Merge pull request #19 from Zymo-Research/kerikssonNamingStandard

Merging on new naming standard

figaroSupport/fileNamingStandards.py

@@ -2,7 +2,8 @@
 aliasList = {"zymo": "zymo",
              "zymoservicesnamingstandard": "zymo",
              "zymoservices": "zymo",
-             "illumina": "illumina"}
+             "illumina": "illumina",
+             "keriksson": "keriksson"}
 
 class NamingStandard(object):
 
@@ -71,6 +72,21 @@ def getSampleInfo(self, fileName:str):
             raise ValueError("%s does not appear to be a valid Illumina file name. Please check file naming convention argument." % fileName)
 
 
+class KErickssonStandard(NamingStandard):
+
+    def getSampleInfo(self, fileName:str):
+        group, sampleAndDirection = fileName.split(".")[:2]
+        try:
+            sample, direction = sampleAndDirection.split("_")
+            direction = direction.replace("R", "")
+            direction = direction.replace("r", "")
+            direction = int(direction)
+        except ValueError:
+            raise ValueError("%s does not appear to be a valid file for this standard. Please check file naming convention argument." %fileName)
+
+        return group, sample, direction
+
+
 class ManualNamingStandard(NamingStandard):
     __slots__ = ["fileName", "fileDirectory", "filePath", "sampleNumber", "group", "direction", "sampleID"]
 
@@ -87,7 +103,8 @@ def __init__(self, filePath: str, group:str, number:int, direction:int):
 
 def loadNamingStandard(name:str):
     aliasObjectKey = {"zymo" : ZymoServicesNamingStandard,
-                      "illumina" : IlluminaStandard}
+                      "illumina" : IlluminaStandard,
+                      "keriksson": KErickssonStandard}
     nameLower = name.lower()
     if not nameLower in aliasList:
         raise ValueError("%s is not a valid naming standard identifier" %name)