format

bin/pharokka.py

@@ -11,42 +11,21 @@
 from custom_db import run_custom_pyhmmer
 from databases import check_db_installation
 from hmm import run_pyhmmer
-from input_commands import (
-    check_dependencies,
-    get_input,
-    instantiate_dirs,
-    instantiate_split_output,
-    validate_and_extract_genbank,
-    validate_custom_hmm,
-    validate_fasta,
-    validate_gene_predictor,
-    validate_meta,
-    validate_terminase,
-    validate_threads,
-)
+from input_commands import (check_dependencies, get_input, instantiate_dirs,
+                            instantiate_split_output,
+                            validate_and_extract_genbank, validate_custom_hmm,
+                            validate_fasta, validate_gene_predictor,
+                            validate_meta, validate_terminase,
+                            validate_threads)
 from loguru import logger
 from post_processing import Pharok, remove_post_processing_files
-from processes import (
-    concat_phanotate_meta,
-    concat_trnascan_meta,
-    convert_gff_to_gbk,
-    reorient_terminase,
-    run_aragorn,
-    run_dnaapler,
-    run_mash_dist,
-    run_mash_sketch,
-    run_minced,
-    run_mmseqs,
-    run_phanotate,
-    run_phanotate_fasta_meta,
-    run_phanotate_txt_meta,
-    run_pyrodigal,
-    run_pyrodigal_gv,
-    run_trna_scan,
-    run_trnascan_meta,
-    split_input_fasta,
-    translate_fastas,
-)
+from processes import (concat_phanotate_meta, concat_trnascan_meta,
+                       convert_gff_to_gbk, reorient_terminase, run_aragorn,
+                       run_dnaapler, run_mash_dist, run_mash_sketch,
+                       run_minced, run_mmseqs, run_phanotate,
+                       run_phanotate_fasta_meta, run_phanotate_txt_meta,
+                       run_pyrodigal, run_pyrodigal_gv, run_trna_scan,
+                       run_trnascan_meta, split_input_fasta, translate_fastas)
 from util import count_contigs, get_version
 
 # add this to make sure of deprecation warning with biopython

bin/pharokka_multiplotter.py

@@ -1,15 +1,14 @@
 #!/usr/bin/env python3
 import argparse
 import os
+import shutil
 import sys
 from argparse import RawTextHelpFormatter
 from pathlib import Path
-import shutil
-from pycirclize.parser import Genbank
-
 
 from loguru import logger
 from plot import create_single_plot
+from pycirclize.parser import Genbank
 from util import get_version
 
 
@@ -29,7 +28,11 @@ def get_input():
         help="Input genbank file from Pharokka.",
     )
     parser.add_argument(
-        "-o", "--outdir", action="store", help="Pharokka output directory.",required=True
+        "-o",
+        "--outdir",
+        action="store",
+        help="Pharokka output directory.",
+        required=True,
     )
     parser.add_argument(
         "-f", "--force", help="Overwrites the output plot file.", action="store_true"
@@ -139,12 +142,9 @@ def get_input():
             f"--annotations {args.annotations} specified is not a float. Please check your input and try again."
         )
 
-
     if args.force == True:
         if os.path.exists(args.outdir) == True:
-            logger.info(
-                f"Removing {args.outdir} as --force was specified."
-            )
+            logger.info(f"Removing {args.outdir} as --force was specified.")
             shutil.rmtree(args.outdir)
         else:
             logger.warning(
@@ -161,7 +161,6 @@ def get_input():
     if Path(args.outdir).exists() is False:
         Path(args.outdir).mkdir(parents=True, exist_ok=True)
 
-
     # check label_ids
 
     # list of all IDs that need to be labelled from file
@@ -237,15 +236,11 @@ def get_input():
                 label_force_list = list(ignore_dict)
 
         except FileNotFoundError:
-            logger.warning(
-                f"{label_ids} contains no text. No contigs will be ignored"
-            )
-
+            logger.warning(f"{label_ids} contains no text. No contigs will be ignored")
 
