| Previous changeset 6:56a0938d534d (2025-04-18) Next changeset 8:87585c392228 (2025-04-18) |
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Commit message:
planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae |
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modified:
get_DB_data.xml get_db_info.py |
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added:
test-data/test_input.tsv |
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removed:
test-data/test_input.csv |
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| diff -r 56a0938d534d -r 8984fabea52c get_DB_data.xml --- a/get_DB_data.xml Fri Apr 18 12:52:49 2025 +0000 +++ b/get_DB_data.xml Fri Apr 18 13:04:32 2025 +0000 |
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| @@ -22,7 +22,7 @@ --output 'outdir' ]]></command> <inputs> - <param name="input" type="data" format="csv" label="Input CSV file" /> + <param name="input" type="data" format="tsv" label="Input TSV file" /> <param name="table" type="text" label="Database Table Name" optional="false" /> <param name="sequence_column" type="text" label="DB column contains sequence for ganbank file" optional="false" /> <param name="annotation_columns" type="text" label="DB column contains annotation for ganbank file" optional="false" /> @@ -35,9 +35,9 @@ </collection> </outputs> <tests> - <!--python get_db_info.py -input 'test-data/test_input.csv' -sequence_column 'sequence' -annotation_column 'annotation' -db_uri 'postgresql://postgres:RK17@localhost:5432/test_fragments_db' -table 'sample' -fragment_column 'fragment' -output 'test-data/output'--> + <!--python get_db_info.py -input 'test-data/test_input.tsv' -sequence_column 'sequence' -annotation_column 'annotation' -db_uri 'postgresql://postgres:RK17@localhost:5432/test_fragments_db' -table 'sample' -fragment_column 'fragment' -output 'test-data/output'--> <test> - <param name="input" value="test_input.csv" /> + <param name="input" value="test_input.tsv" /> <param name="table" value="sample" /> <param name="sequence_column" value="sequence" /> <param name="annotation_columns" value="annotation" /> @@ -72,7 +72,7 @@ Pick Data From DB =================== -generate GanDank files from csv file based on SQL DB. +generate GanDank files from tsv file based on SQL DB. ]]></help> <citations> <citation type="bibtex"> |
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| diff -r 56a0938d534d -r 8984fabea52c get_db_info.py --- a/get_db_info.py Fri Apr 18 12:52:49 2025 +0000 +++ b/get_db_info.py Fri Apr 18 13:04:32 2025 +0000 |
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| @@ -81,10 +81,10 @@ time.sleep(2) raise Exception("Database connection failed after timeout.") -def fetch_annotations(csv_file, sequence_column, annotation_columns, db_uri, table_name, fragment_column_name, output): +def fetch_annotations(tsv_file, sequence_column, annotation_columns, db_uri, table_name, fragment_column_name, output): """Fetch annotations from the database and save the result as GenBank files.""" db_uri = fix_db_uri(db_uri) - df = pd.read_csv(csv_file, sep=',') + df = pd.read_csv(tsv_file, sep='\t') engine = create_engine(db_uri) connection = engine.connect() @@ -216,7 +216,7 @@ def main(): parser = argparse.ArgumentParser(description="Fetch annotations from PostgreSQL database and save as JSON.") - parser.add_argument("--input", required=True, help="Input CSV file") + parser.add_argument("--input", required=True, help="Input TSV file") parser.add_argument("--sequence_column", required=True, help="DB column contains sequence for ganbank file") parser.add_argument("--annotation_columns", required=True, help="DB column contains head for ganbank file") parser.add_argument("--db_uri", required=True, help="Database URI connection string") |
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| diff -r 56a0938d534d -r 8984fabea52c test-data/test_input.csv --- a/test-data/test_input.csv Fri Apr 18 12:52:49 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -ID,Frag1,Frag2,Frag3 -Sample-1,ACP10001AaCbbBS,CFP10002AaCbbBS,XYZ10003AaCbbBS -Sample-2,CFP10002AaCbbBS,ACP10001AaCbbBS,QWE10004AaCbbBS -Sample-3,XYZ10003AaCbbBS,QWE10004AaCbbBS,ACP10001AaCbbBS -Sample-4,QWE10004AaCbbBS,XYZ10003AaCbbBS,CFP10002AaCbbBS |
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| diff -r 56a0938d534d -r 8984fabea52c test-data/test_input.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_input.tsv Fri Apr 18 13:04:32 2025 +0000 |
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| @@ -0,0 +1,5 @@ +ID Frag1 Frag2 Frag3 +Sample-1 ACP10001AaCbbBS CFP10002AaCbbBS XYZ10003AaCbbBS +Sample-2 CFP10002AaCbbBS ACP10001AaCbbBS QWE10004AaCbbBS +Sample-3 XYZ10003AaCbbBS QWE10004AaCbbBS ACP10001AaCbbBS +Sample-4 QWE10004AaCbbBS XYZ10003AaCbbBS CFP10002AaCbbBS |