Attempt to guess raw sequence type for a run.

[htsworkflow.git] / htsworkflow / pipelines / bustard.py

diff --git a/htsworkflow/pipelines/bustard.py b/htsworkflow/pipelines/bustard.py
index cb32515dca06e2f22fed1e836a1c30288d33940b..eefaef4d82acc122b8fda2e35ffcbb9cfca100b5 100644 (file)
--- a/htsworkflow/pipelines/bustard.py
+++ b/htsworkflow/pipelines/bustard.py
@@ -239,6 +239,22 @@ class Bustard(object):
         self.date = date(*t[0:3])
         self.user = groups[2]
 
+    def _get_sequence_format(self):
+        """Guess sequence format"""
+        projects = glob(os.path.join(self.pathname, 'Project_*'))
+        if len(projects) > 0:
+            # Hey we look like a demultiplexed run
+            return 'fastq'
+        return 'qseq'
+        #qseqs = glob(os.path.join(self.pathname, '*_qseq.txt'))
+        #if len(qseqs) > 0:
+        #    return 'qseq'
+        #seqs = glob(os.path.join(self.pathname, '*_seq.txt'))
+        #if len(seqs) > 0:
+        #    return 'srf'
+        return None
+    sequence_format = property(_get_sequence_format)
+
     def _get_software_version(self):
         """return software name, version tuple"""
         if self.bustard_config is None: