formating

metagenome-atlas · Aug 3, 2022 · 1eee69c · 1eee69c
1 parent 144a13c
commit 1eee69c
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Showing 6 changed files with 30 additions and 28 deletions.
diff --git a/atlas/workflow/rules/genecatalog.smk b/atlas/workflow/rules/genecatalog.smk
@@ -156,6 +156,7 @@ if (config["genecatalog"]["clustermethod"] == "linclust") or (
 # cluster genes with cd-hit-est
 
 
+
 elif config["genecatalog"]["clustermethod"] == "cd-hit-est":
 
     include: "cdhit.smk"
@@ -280,7 +281,6 @@ rule combine_gene_coverages:
         "../scripts/combine_gene_coverages.py"
 
 
-
 ###########
 ## EGG NOG
 ##########
@@ -437,7 +437,7 @@ checkpoint gene_subsets:
     params:
         subset_size=config["genecatalog"]["SubsetSize"],
     conda:
-        "../envs/sequence_utils.yaml",
+        "../envs/sequence_utils.yaml"
     log:
         "logs/Genecatalog/clustering/split_genecatalog.log",
     script:
@@ -490,8 +490,7 @@ rule gene2genome:
     log:
         "logs/genomes/annotations/gene2genome.log",
     script:
-        "../scripts/gene2genome.py",
-
+        "../scripts/gene2genome.py"
 
 
 # after combination need to add eggNOG headerself.

diff --git a/atlas/workflow/rules/qc.smk b/atlas/workflow/rules/qc.smk
@@ -158,20 +158,20 @@ rule get_read_stats:
             tmp_file = os.path.join(subfolder, "read_stats.tmp")
             shell(
                 """
-                                mkdir -p {subfolder} 2> {log}
-
-                                reformat.sh {params_in} \
-                                bhist={subfolder}/base_hist.txt \
-                                qhist={subfolder}/quality_by_pos.txt \
-                                lhist={subfolder}/readlength.txt \
-                                gchist={subfolder}/gc_hist.txt \
-                                gcbins=auto \
-                                bqhist={subfolder}/boxplot_quality.txt \
-                                threads={threads} \
-                                overwrite=true \
-                                -Xmx{mem}G \
-                                2> >(tee -a {log} {tmp_file} )
-                                """.format(
+                                        mkdir -p {subfolder} 2> {log}
+
+                                        reformat.sh {params_in} \
+                                        bhist={subfolder}/base_hist.txt \
+                                        qhist={subfolder}/quality_by_pos.txt \
+                                        lhist={subfolder}/readlength.txt \
+                                        gchist={subfolder}/gc_hist.txt \
+                                        gcbins=auto \
+                                        bqhist={subfolder}/boxplot_quality.txt \
+                                        threads={threads} \
+                                        overwrite=true \
+                                        -Xmx{mem}G \
+                                        2> >(tee -a {log} {tmp_file} )
+                                        """.format(
                     subfolder=subfolder,
                     params_in=params_in,
                     log=log,

diff --git a/atlas/workflow/scripts/combine_gene_coverages.py b/atlas/workflow/scripts/combine_gene_coverages.py
@@ -63,9 +63,7 @@ def handle_exception(exc_type, exc_value, exc_traceback):
 
     # add gene length to dataframe of counts
     if cov_file == snakemake.input.covstats[0]:
-        combined_N_reads["Length"] = pd.to_numeric(
-            data.Length, downcast="unsigned"
-        )
+        combined_N_reads["Length"] = pd.to_numeric(data.Length, downcast="unsigned")
 
     combined_cov[sample] = pd.to_numeric(data.Avg_fold, downcast="float")
     combined_N_reads[sample] = pd.to_numeric(data.Reads, downcast="unsigned")
@@ -86,4 +84,4 @@ def handle_exception(exc_type, exc_value, exc_traceback):
 gc.collect()
 
 combined_cov.reset_index().to_parquet(snakemake.output[0])
-del combined_cov
+del combined_cov
diff --git a/atlas/workflow/scripts/gene2genome.py b/atlas/workflow/scripts/gene2genome.py
@@ -46,9 +46,7 @@ def handle_exception(exc_type, exc_value, exc_traceback):
         snakemake.input.old2newID, index_col=0, squeeze=True, sep="\t"
     )
 
-    contigs2genome = (
-        contigs2bins.join(old2newID, on="Bin").dropna().drop("Bin", axis=1)
-    )
+    contigs2genome = contigs2bins.join(old2newID, on="Bin").dropna().drop("Bin", axis=1)
 else:
     contigs2genome = pd.read_csv(
         snakemake.input.contigs2mags, index_col=0, squeeze=False, sep="\t", header=None
@@ -76,4 +74,4 @@ def handle_exception(exc_type, exc_value, exc_traceback):
 ).unstack(fill_value=0)
 
 # save as parquet
-gene2genome.reset_index().to_parquet(snakemake.output[0])
+gene2genome.reset_index().to_parquet(snakemake.output[0])
diff --git a/atlas/workflow/scripts/rename_genecatalog.py b/atlas/workflow/scripts/rename_genecatalog.py
@@ -44,7 +44,9 @@ def handle_exception(exc_type, exc_value, exc_traceback):
 # from gene Nr to gene name
 rep2gene = geneNr_to_string(map_genenr)
 
-logging.info(f"Collect and rename representative genes according to:\n {rep2gene.head()}")
+logging.info(
+    f"Collect and rename representative genes according to:\n {rep2gene.head()}"
+)
 
 assert rep2gene.shape[0] > 0
 

diff --git a/atlas/workflow/scripts/split_genecatalog.py b/atlas/workflow/scripts/split_genecatalog.py
@@ -35,4 +35,9 @@ def handle_exception(exc_type, exc_value, exc_traceback):
 
 from utils import fasta
 
-fasta.split(snakemake.input[0], snakemake.params.subset_size, snakemake.output[0], simplify_headers=True)
+fasta.split(
+    snakemake.input[0],
+    snakemake.params.subset_size,
+    snakemake.output[0],
+    simplify_headers=True,
+)