From 0b9ecdc880eea6062c8771c7809542cba80211d5 Mon Sep 17 00:00:00 2001
From: iquasere <maildosequeira@gmail.com>
Date: Thu, 23 Nov 2023 11:43:13 +0000
Subject: [PATCH] Minor code formatting

---
 workflow/scripts/metaproteomics.py | 4 ++--
 workflow/scripts/quantification.py | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/workflow/scripts/metaproteomics.py b/workflow/scripts/metaproteomics.py
index e568336..f05c897 100644
--- a/workflow/scripts/metaproteomics.py
+++ b/workflow/scripts/metaproteomics.py
@@ -299,7 +299,7 @@ def select_proteins_for_second_search(self, original_db, output, results_files,
             output=f'{output}/2nd_search_database.fasta')
 
     def run(self):
-        """
+
         Path(snakemake.params.output).mkdir(parents=True, exist_ok=True)
         # 1st database construction
         self.database_generation(
@@ -313,7 +313,7 @@ def run(self):
             self.generate_parameters_file(f'{snakemake.params.output}/1st_params.par', protein_fdr=100)
         except:
             print('An illegal reflective access operation has occurred. But MOSCA can handle it.')
-        """
+
         # 2nd database construction
         proteins_for_second_search = []
         for i in range(len(snakemake.params.names)):
diff --git a/workflow/scripts/quantification.py b/workflow/scripts/quantification.py
index f83c65d..b356e7e 100644
--- a/workflow/scripts/quantification.py
+++ b/workflow/scripts/quantification.py
@@ -27,8 +27,8 @@ def run():
             else:
                 continue
             if ',' in pexps.loc[i]['Files']:
-                reads = [f"{snakemake.params.output}/Preprocess/Trimmomatic/quality_trimmed_{pexps.loc[i]['Name']}_{fr}_paired.fq"
-                         for fr in ['forward', 'reverse']]
+                reads = [(f"{snakemake.params.output}/Preprocess/Trimmomatic/quality_trimmed_{pexps.loc[i]['Name']}_"
+                          f"{fr}_paired.fq") for fr in ['forward', 'reverse']]
             else:
                 reads = [f"{snakemake.params.output}/Preprocess/Trimmomatic/quality_trimmed_{pexps.loc[i]['Name']}.fq"]
             perform_alignment(
@@ -38,8 +38,8 @@ def run():
                 f"{snakemake.params.output}/Quantification/{pexps.loc[i]['Name']}.readcounts", reference)
             # Read the results of alignment and add them to the readcounts result at sample level
             normalized_by_gene_size = pd.read_csv(
-                f"{snakemake.params.output}/Quantification/{pexps.loc[i]['Name']}.readcounts.norm", sep='\t',
-                names=['Gene' if pexps.loc[i]['Data type'] == 'mrna' else 'Contig', pexps.loc[i]['Name']])
+                f"{snakemake.params.output}/Quantification/{pexps.loc[i]['Name']}.readcounts.norm",
+                sep='\t', names=['Gene' if pexps.loc[i]['Data type'] == 'mrna' else 'Contig', pexps.loc[i]['Name']])
             if pexps.loc[i]['Data type'] == 'dna':
                 mg_result = pd.merge(mg_result, normalized_by_gene_size, how='outer', on='Contig')
             else: