minor changes in code.

pypgatk/commands/blast_get_position.py

@@ -16,7 +16,7 @@
 @click.option('-n', '--number_of_processes', help='Used to specify the number of processes. Default is 40.')
 
 @click.pass_context
-def blast_get_position(ctx, config_file, input_psm_to_blast, output_psm, input_reference_database, number_of_processes):  
+def blast_get_position(ctx, config_file, input_psm_to_blast, output_psm, input_reference_database, number_of_processes):
     config_data = None
     if config_file is not None:
         config_data = read_yaml_from_file(config_file)

pypgatk/commands/mztab_class_fdr.py

@@ -19,7 +19,6 @@
                                               "groups e.g. \"{non_canonical:[altorf,pseudo,ncRNA];mutations:[COSMIC,cbiomut];variants:[var_mut,var_rs]}\"")
 @click.pass_context
 def mztab_class_fdr(ctx, config_file, input_mztab, outfile_name, decoy_prefix, global_fdr_cutoff, class_fdr_cutoff, peptide_groups_prefix):
-
     config_data = None
     if config_file is not None:
         config_data = read_yaml_from_file(config_file)

pypgatk/commands/validate_peptides.py

@@ -8,26 +8,31 @@
 
 log = logging.getLogger(__name__)
 
-@click.command('validate_peptides', short_help='Command to inspect MS2 spectra of single-subsititution peptide identifications')
+
+@click.command('validate_peptides',
+               short_help='Command to inspect MS2 spectra of single-subsititution peptide identifications')
 @click.option('-c', '--config_file', help='Configuration file for the validate peptides pipeline')
 @click.option('-p', '--mzml_path', help='The mzml file path.You only need to use either mzml_path or mzml_files')
-@click.option('-f', '--mzml_files', help='The mzml files.Different files are separated by ",".You only need to use either mzml_path or mzml_files')
+@click.option('-f', '--mzml_files',
+              help='The mzml files.Different files are separated by ",".You only need to use either mzml_path or mzml_files')
 @click.option('-i', '--infile_name', help='Variant peptide PSMs table')
 @click.option('-o', '--outfile_name', help='Output file for the results')
 @click.option('-ion', '--ions_tolerance', help='MS2 fragment ions mass accuracy')
 @click.option('-n', '--number_of_processes', help='Used to specify the number of processes. Default is 40.')
-@click.option('-r', '--relative', help='When using ppm as ions_tolerance (not Da), it needs to be turned on', is_flag=True)
-@click.option('-msgf', '--msgf', help='If it is the standard format of MSGF output, please turn on this switch, otherwise it defaults to mzTab format', is_flag=True)
-
+@click.option('-r', '--relative', help='When using ppm as ions_tolerance (not Da), it needs to be turned on',
+              is_flag=True)
+@click.option('-msgf', '--msgf',
+              help='If it is the standard format of MSGF output, please turn on this switch, otherwise it defaults to mzTab format',
+              is_flag=True)
 @click.pass_context
-
-def validate_peptides(ctx, config_file, mzml_path, mzml_files, infile_name, outfile_name, ions_tolerance, number_of_processes, relative, msgf):
+def validate_peptides(ctx, config_file, mzml_path, mzml_files, infile_name, outfile_name, ions_tolerance,
+                      number_of_processes, relative, msgf):
     config_data = None
     if config_file is not None:
         config_data = read_yaml_from_file(config_file)
 
     validate_flag = bool(infile_name and (mzml_path or mzml_files) and outfile_name)
-    if not validate_flag :
+    if not validate_flag:
         print_help()
 
     pipeline_arguments = {}
@@ -44,9 +49,7 @@ def validate_peptides(ctx, config_file, mzml_path, mzml_files, infile_name, outf
         pipeline_arguments[ValidatePeptidesService.CONFIG_RELATIVE] = relative
     if msgf is not None:
         pipeline_arguments[ValidatePeptidesService.CONFIG_MSGF] = msgf
-    
+
     validate_peptides_service = ValidatePeptidesService(config_data, pipeline_arguments)
     if validate_flag:
         validate_peptides_service.validate(infile_name, outfile_name)
-
-