mgnify-pipelines-toolkit 1.0.5__py3-none-any.whl → 1.0.6__py3-none-any.whl

mgnify_pipelines_toolkit/analysis/assembly/gff_toolkit.py

@@ -29,24 +29,27 @@ from mgnify_pipelines_toolkit.analysis.assembly.gff_file_utils import (
 )
 
 
-def main(
-    gff,
-    ipr_file,
-    eggnog_file,
-    sanntis_file,
-    crispr_file,
-    amr_file,
-    antismash_file,
-    gecco_file,
-    dbcan_file,
-    dbcan_cazys_file,
-    defense_finder_file,
-    pseudofinder_file,
-    rfam_file,
-    trnascan_file,
-    outfile,
-    pseudogene_report_file,
-):
+def main():
+
+    (
+        gff,
+        ipr_file,
+        eggnog_file,
+        sanntis_file,
+        crispr_file,
+        amr_file,
+        antismash_file,
+        gecco_file,
+        dbcan_file,
+        dbcan_cazys_file,
+        defense_finder_file,
+        pseudofinder_file,
+        rfam_file,
+        trnascan_file,
+        outfile,
+        pseudogene_report_file,
+    ) = parse_args()
+
     # load annotations and add them to existing CDS
     # here header contains leading GFF lines starting with "#",
     # main_gff_extended is a dictionary that contains GFF lines with added in additional annotations
@@ -163,12 +166,8 @@ def parse_args():
         "--pseudogene-report", help="Pseudogene report filename", required=False
     )
 
-    return parser.parse_args()
-
-
-if __name__ == "__main__":
-    args = parse_args()
-    main(
+    args = parser.parse_args()
+    return (
         args.gff_input,
         args.ips,
         args.eggnog,
@@ -186,3 +185,7 @@ if __name__ == "__main__":
         args.outfile,
         args.pseudogene_report,
     )
+
+
+if __name__ == "__main__":
+    main()

mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_cazys.py

@@ -24,7 +24,16 @@ import re
 logging.basicConfig(level=logging.INFO)
 
 
-def main(hmm_file, overview_file, genome_gff, outfile, dbcan_version):
+def main():
+
+    args = parse_args()
+    hmm_file, overview_file, genome_gff, outfile, dbcan_ver = (
+        args.hmm_file,
+        args.overview_file,
+        args.genome_gff,
+        args.outfile,
+        args.dbcan_ver,
+    )
 
     hmm_path = Path(hmm_file)
     overview_path = Path(overview_file)
@@ -38,7 +47,7 @@ def main(hmm_file, overview_file, genome_gff, outfile, dbcan_version):
     substrates = load_substrates(hmm_path)
     genome_gff_lines = load_gff(genome_gff)
 
-    print_gff(overview_file, outfile, dbcan_version, substrates, genome_gff_lines)
+    print_gff(overview_file, outfile, dbcan_ver, substrates, genome_gff_lines)
 
 
 def load_gff(gff):
@@ -205,7 +214,4 @@ def parse_args():
 
 
 if __name__ == "__main__":
-    args = parse_args()
-    main(
-        args.hmm_file, args.overview_file, args.genome_gff, args.outfile, args.dbcan_ver
-    )
+    main()

mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_clusters.py

@@ -22,7 +22,15 @@ from pathlib import Path
 logging.basicConfig(level=logging.INFO)
 
 
-def main(standard_file, substrate_file, outfile, dbcan_version):
+def main():
+
+    args = parse_args()
+    standard_file, substrate_file, outfile, dbcan_ver = (
+        args.standard_file,
+        args.substrate_file,
+        args.outfile,
+        args.dbcan_ver,
+    )
     standard_path = Path(standard_file)
     substrate_path = Path(substrate_file)
 
@@ -36,7 +44,7 @@ def main(standard_file, substrate_file, outfile, dbcan_version):
 
     substrates = load_substrates(substrate_path)
     cgc_locations = load_cgcs(standard_path)
-    print_gff(standard_path, outfile, dbcan_version, substrates, cgc_locations)
+    print_gff(standard_path, outfile, dbcan_ver, substrates, cgc_locations)
 
 
 def load_cgcs(standard_path):
@@ -158,5 +166,4 @@ def parse_args():
 
 
 if __name__ == "__main__":
-    args = parse_args()
-    main(args.standard_file, args.substrate_file, args.outfile, args.dbcan_ver)
+    main()

{mgnify_pipelines_toolkit-1.0.5.dist-info → mgnify_pipelines_toolkit-1.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mgnify_pipelines_toolkit
-Version: 1.0.5
+Version: 1.0.6
 Summary: Collection of scripts and tools for MGnify pipelines
 Author-email: MGnify team <metagenomics-help@ebi.ac.uk>
 License: Apache Software License 2.0

{mgnify_pipelines_toolkit-1.0.5.dist-info → mgnify_pipelines_toolkit-1.0.6.dist-info}/RECORD

