From 0e90b30e42f4cd52cf0e5df6283957b57098157b Mon Sep 17 00:00:00 2001 From: Dakota Howard <58985143+dthoward96@users.noreply.github.com> Date: Mon, 20 May 2024 14:35:03 -0400 Subject: [PATCH 1/2] Table2asn bug fixes Resolve issue with table2asn not allowing multiple sequences in the fasta file and for the table2asn sendmail function not properly grabbing the sqn file. --- create.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/create.py b/create.py index 1eea1ae..7e0f5e2 100644 --- a/create.py +++ b/create.py @@ -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 @@ -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")) From 92a2b6a27313beef14fecdb77c41e02e70906234 Mon Sep 17 00:00:00 2001 From: Dakota Howard <58985143+dthoward96@users.noreply.github.com> Date: Mon, 20 May 2024 14:37:17 -0400 Subject: [PATCH 2/2] Update submit.py --- submit.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/submit.py b/submit.py index 645c01e..2b39dad 100644 --- a/submit.py +++ b/submit.py @@ -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)