diann_convert

python/quantmsio/quantms_io/commands/diann_convert_command.py

@@ -0,0 +1,93 @@
+from quantms_io.core.diann_convert import DiaNNConvert
+import click
+from quantms_io.core.project import create_uuid_filename
+from typing import List
+import os
+CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
+@click.group(context_settings=CONTEXT_SETTINGS)
+def cli():
+    """
+    This is the main tool that gives access to all commands.
+    """
+
+@click.command(
+    "diann_convert_to_parquet", short_help="Convert diann_report to parquet and psm file"
+)
+@click.option(
+    "--report_path",
+    help="the diann report file path",
+    required=True,
+)
+@click.option(
+    "--design_file",
+    help="the disign file path",
+    required=True,
+)
+@click.option(
+    "--fasta_path",
+    help="Reference fasta database file",
+    required=True,
+)
+@click.option(
+    "--modifications",
+    help="a list contains fix modifications and variable modifications",
+    required=True,
+)
+@click.option(
+    "--pg_path",
+    help="pg_matrix file",
+    required=True,
+)
+@click.option(
+    "--pr_path",
+    help="pr_matrix file",
+    required=True,
+)
+@click.option(
+    "--qvalue_threshold",
+    help="qvalue_threshold",
+    required=True,
+    default= 0.05
+)
+@click.option(
+    "--mzml_info_folder",
+    help="mzml info tsv file",
+    required=True,
+)
+@click.option(
+    "--sdrf_path",
+    help="sdrf file path",
+    required=True,
+)
+@click.option(
+    "--output_folder",
+    help="Folder where the Json file will be generated",
+    required=True,
+)
+@click.option("--output_prefix_file", help="Prefix of the Json file needed to generate the file name", required=False)
+@click.option(
+    "--chunksize",
+    help="mzml info tsv file",
+    required=False,
+    default = 100000
+)
+@click.pass_context
+def diann_convert_to_parquet(report_path:str,design_file:str,fasta_path:str,modifications:List,pg_path:str,pr_path:str,qvalue_threshold: float,mzml_info_folder:str,sdrf_path:str,output_folder:str,output_prefix_file:str,chunksize:int):
+
+    if os.path.exists(output_folder):
+        os.makedirs(output_folder)
+
+    if not output_prefix_file:
+        output_prefix_file = ''
+
+    feature_output_path = output_folder + "/" + create_uuid_filename(output_prefix_file,'.feature.parquet')
+    psm_output_path = output_folder + "/" + create_uuid_filename(output_prefix_file,'.psm.parquet')
+
+    DiaNN = DiaNNConvert()
+
+    DiaNN.generate_feature_file(report_path,design_file,fasta_path,modifications,pg_path,pr_path,qvalue_threshold,mzml_info_folder,sdrf_path,feature_output_path,chunksize)
+    DiaNN.generate_psm_file(report_path,design_file,fasta_path,modifications,pg_path,qvalue_threshold,mzml_info_folder,psm_output_path,chunksize)
+
+cli.add_command(diann_convert_to_parquet)
+if __name__ == '__main__':
+    cli()