def taxonomic_classification_setup(_id, feature_table, rep_seqs): denoise_dir = get_denoise_dir(_id) feature_table_destination = os.path.join(denoise_dir, "merged_table.qza") rep_seqs_destination = os.path.join(denoise_dir, "merged_rep_seqs.qza") responseIfError(make_dir, dirpath=denoise_dir) responseIfError(copy_file, source=feature_table, destination=feature_table_destination) responseIfError(copy_file, source=rep_seqs, destination=rep_seqs_destination)
def denoise_feature_table():
uid = request.form["uid"]
DENOISE_DIR = get_denoise_dir(uid)
if(uid == ''):
# return sample output if uid not specified
feature_table = os.path.join('/data/output/dada2/merged', 'merged_table.qza')
else:
feature_table = os.path.join(DENOISE_DIR, 'merged_table.qza')
return send_file(feature_table, mimetype='application/octet-stream', as_attachment=True)
def denoise_summary_qzv():
uid = request.form["uid"]
DENOISE_DIR = get_denoise_dir(uid)
if(uid == ''):
# return sample output if uid not specified
stats_qzv = os.path.join('/data/output/dada2/merged', 'merged_stats_dada2.qzv')
else:
stats_qzv = os.path.join(DENOISE_DIR, 'merged_stats_dada2.qzv')
return send_file(stats_qzv, mimetype='application/octet-stream', as_attachment=True)
def dada2_summary():
uid = request.form["uid"]
DENOISE_DIR = get_denoise_dir(uid)
if(uid == ''):
# return sample output if uid not specified
dada2_summary = os.path.join('/data/output/dada2/merged', 'merged_stats_dada2.json')
else:
dada2_summary = os.path.join(DENOISE_DIR, 'merged_stats_dada2.json')
return send_file(dada2_summary, mimetype='application/json', as_attachment=True)
def analysis_setup(_id, feature_table, rep_seqs, taxonomy):
denoise_dir = get_denoise_dir(_id)
feature_table_destination = os.path.join(denoise_dir, "merged_table.qza")
rep_seqs_destination = os.path.join(denoise_dir, "merged_rep_seqs.qza")
taxonomy_dir = get_taxonomic_classification_dir(_id)
taxonomy_destination = os.path.join(taxonomy_dir, "taxonomy.qza")
# pre-make input dir and copy files
# pipeline requires input files to be present in specific dirs
responseIfError(make_dir, dirpath=denoise_dir)
responseIfError(copy_file,
source=feature_table,
destination=feature_table_destination)
responseIfError(copy_file,
source=rep_seqs,
destination=rep_seqs_destination)
responseIfError(make_dir, dirpath=taxonomy_dir)
responseIfError(copy_file,
source=taxonomy,
destination=taxonomy_destination)