@@ -18,11 +18,11 @@ mgnify_pipelines_toolkit/analysis/assembly/combined_gene_caller_merge.py,sha256=
 mgnify_pipelines_toolkit/analysis/assembly/generate_gaf.py,sha256=2T4T7aXMGPac-LZUXJF3lOUzZZF50dAKkKTSaO-4idQ,3587
 mgnify_pipelines_toolkit/analysis/assembly/gff_annotation_utils.py,sha256=6gbCRlEX1eBqzFYjOt3og-961dZ--QsCJL-7l5nzg1k,33992
 mgnify_pipelines_toolkit/analysis/assembly/gff_file_utils.py,sha256=_4J31wAjK5B15p9lDzTG2wmZdyoZkOgmy7Kp_w8lTeE,3812
-mgnify_pipelines_toolkit/analysis/assembly/gff_toolkit.py,sha256=n2rbS8UHevF8OB4umo7QivS6v4avlgsCaRwrBbVmZ24,5398
+mgnify_pipelines_toolkit/analysis/assembly/gff_toolkit.py,sha256=_iaTBvMKbQDi_02_QuSPqLJ_rC37ruxiPHv5lLQmI-w,5480
 mgnify_pipelines_toolkit/analysis/assembly/go_utils.py,sha256=eay9e3Xdc8XxnlC_4SHHjN89k-M9i_cFMc2lI_ZFxqY,5596
 mgnify_pipelines_toolkit/analysis/assembly/krona_txt_from_cat_classification.py,sha256=uex2T6GagtYFBIc39-Xm4SFHL06KAQ5v0_loOmY_eaw,4289
-mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_cazys.py,sha256=dlsXfLPvm1qXRQplM0d5q0JMv9AuD9ytZn3utgYDYAM,7712
-mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_clusters.py,sha256=61zVSuQ6Jw2hZU6QOa05lNcrr8Ylzpy2Tes-QaX8kFw,5888
+mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_cazys.py,sha256=5lbVSWRZoi61cKvuolzUJlhUBzpx8DgWMH0Vzw1HcHA,7748
+mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_clusters.py,sha256=i4uYdqY6y2ee72vl0sLkHeJvigHGKJMzdyR3HEIK1Mk,5930
 mgnify_pipelines_toolkit/analysis/assembly/summarise_antismash_bgcs.py,sha256=eRAQ0vFbqnWreiBdtFuwLKve9WwYwv9dYQtD1pumaZs,10776
 mgnify_pipelines_toolkit/analysis/assembly/summarise_goslims.py,sha256=TPaKlYkoy37_XgYNOskWCCoXtPNku_k5ygSeK4fT1VQ,6689
 mgnify_pipelines_toolkit/analysis/assembly/summarise_sanntis_bgcs.py,sha256=65szj-H8Hxy_eXy3TyTs48EhPJbJ2w1skHlVbH2YeVM,4538
@@ -48,9 +48,9 @@ mgnify_pipelines_toolkit/schemas/schemas.py,sha256=pnH8LUH8i2ACNvFNWyG-n-eIHZcI5
 mgnify_pipelines_toolkit/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mgnify_pipelines_toolkit/utils/fasta_to_delimited.py,sha256=lgYIR1S4crURY7C7nFtgE6QMV4u4zCNsUrVkcRnsEEo,3996
 mgnify_pipelines_toolkit/utils/get_mpt_version.py,sha256=aS9bWrC9CP7tpxoEVg6eEYt18-pmjG7fJl5Mchz4YOU,798
-mgnify_pipelines_toolkit-1.0.5.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-mgnify_pipelines_toolkit-1.0.5.dist-info/METADATA,sha256=fp1mfamjDfteh42zghP_y8br_zRaEYGzAhbDB7O72mc,5810
-mgnify_pipelines_toolkit-1.0.5.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-mgnify_pipelines_toolkit-1.0.5.dist-info/entry_points.txt,sha256=T8soGT2to8c_qafw-0itqCn4sjOnxlfaNWHIaHz4H54,3416
-mgnify_pipelines_toolkit-1.0.5.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
-mgnify_pipelines_toolkit-1.0.5.dist-info/RECORD,,
+mgnify_pipelines_toolkit-1.0.6.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+mgnify_pipelines_toolkit-1.0.6.dist-info/METADATA,sha256=b9Hoo0e0xVvL4erImJgt_7gtbb-5Yx8TZNlf9KZcQIY,5810
+mgnify_pipelines_toolkit-1.0.6.dist-info/WHEEL,sha256=pxyMxgL8-pra_rKaQ4drOZAegBVuX-G_4nRHjjgWbmo,91
+mgnify_pipelines_toolkit-1.0.6.dist-info/entry_points.txt,sha256=T8soGT2to8c_qafw-0itqCn4sjOnxlfaNWHIaHz4H54,3416
+mgnify_pipelines_toolkit-1.0.6.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
+mgnify_pipelines_toolkit-1.0.6.dist-info/RECORD,,

{mgnify_pipelines_toolkit-1.0.5.dist-info → mgnify_pipelines_toolkit-1.0.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (79.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any