Commit b4a980d5 authored by MARIJON Pierre's avatar MARIJON Pierre

If we didn't have assembly_len skip the assembly

parent 25967ec9
...@@ -85,7 +85,11 @@ def finish(args): ...@@ -85,7 +85,11 @@ def finish(args):
logging.info("begin of get information for "+accession) logging.info("begin of get information for "+accession)
run_id, assembly_len = get_info_about_ERS(ERS_accession) run_id, assembly_len = get_info_about_ERS(ERS_accession)
logging.info("end of get information for "+accession) logging.info("end of get information for "+accession)
if not assembly_len:
logging.error("We didn't find any assembly len, we skip this !")
continue
data_path = args["data"] / accession data_path = args["data"] / accession
data_path.mkdir(parents=True, exist_ok=True) data_path.mkdir(parents=True, exist_ok=True)
...@@ -161,6 +165,10 @@ def select(args): ...@@ -161,6 +165,10 @@ def select(args):
run_id, assembly_len = get_info_about_ERS(ERS_accession) run_id, assembly_len = get_info_about_ERS(ERS_accession)
download_extract_merge(data_path, accession) download_extract_merge(data_path, accession)
logging.info("end of download data for "+accession) logging.info("end of download data for "+accession)
if not assembly_len:
logging.error("We didn't find any assembly len, we skip this !")
continue
# compute coverage # compute coverage
logging.info("begin of compute canu parametre for "+accession) logging.info("begin of compute canu parametre for "+accession)
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment