mimseq - npm Package Compare versions

Comparing version 1.3.10 to 1.3.11

mimseq.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: mimseq
-Version: 1.3.10
+Version: 1.3.11
 Summary: Custom high-throughput tRNA sequencing alignment and quantification pipeline based on modification induced misincorporation cDNA synthesis.
@@ -5,0 +5,0 @@ Home-page: https://github.com/nedialkova-lab/mim-tRNAseq

mimseq/tRNAtools.py

@@ -18,2 +18,3 @@ #!/usr/bin/env python3
 from .ssAlign import aligntRNA, extraCCA, tRNAclassifier, tRNAclassifier_nogaps, getAnticodon, clusterAnticodon
+import unicodedata
 
@@ -269,3 +270,3 @@ log = logging.getLogger(__name__)
 def modificationParser(modifications_table, fetch):
-	# Read in modifications and build dictionary
+    # Read in modifications and build dictionary
 
@@ -277,4 +278,13 @@ modifications = {}
 		for data in modifications_table.values():
-			modifications[data["new_abbrev"].strip()] = {'name':data["name"].strip(), 'abbr':data["short_name"].strip(), 'ref':data["reference_moiety"][0].strip()}
-		
+			key = unicodedata.normalize(
+                    "NFKC", 
+                    data["new_abbrev"].strip()
+                    )
+
+			modifications[key] = {
+                    'name':data["name"].strip(),
+                    'abbr':data["short_name"].strip(), 
+                    'ref':data["reference_moiety"][0].strip()
+                    }
+            
 	elif not fetch:
@@ -289,5 +299,10 @@ log.info("Parsing local Modification data...")
 				if mod and not mod.isspace():
-					modifications[mod.strip()] = {'name':name.strip(), 'abbr':abbr.strip(), 'ref':ref.strip()}
+					key = unicodedata.normalize("NFKC", mod.strip())
+					modifications[key] = {
+                            'name':name.strip(), 
+                            'abbr':abbr.strip(), 
+                            'ref':ref.strip()
+                            }
 
-	return(modifications)
+	return modifications
 
@@ -300,4 +315,7 @@ def getUnmodSeq(seq, modification_table):
 		# for insertions ('_') make reference N - this is not described in the modifications table
-		if char == '_':
+		if char == '_': 
 			char = 'N'
+		elif char not in modification_table:
+			log.info(f"Unknown modification {char} found - changing to N")
+			char = 'N'
 		else:
@@ -304,0 +322,0 @@ char = modification_table[char]['ref']

mimseq/version.py

@@ -1,1 +0,1 @@
-__version__ = "v1.3.10"
+__version__ = "v1.3.11"

PKG-INFO

 Metadata-Version: 2.1
 Name: mimseq
-Version: 1.3.10
+Version: 1.3.11
 Summary: Custom high-throughput tRNA sequencing alignment and quantification pipeline based on modification induced misincorporation cDNA synthesis.
@@ -5,0 +5,0 @@ Home-page: https://github.com/nedialkova-lab/mim-tRNAseq

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3672

0.47%