     # if there is 1 contig, then all the parameters will apply
-
-    for contig_id, contig_sequence in gb_seq_dict.items():
 
+    for contig_id, contig_sequence in gb_seq_dict.items():
         logger.info(f"Plotting {contig_id}")
 
         create_single_plot(

bin/pharokka_proteins.py

@@ -6,20 +6,12 @@
 from pathlib import Path
 
 from databases import check_db_installation
-from input_commands import (
-    check_dependencies,
-    instantiate_dirs,
-    validate_fasta,
-    validate_threads,
-)
+from input_commands import (check_dependencies, instantiate_dirs,
+                            validate_fasta, validate_threads)
 from loguru import logger
 from post_processing import remove_directory, remove_file
-from proteins import (
-    Pharok_Prot,
-    get_input_proteins,
-    run_mmseqs_proteins,
-    run_pyhmmer_proteins,
-)
+from proteins import (Pharok_Prot, get_input_proteins, run_mmseqs_proteins,
+                      run_pyhmmer_proteins)
 from util import get_version
 
 

bin/plot.py

@@ -1,14 +1,15 @@
+from pathlib import Path
+from typing import Dict, List
+
 import numpy as np
+from Bio import SeqUtils
+from Bio.Seq import Seq
+from Bio.SeqFeature import SeqFeature
 from loguru import logger
 from matplotlib.lines import Line2D
 from matplotlib.patches import Patch
 from pycirclize import Circos
 from pycirclize.parser import Genbank, Gff
-from Bio.Seq import Seq
-from Bio.SeqFeature import SeqFeature
-from Bio import SeqUtils
-from typing import List, Dict
-from pathlib import Path
 
 # Load GFF file
 
@@ -596,6 +597,7 @@ def create_plot(
 
 ### for multiplotter
 
+
 def create_single_plot(
     contig_id: str,
     contig_sequence: Seq,
@@ -1099,7 +1101,10 @@ def create_single_plot(
         Patch(color=data_dict["head"]["col"], label="Head & packaging"),
         Patch(color=data_dict["con"]["col"], label="Connector"),
         Patch(color=data_dict["tail"]["col"], label="Tail"),
-        Patch(color=data_dict["acr_defense_vfdb_card"]["col"], label="Virulence Factor/AMR"),
+        Patch(
+            color=data_dict["acr_defense_vfdb_card"]["col"],
+            label="Virulence Factor/AMR",
+        ),
     ]
 
     fig = circos.plotfig()

bin/proteins.py

@@ -16,14 +16,12 @@
 from Bio import SeqIO
 from external_tools import ExternalTool
 from loguru import logger
-from post_processing import (
-    process_card_results,
-    process_pyhmmer_results,
-    process_vfdb_results,
-)
+from post_processing import (process_card_results, process_pyhmmer_results,
+                             process_vfdb_results)
 from pyhmmer.easel import SequenceFile
 from pyhmmer.plan7 import HMM, HMMFile
-from util import count_contigs, get_contig_headers, get_version, remove_directory
+from util import (count_contigs, get_contig_headers, get_version,
+                  remove_directory)
 
 Result = collections.namedtuple("Result", ["protein", "phrog", "bitscore", "evalue"])
 

tests/test_external_commands.py

@@ -14,15 +14,8 @@
 import pytest
 from loguru import logger
 
-from bin.processes import (
-    run_aragorn,
-    run_mash_sketch,
-    run_minced,
-    run_phanotate,
-    run_pyrodigal,
-    run_pyrodigal_gv,
-)
-
+from bin.processes import (run_aragorn, run_mash_sketch, run_minced,
+                           run_phanotate, run_pyrodigal, run_pyrodigal_gv)
 # import functions
 from bin.util import remove_directory
 

tests/test_input_commands.py

@@ -6,7 +6,6 @@
 """
 
 import sys
-
 # import
 import unittest
 from pathlib import Path
@@ -15,16 +14,10 @@
 import pytest
 from loguru import logger
 
-from bin.input_commands import (
-    instantiate_dirs,
-    validate_fasta,
-    validate_gene_predictor,
-    validate_meta,
-    validate_strand,
-    validate_terminase,
-    validate_terminase_start,
-    validate_threads,
-)
+from bin.input_commands import (instantiate_dirs, validate_fasta,
+                                validate_gene_predictor, validate_meta,
+                                validate_strand, validate_terminase,
+                                validate_terminase_start, validate_threads)
 from bin.util import remove_directory
 
 # test data

tests/test_overall.py

@@ -7,7 +7,6 @@
 # import
 import os
 import shutil
-
 # import functions
 import subprocess
 import sys

tests/test_proteins.py

@@ -8,7 +8,6 @@
 # import
 import os
 import shutil
-
 # import functions
 import subprocess
 import sys