mgnify-pipelines-toolkit 0.1.5__tar.gz → 0.1.7__tar.gz

{mgnify_pipelines_toolkit-0.1.5 → mgnify_pipelines_toolkit-0.1.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mgnify_pipelines_toolkit
-Version: 0.1.5
+Version: 0.1.7
 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-0.1.5 → mgnify_pipelines_toolkit-0.1.7}/mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py

@@ -58,19 +58,20 @@ def parse_args():
     return input, fasta, sample
 
 
-def get_amp_region(beg, strand, model):
+def get_amp_region(beg, end, strand, model):
     prev_region = ""
 
     for region, region_coords in model.items():
 
         region_beg = region_coords[0]
         beg_diff = region_beg - beg
+        end_diff = region_beg - end
 
         if strand == STRAND_FWD:
-            if beg_diff > 0:
+            if beg_diff > 0 and end_diff > 0:
                 return region
         else:
-            if beg_diff > 0:
+            if beg_diff > 0 and end_diff > 0:
                 return prev_region
 
         prev_region = region
@@ -92,6 +93,7 @@ def main():
             primer_name = line_lst[0]
             rfam = line_lst[3]
             beg = float(line_lst[5])
+            end = float(line_lst[6])
 
             if rfam == "RF00177":
                 gene = "16S"
@@ -116,7 +118,7 @@ def main():
             elif "R" in primer_name:
                 strand = STRAND_REV
 
-            amp_region = get_amp_region(beg, strand, model)
+            amp_region = get_amp_region(beg, end, strand, model)
             primer_seq = str(fasta_dict[primer_name].seq)
 
             res_dict["Gene"].append(gene)

{mgnify_pipelines_toolkit-0.1.5 → mgnify_pipelines_toolkit-0.1.7}/mgnify_pipelines_toolkit/analysis/shared/fastq_suffix_header_check.py

@@ -77,12 +77,10 @@ def main():
                 'No reverse file given, yet given forward file has the "_1" suffix implying it\'s paired-end. '
                 + "Either supply the reverse file, or supply a single-end file."
             )
-            exit(1)
         elif "_2" not in rev:
             logging.error(
                 'The expected suffix "_2" for a supplied reverse file is missing. Please verify your inputs.'
             )
-            exit(1)
         else:
             files_to_parse = [fwd, rev]
 

{mgnify_pipelines_toolkit-0.1.5 → mgnify_pipelines_toolkit-0.1.7}/mgnify_pipelines_toolkit/analysis/shared/get_subunits.py

@@ -102,7 +102,7 @@ def main():
     ]
     open_files = {}
     for record in SeqIO.parse(args.input, "fasta"):
-        model = "-".join(record.id.split("/")[0].split("-")[1:])
+        model = "-".join(record.id.split("/")[0].split("-")[-1:])
         if model in coding_rna:
             filename = pattern_dict[model]
         else:

mgnify_pipelines_toolkit-0.1.7/mgnify_pipelines_toolkit/utils/get_mpt_version.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# Copyright 2024 EMBL - European Bioinformatics Institute
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import importlib.metadata
+
+
+def main():
+
+    print(importlib.metadata.version("mgnify-pipelines-toolkit"))
+
+
+if __name__ == "__main__":
+    main()

{mgnify_pipelines_toolkit-0.1.5 → mgnify_pipelines_toolkit-0.1.7}/mgnify_pipelines_toolkit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: mgnify_pipelines_toolkit
-Version: 0.1.5
+Version: 0.1.7
 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-0.1.5 → mgnify_pipelines_toolkit-0.1.7}/mgnify_pipelines_toolkit.egg-info/SOURCES.txt

@@ -33,4 +33,5 @@ mgnify_pipelines_toolkit/constants/tax_ranks.py
 mgnify_pipelines_toolkit/constants/thresholds.py
 mgnify_pipelines_toolkit/constants/var_region_coordinates.py
 mgnify_pipelines_toolkit/utils/__init__.py
-mgnify_pipelines_toolkit/utils/fasta_to_delimited.py
+mgnify_pipelines_toolkit/utils/fasta_to_delimited.py
+mgnify_pipelines_toolkit/utils/get_mpt_version.py

{mgnify_pipelines_toolkit-0.1.5 → mgnify_pipelines_toolkit-0.1.7}/mgnify_pipelines_toolkit.egg-info/entry_points.txt

@@ -6,6 +6,7 @@ classify_var_regions = mgnify_pipelines_toolkit.analysis.amplicon.classify_var_r
 fasta_to_delimited = mgnify_pipelines_toolkit.utils.fasta_to_delimited:main
 fastq_suffix_header_check = mgnify_pipelines_toolkit.analysis.shared.fastq_suffix_header_check:main
 find_mcp_inflection_points = mgnify_pipelines_toolkit.analysis.amplicon.find_mcp_inflection_points:main
+get_mpt_version = mgnify_pipelines_toolkit.utils.get_mpt_version:main
 get_subunits = mgnify_pipelines_toolkit.analysis.shared.get_subunits:main
 get_subunits_coords = mgnify_pipelines_toolkit.analysis.shared.get_subunits_coords:main
 library_strategy_check = mgnify_pipelines_toolkit.analysis.shared.library_strategy_check:main

{mgnify_pipelines_toolkit-0.1.5 → mgnify_pipelines_toolkit-0.1.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mgnify_pipelines_toolkit"
-version = "0.1.5"
+version = "0.1.7"
 readme = "README.md"
 license = {text = "Apache Software License 2.0"}
 authors = [
@@ -56,6 +56,7 @@ mapseq_to_asv_table = "mgnify_pipelines_toolkit.analysis.amplicon.mapseq_to_asv_
 primer_val_classification = "mgnify_pipelines_toolkit.analysis.amplicon.primer_val_classification:main"
 # utils
 fasta_to_delimited = "mgnify_pipelines_toolkit.utils.fasta_to_delimited:main"
+get_mpt_version = "mgnify_pipelines_toolkit.utils.get_mpt_version:main"
 
 [project.optional-dependencies]
 tests = [