add to scripts

bin/databases.py

@@ -26,7 +26,6 @@
 import requests
 from alive_progress import alive_bar
 from loguru import logger
-
 from post_processing import remove_directory
 
 # to hold information about the different DBs

bin/input_commands.py

@@ -2,12 +2,10 @@
 import os
 import shutil
 import subprocess as sp
-import sys
 from argparse import RawTextHelpFormatter
 
 from Bio import SeqIO
 from loguru import logger
-
 from util import get_version
 
 
@@ -17,10 +15,7 @@ def get_input():
         formatter_class=RawTextHelpFormatter,
     )
     parser.add_argument(
-        "-i", 
-        "--infile", 
-        action="store", 
-        help="Input genome file in fasta format."
+        "-i", "--infile", action="store", help="Input genome file in fasta format."
     )
     parser.add_argument(
         "-o",

bin/install_databases.py

@@ -3,9 +3,9 @@
 import os
 import sys
 from argparse import RawTextHelpFormatter
-from loguru import logger
 
 from databases import instantiate_install
+from loguru import logger
 
 
 def get_db_input():

bin/pharokka.py

@@ -6,42 +6,21 @@
 import time
 from pathlib import Path
 
-from loguru import logger
-
 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_fasta,
-    validate_gene_predictor,
-    validate_meta,
-    validate_terminase,
-    validate_threads,
-)
+from input_commands import (check_dependencies, get_input, instantiate_dirs,
+                            instantiate_split_output, 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_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_trna_scan, run_trnascan_meta,
+                       split_input_fasta, translate_fastas)
 from util import get_version
 
 

bin/pharokka_plotter.py

@@ -3,10 +3,10 @@
 import os
 import sys
 from argparse import RawTextHelpFormatter
-from loguru import logger
 from pathlib import Path
 
 from input_commands import validate_fasta
+from loguru import logger
 from plot import create_plot
 from util import get_version
 
@@ -247,12 +247,12 @@ def get_input():
     label_force_list = []
 
     if args.label_ids != "":
-        logger.info(f"You have specified a file {args.label_ids} containing a list of CDS IDs to force label.")
+        logger.info(
+            f"You have specified a file {args.label_ids} containing a list of CDS IDs to force label."
+        )
         # check if it is a file
         if os.path.isfile(args.label_ids) == False:
-            logger.error(
-                f"{args.label_ids} was not found."
-            )
+            logger.error(f"{args.label_ids} was not found.")
         # check if it contains text
         try:
             # Open the file in read mode
@@ -267,7 +267,9 @@ def get_input():
                 label_force_list = list(ignore_dict)
 
         except FileNotFoundError:
-            logger.warning(f"{args.label_id} contains no text. No contigs will be ignored")
+            logger.warning(
+                f"{args.label_id} contains no text. No contigs will be ignored"
+            )
 
     logger.info("All files checked.")
     logger.info("Plotting the phage.")
@@ -285,5 +287,5 @@ def get_input():
         args.label_size,
         args.label_hypotheticals,
         args.remove_other_features_labels,
-        label_force_list
+        label_force_list,
     )

bin/pharokka_proteins.py

@@ -5,23 +5,13 @@
 import time
 from pathlib import Path
 
-from loguru import logger
-
 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

@@ -1,9 +1,9 @@
 import numpy as np
+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 loguru import logger
 
 # Load GFF file
 
@@ -21,7 +21,7 @@ def create_plot(
     label_size,
     label_hypotheticals,
     remove_other_features_labels,
-    label_force_list
+    label_force_list,
 ):
     gff = Gff(gff_file)
 
@@ -136,7 +136,7 @@ def create_plot(
             r_lim=(75, 80),
             fc=data_dict[key]["col"],
         )
-    # rev
+        # rev
         cds_track.genomic_features(
             data_dict[key]["rev_list"],
             plotstyle="arrow",
@@ -293,31 +293,30 @@ def create_plot(
         id = f.qualifiers.get("ID", [""])[0]
 
