mgnify-pipelines-toolkit 1.0.6__tar.gz → 1.0.7__tar.gz

{mgnify_pipelines_toolkit-1.0.6 → mgnify_pipelines_toolkit-1.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mgnify_pipelines_toolkit
-Version: 1.0.6
+Version: 1.0.7
 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-1.0.6 → mgnify_pipelines_toolkit-1.0.7}/mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_cazys.py

@@ -52,7 +52,7 @@ def main():
 
 def load_gff(gff):
     genome_gff_lines = dict()
-    with fileinput.hook_compressed(gff, "rt") as gff:
+    with fileinput.hook_compressed(gff, "r", encoding="utf-8") as gff:
         for line in gff:
             if line.startswith("##FASTA"):
                 return genome_gff_lines
@@ -81,7 +81,7 @@ def load_gff(gff):
 def print_gff(overview_file, outfile, dbcan_version, substrates, genome_gff_lines):
     with open(outfile, "w") as file_out:
         file_out.write("##gff-version 3\n")
-        with fileinput.hook_compressed(overview_file, "rt") as file_in:
+        with fileinput.hook_compressed(overview_file, "r", encoding="utf-8") as file_in:
             for line in file_in:
                 if line.startswith("MGYG") or line.startswith("ERZ"):
                     (
@@ -151,7 +151,7 @@ def print_gff(overview_file, outfile, dbcan_version, substrates, genome_gff_line
 
 def load_substrates(hmm_path):
     substrates = dict()
-    with fileinput.hook_compressed(hmm_path, "rt") as file_in:
+    with fileinput.hook_compressed(hmm_path, "r", encoding="utf-8") as file_in:
         header = next(file_in)
         header_fields = header.strip().split("\t")
         substrate_idx = header_fields.index("Substrate")

{mgnify_pipelines_toolkit-1.0.6 → mgnify_pipelines_toolkit-1.0.7}/mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_clusters.py

@@ -49,7 +49,7 @@ def main():
 
 def load_cgcs(standard_path):
     cgc_locations = dict()
-    with fileinput.hook_compressed(standard_path, "rt") as file_in:
+    with fileinput.hook_compressed(standard_path, "r", encoding="utf-8") as file_in:
         for line in file_in:
             if not line.startswith("CGC#"):
                 cgc, _, contig, _, start, end, _, _ = line.strip().split("\t")
@@ -72,7 +72,7 @@ def print_gff(standard_path, outfile, dbcan_version, substrates, cgc_locations):
     with open(outfile, "w") as file_out:
         file_out.write("##gff-version 3\n")
         cgcs_printed = list()
-        with fileinput.hook_compressed(standard_path, "rt") as file_in:
+        with fileinput.hook_compressed(standard_path, "r", encoding="utf-8") as file_in:
             for line in file_in:
                 if not line.startswith("CGC#"):
                     cgc, gene_type, contig, prot_id, start, end, strand, protein_fam = (
@@ -107,7 +107,7 @@ def print_gff(standard_path, outfile, dbcan_version, substrates, cgc_locations):
 
 def load_substrates(substrate_path):
     substrates = dict()
-    with fileinput.hook_compressed(substrate_path, "rt") as file_in:
+    with fileinput.hook_compressed(substrate_path, "r", encoding="utf-8") as file_in:
         for line in file_in:
             if not line.startswith("#"):
                 parts = line.strip().split("\t")

{mgnify_pipelines_toolkit-1.0.6 → mgnify_pipelines_toolkit-1.0.7}/mgnify_pipelines_toolkit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mgnify_pipelines_toolkit
-Version: 1.0.6
+Version: 1.0.7
 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-1.0.6 → mgnify_pipelines_toolkit-1.0.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mgnify_pipelines_toolkit"
-version = "1.0.6"
+version = "1.0.7"
 readme = "README.md"
 license = {text = "Apache Software License 2.0"}
 authors = [