Merge pull request #322 from gbouras13/dev

Update biopython <1.82 [skip ci]

bin/pharokka.py

@@ -4,28 +4,54 @@
 import shutil
 import sys
 import time
+import warnings
 from pathlib import Path
 
+from Bio import BiopythonDeprecationWarning
 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
+warnings.simplefilter("default", BiopythonDeprecationWarning)
+
 
 def main():
     # get the args

bin/pharokka_proteins.py

@@ -6,12 +6,20 @@
 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/proteins.py

@@ -16,12 +16,14 @@
 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"])
 

environment.yml

@@ -5,7 +5,7 @@ channels:
   - defaults
 dependencies:
   - bcbio-gff >=0.7.0
-  - biopython >=1.78
+  - biopython >=1.78,<1.82
   - phanotate >=1.5.0
   - mmseqs2 ==13.45111
   - trnascan-se >=2.0.9

tests/test_external_commands.py

@@ -14,8 +14,15 @@
 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

@@ -6,6 +6,7 @@
 """
 
 import sys
+
 # import
 import unittest
 from pathlib import Path
@@ -14,10 +15,16 @@
 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

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

tests/test_proteins.py

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