, proteome, gff)
- # Triggers when a dataset path is empty
- # Exits after a single iteration to not replicate the search
- # This is VERY specific to phaeoexplorer, as the search depends on how the folders and datasets are named
- for k, v in datasets_to_get.items():
- if k not in search_excluded_datasets and v == "":
- print("Dataset not specified (%s), searching datasets" % k)
- self.find_dataset_from_source_data_parent_dir()
- break
-
# Copy dataset in the organism src_data dir tree correct folder
for k, v in datasets_to_get.items():
if k in genome_datasets:
@@ -177,50 +102,6 @@ class GetData(speciesData.SpeciesData):
os.chdir(self.main_dir)
- def find_dataset_from_source_data_parent_dir(self):
- """
- "Fail case" func if a dataset isn't specified in the input file. This func will search the specified "parent directory" for files matching
- the current species
-
- Highly specific to the phaeoexplorer project!
- Doesn't work for interpro, orthofinder and blast datasets at the moment, those absolutely need to be written in the input file
-
- :return
- """
-
- organism_annotation_dir = os.path.abspath("./src_data/annotation/{0}/OGS{1}".format(self.species_folder_name, self.genome_version))
- organism_genome_dir = os.path.abspath("./src_data/genome/{0}/v{1}".format(self.species_folder_name, self.genome_version))
-
- for dirpath, dirnames, files in os.walk(self.source_data_dir):
- if self.genus_upper and self.species in str(dirpath):
- for f in files:
- if "Contaminants" not in str(f):
- try:
- if fnmatch.fnmatch(f, "*" + self.species[1:] + "_" + self.sex.upper() + ".fa"):
- logging.info("Genome assembly file found - " + str(f))
- self.genome_path = os.path.abspath(f)
- elif fnmatch.fnmatch(f, "*" + self.species[1:] + "_" + self.sex.upper() + ".gff"):
- logging.info("GFF file - " + str(f))
- self.gff_path = os.path.abspath(f)
- elif fnmatch.fnmatch(f, "*" + self.species[1:] + "_" + self.sex.upper() + "_transcripts-gff.fa"):
- logging.info("Transcripts file - " + str(f))
- self.transcripts_path = os.path.abspath(f)
- elif fnmatch.fnmatch(f, "*" + self.species[1:] + "_" + self.sex.upper() + "_proteins.fa"):
- logging.info("Proteins file - " + str(f))
- self.proteins_path = os.path.abspath(f)
- except Exception as exc:
- logging.debug("Error raised %s" % exc)
-
- def generate_blast_banks(self):
- """
- TODO
- Do we need to generate blast banks?
-
- :return:
- """
-
- return 0
-
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Automatic data loading in containers and interaction "
diff --git a/speciesData.py b/speciesData.py
index db78196a11efa6080f192ade6c0ca42611841189..a099078fa620fa73232c101f14ebbd43da9fd298 100644
--- a/speciesData.py
+++ b/speciesData.py
@@ -49,7 +49,6 @@ class SpeciesData:
self.genus_lowercase = self.genus[0].lower() + self.genus[1:]
self.genus_uppercase = self.genus[0].upper() + self.genus[1:]
self.chado_species_name = "{0} {1}".format(self.species, self.sex)
- self.species_folder_name = "_".join([self.genus_lowercase, self.species, self.strain, self.sex])
self.full_name = ' '.join(utilities.filter_empty_not_empty_items([self.genus_uppercase, self.species, self.strain, self.sex])["not_empty"])
self.full_name_lowercase = self.full_name.lower()
self.abbreviation = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase[0], self.species, self.strain, self.sex])["not_empty"])
@@ -79,6 +78,6 @@ class SpeciesData:
self.source_data_dir = "/shared/projects/phaeoexplorer/" # Testing path for phaeoexplorer data - TODO: REMOVE IN PRODUCTION
else:
self.source_data_dir = parameters_dictionary["data"]["parent_directory"]
- self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase, self.species, self.strain, self.sex])["not_empty"])
+ self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase.lower(), self.species.lower(), self.sex.lower()])["not_empty"])
self.existing_folders_cache = {}
self.bam_metadata_cache = {}