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alphabetized checksum processing for bigwigs, changed delimiter count… #38

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alphabetized checksum processing for bigwigs, changed delimiter count… #38

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15 changes: 12 additions & 3 deletions scripts/process_collections.py
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Original file line number Diff line number Diff line change
Expand Up @@ -201,8 +201,13 @@ def process_collections(self, cmds_only, mode):
bw_name = self.files[collection_type][dsfile].get(
"name", None
)
bw_id = bw_name.split(".")[-2:]
project_id = ".".join(bw_name.split(".")[1:-2])
#bw_id = bw_name.split(".")[-2:]
#project_id = ".".join(bw_name.split(".")[1:-2])

# count from left side instead
bw_id = bw_name.split(".")[7:]
project_id = ".".join(bw_name.split(".")[1:7])

cmd = f"jbrowse add-track {url} --name {bw_id[0]} --assemblyNames {parent[0]} --category expression,{project_id} --out {os.path.abspath(self.out_dir)} --force"

elif mode == "blast": # for blast
Expand Down Expand Up @@ -595,7 +600,11 @@ def add_collections(self, collection_type, genus, species):
logger.debug(checksum_response)
# print('\nchecksum_response: ', checksum_response,'\n')
if checksum_response: # checksum SUCCESS 200
for line in checksum_response.split("\n"):
sorted_lines = sorted(
(line for line in checksum_response.split("\n") if line.strip()),
key=lambda line: line.split()[1]
)
for line in sorted_lines:
logger.debug(line)
fields = line.split()
if fields: # process if fields exists
Expand Down
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