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Table2asn bug fixes #57

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merged 2 commits into from
May 20, 2024
Merged

Table2asn bug fixes #57

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0e90b30
Table2asn bug fixes
dthoward96 May 20, 2024
92a2b6a
Update submit.py
dthoward96 May 20, 2024
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4 changes: 2 additions & 2 deletions create.py
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Original file line number Diff line number Diff line change
Expand Up @@ -394,7 +394,7 @@ def create_genbank_files(organism, config_dict, metadata, submission_name, submi
create_authorset(config_dict=config_dict, metadata=metadata, submission_name=submission_name, submission_files_dir=submission_files_dir)
create_fasta(organism=organism, database="GENBANK", metadata=metadata, submission_files_dir=submission_files_dir)
# Retrieve the source df"
source_df = metadata.filter(regex="^gb-seq_id$|^src-|^ncbi-spuid$|^ncbi-bioproject$|^organism$|^collection_date$").copy()
source_df = metadata.filter(regex="^gb-seq_id$|^src-|^ncbi-bioproject$|^organism$|^collection_date$").copy()
source_df.columns = source_df.columns.str.replace("src-","").str.strip()
source_df = source_df.rename(columns = {"gb-seq_id":"Sequence_ID", "collection_date":"Collection_date"})
# Add BioProject if available
Expand Down Expand Up @@ -437,7 +437,7 @@ def create_genbank_table2asn(submission_name, submission_files_dir, gff_file=Non
print("Downloading Table2asn.", file=sys.stdout)
setup.download_table2asn(table2asn_dir=table2asn_dir)
# Command to generate table2asn submission file
command = [table2asn_dir, "-t", os.path.join(submission_files_dir, "authorset.sbt"), "-i", os.path.join(submission_files_dir, "sequence.fsa"), "-src-file", os.path.join(submission_files_dir, "source.src"), "-o", os.path.join(submission_files_dir, submission_name + ".sqn")]
command = [table2asn_dir, "-a", "s", "-t", os.path.join(submission_files_dir, "authorset.sbt"), "-i", os.path.join(submission_files_dir, "sequence.fsa"), "-src-file", os.path.join(submission_files_dir, "source.src"), "-o", os.path.join(submission_files_dir, submission_name + ".sqn")]
if os.path.isfile(os.path.join(submission_files_dir, "comment.cmt")):
command.append("-w")
command.append( os.path.join(submission_files_dir, "comment.cmt"))
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2 changes: 1 addition & 1 deletion submit.py
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Expand Up @@ -210,7 +210,7 @@ def sendmail(database, submission_name, submission_dir, config_dict, test):
msg['To'] = ", ".join(to_email)
if len(cc_email) != 0:
msg['Cc'] = ", ".join(cc_email)
with open(os.path.join(submission_dir, submission_name + ".sqn"), 'rb') as file_input:
with open(os.path.join(submission_files_dir, submission_name + ".sqn"), 'rb') as file_input:
part = MIMEApplication(file_input.read(), Name=submission_name + ".sqn")
part['Content-Disposition'] = "attachment; filename=" + submission_name + ".sqn"
msg.attach(part)
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