         # skip hypotheticals if the flag is false (default)
-        if id in label_force_list: # if in the list
+        if id in label_force_list:  # if in the list
             if len(label) > truncate:
                 label = label[:truncate] + "..."
             pos_list.append(pos)
             labels.append(label)
             length_list.append(length)
             id_list.append(id)
-            continue # to break if in the list
+            continue  # to break if in the list
         else:
             if label_hypotheticals == False:
                 if (
-                label == ""
-                or label.startswith("hypothetical")
-                or label.startswith("unknown")
-                    ):
-                    continue # if hypothetical not in the list
-                else: # all others
-                    if len(label) > truncate: 
+                    label == ""
+                    or label.startswith("hypothetical")
+                    or label.startswith("unknown")
+                ):
+                    continue  # if hypothetical not in the list
+                else:  # all others
+                    if len(label) > truncate:
                         label = label[:truncate] + "..."
                     pos_list.append(pos)
                     labels.append(label)
                     length_list.append(length)
                     id_list.append(id)
 
-
     ###################################################
     #### thin out CDS annotations
     ###################################################
@@ -360,7 +359,6 @@ def create_plot(
     labels = [labels[i] for i in filtered_indices]
     length_list = [length_list[i] for i in filtered_indices]
 
-
     # Plot CDS product labels on outer position
     cds_track.xticks(
         pos_list,

bin/post_processing.py

@@ -11,7 +11,6 @@
 from Bio import SeqIO
 from Bio.SeqUtils import GC
 from loguru import logger
-
 from processes import convert_gff_to_gbk
 from util import remove_directory, remove_file, touch_file
 
@@ -529,8 +528,8 @@ def create_gff(self):
             locus_df["locus_tag"] = locus_df.contig + "_CDS_" + locus_df["count"]
 
         # assign count and locus_tag to merged_df (for meta)
-        self.merged_df["locus_tag"] =  locus_df["locus_tag"]
-        self.merged_df["count"] =  locus_df["count"]
+        self.merged_df["locus_tag"] = locus_df["locus_tag"]
+        self.merged_df["count"] = locus_df["count"]
         #################################
 
         #########

bin/processes.py

@@ -11,9 +11,8 @@
 from Bio import SeqIO
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
-from loguru import logger
-
 from external_tools import ExternalTool
+from loguru import logger
 from util import count_contigs, remove_directory
 
 ##### phanotate meta mode ########

bin/proteins.py

@@ -15,24 +15,15 @@
 import pyhmmer
 from Bio import SeqIO
 from Bio.SeqUtils import GC
+from external_tools import ExternalTool
+from lib.util import (count_contigs, get_contig_headers, get_version,
+                      remove_directory)
 from loguru import logger
+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 external_tools import ExternalTool
-from post_processing import (
-    process_card_results,
-    process_pyhmmer_results,
-    process_vfdb_results,
-)
-
-from lib.util import (
-    count_contigs,
-    get_contig_headers,
-    get_version,
-    remove_directory
-)
-
 Result = collections.namedtuple("Result", ["protein", "phrog", "bitscore", "evalue"])
 
 

bin/util.py

@@ -4,9 +4,8 @@
 import click
 import pandas as pd
 from Bio import SeqIO
-from loguru import logger
-
 from citation import __citation__
+from loguru import logger
 from version import __version__
 
 

setup.py

@@ -1,6 +1,6 @@
 import os
 
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 
 def get_version():
@@ -45,17 +45,18 @@ def package_files(directory):
         "bin/citation.py",
         "bin/databases.py",
         "bin/external_tools.py",
+        "bin/input_commands.py",
         "bin/hmm.py",
         "bin/plot.py",
         "bin/post_processing.py",
         "bin/processes.py",
         "bin/proteins.py",
         "bin/util.py",
-        "bin/version.py"
+        "bin/version.py",
     ],
-    packages=['pharokka_runner'],                           
-    package_dir=dict(pharokka_runner='bin'),                        
-    package_data=dict(pharokka_runner=package_files('bin/')),
+    packages=["pharokka_runner"],
+    package_dir=dict(pharokka_runner="bin"),
+    package_data=dict(pharokka_runner=package_files("bin/")),
     include_package_data=True,
     license="MIT License",
     platforms=["Unix"],

tests/test_external_commands.py

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