Solved a couple of bugs in picker

Mikado/picking/picker.py

@@ -822,7 +822,7 @@ def __test_sortedness(self, row, coords):
         else:
             chrom, start, end = coords.chrom, coords.start, coords.end
 
-        if chrom is None:
+        if any(_ is True for _ in coords):
             return True
         if chrom > row.chrom:
             test = False
@@ -974,6 +974,7 @@ def __check_max_intron(self, current, invalids, row, max_intron):
                 previous = exon
                 break
 
+        current["transcripts"][row.transcript]["exon_lines"].append((row.start, row.end, row.feature, row.phase))
         if previous:
             # I have to compare like with like.
             intron_length = (row.start - 1) - (previous[1] + 1) + 1
@@ -984,14 +985,15 @@ def __check_max_intron(self, current, invalids, row, max_intron):
                 )
                 del current["transcripts"][row.transcript]
                 invalids.add(row.transcript)
-                current["start"] = min([
-                    min([exon[0] for exon in current["transcripts"][trans]["exon_lines"]])
-                    for trans in current["transcripts"]])
-                current["end"] = max([
-                    max([exon[1] for exon in current["transcripts"][trans]["exon_lines"]])
-                    for trans in current["transcripts"]])
-        current["transcripts"][row.transcript]["exon_lines"].append(
-            (row.start, row.end, row.feature, row.phase))
+                if current["transcripts"]:
+                    current["start"] = min([
+                        min([exon[0] for exon in current["transcripts"][trans]["exon_lines"]])
+                        for trans in current["transcripts"]])
+                    current["end"] = max([
+                        max([exon[1] for exon in current["transcripts"][trans]["exon_lines"]])
+                        for trans in current["transcripts"]])
+                else:
+                    current["start"], current["end"] = None, None
         return current, invalids
 
     def __parse_multithreaded(self, locus_queue, conn, cursor):
@@ -1004,11 +1006,11 @@ def __parse_multithreaded(self, locus_queue, conn, cursor):
             max_intron = self.json_conf["prepare"]["max_intron_length"]
             for row in input_annotation:
                 if row.is_exon is True:
-                    if row.transcript not in current["transcripts"]:
-                        self.logger.error("Transcript %s is invalid", row.id)
-                        invalids.add(row.transcript)
-                    elif row.transcript in invalids:
+                    if row.transcript in invalids:
                         continue
+                    elif row.transcript not in current["transcripts"]:
+                        self.logger.error("Transcript %s is invalid", row.transcript)
+                        invalids.add(row.transcript)
                     else:
                         # Check max intron length. We presume that exons are sorted correctly.
                         current, invalids = self.__check_max_intron(current, invalids, row, max_intron=max_intron)