[tred] Parse sites folder when --workdir is not cwd

sites/README.md

@@ -2,7 +2,7 @@
 
 Use the template in this folder to add additional STR sites to the TREDPARSE
 run. By default, in addition to the 30 standard STR loci, TREDPARSE also look
-for JSON files in `sites`` in the current working directory.
+for JSON files in ``sites`` in the current working directory.
 
 Most of the details can be manually filled out, however, the ``prefix`` and
 ``suffix`` fields need to be computed from the reference FASTA. Therefore we've

tredparse/meta.py

@@ -28,7 +28,7 @@
 
 class TREDsRepo(dict):
 
-    def __init__(self, ref=REF, toy=False, use_sites=True):
+    def __init__(self, ref=REF, toy=False, sites=SITES):
 
         # Parse ALTS first
         alts = self.get_alts(ref)
@@ -41,13 +41,12 @@ def __init__(self, ref=REF, toy=False, use_sites=True):
         self.df = df
 
         # Get all user loci names by searching within sites folder
-        if use_sites:
-            for sites in glob("{}/*.json".format(SITES)):
-                sites = byteify(json.load(open(sites)))
-                for name, row in sites.items():
-                    name = str(name)  # json.loads gets a unicode
-                    self[name] = TRED(name, row, ref=ref, alt=alts.get(name, []))
-                    self.names.append(name)
+        for s in glob("{}/*.json".format(sites)):
+            s = byteify(json.load(open(s)))
+            for name, row in s.items():
+                name = str(name)  # json.loads gets a unicode
+                self[name] = TRED(name, row, ref=ref, alt=alts.get(name, []))
+                self.names.append(name)
 
         if toy:
             tr = self.get("HD")

tredparse/tred.py

@@ -472,10 +472,11 @@ def main(args):
     logger.debug("Total samples: {}".format(len(samples)))
 
     task_args = []
+    sites = op.join(os.getcwd(), "sites")
     os.chdir(workdir)
 
     ref = args.ref
-    repo = TREDsRepo(ref=ref, toy=args.toy)
+    repo = TREDsRepo(ref=ref, toy=args.toy, sites=sites)
     repo.set_ploidy(args.haploid)
     TRED_NAMES = repo.names
     treds = args.tred or TRED_NAMES