Remove prints that were being called in test code.

[htsworkflow.git] / htsworkflow / pipelines / test / simulate_runfolder.py

diff --git a/htsworkflow/pipelines/test/simulate_runfolder.py b/htsworkflow/pipelines/test/simulate_runfolder.py
index 4e462073ccfe668002ef5e1efd1e198401a1bb88..afa2edfe003736605761cdb459c5ba875240ae68 100644 (file)
--- a/htsworkflow/pipelines/test/simulate_runfolder.py
+++ b/htsworkflow/pipelines/test/simulate_runfolder.py
@@ -50,6 +50,31 @@ def make_flowcell_id(runfolder_dir, flowcell_id=None):
     f.write(config)
     f.close()
 
+def make_runinfo(runfolder_dir, flowcell_id):
+    """Simulate a RunInfo.xml file created by >= RTA 1.9
+    """
+    xml = '''<?xml version="1.0"?>
+<RunInfo xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Version="2">
+  <Run Id="{runfolder}" Number="101">
+    <Flowcell>{flowcell}</Flowcell>
+    <Instrument>SN787</Instrument>
+    <Date>110815</Date>
+    <Reads>
+      <Read Number="1" NumCycles="50" IsIndexedRead="N" />
+      <Read Number="2" NumCycles="7" IsIndexedRead="Y" />
+    </Reads>
+    <FlowcellLayout LaneCount="8" SurfaceCount="2" SwathCount="3" TileCount="8" />
+    <AlignToPhiX />
+  </Run>
+</RunInfo>
+'''
+    path, runfolder = os.path.split(runfolder_dir)
+    runinfo = os.path.join(runfolder_dir, 'RunInfo.xml')
+    stream = open(runinfo, 'w')
+    stream.write(xml.format(runfolder=runfolder, flowcell=flowcell_id))
+    stream.close()
+    return runinfo
+
 def make_bustard_config132(image_dir):
     source = os.path.join(TESTDATA_DIR, 'bustard-config132.xml')
     destination = os.path.join(image_dir, 'config.xml')
@@ -651,12 +676,14 @@ CCCFFFFFHHHFHJGIGHIJHIIGHIGIGIGEHFIJJJIHIJHJIIJJIH
 def get_aligned_sample_export(lane, index_seq):
     body = """HWI-ST0787\t102\t{lane}\t1101\t1207\t1993\t{index}\t1\tAANGGATTCGATCCGGCTTAAGAGATGAAAACCGAAAGGGCCGACCGAA\taaBS`ccceg[`ae[dRR_[[SPPPP__ececfYYWaegh^\\ZLLY\\X`\tNM\t\t\t\t\t\t
 HWI-ST0787\t102\t{lane}\t1101\t1478\t1997\t{index}\t1\tCAAGAACCCCGGGGGGGGGGGGGCAGAGAGGGGGAATTTTTTTTTTGTT\tBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\tNM\t\t\t\t\t\t\t\t\t\t\tN
-HWI-ST0787\t102\t{lane}\t1101\t1625\t1994\t{index}\t1\tAANAATGCTACAGAGACAAAACAAAACTGATATGAAAGTTGAGAATAAA\tB^BS\cccgegg[Q[QQQ[`egdgffbeggfgh^^YcfgfhXaHY^O^c\tchrII.fa\t67717938\tR\t99\t72
+HWI-ST0787\t102\t{lane}\t1101\t1625\t1994\t{index}\t1\tAANAATGCTACAGAGACAAAACAAAACTGATATGAAAGTTGAGAATAAA\tB^BS\cccgegg[Q[QQQ[`egdgffbeggfgh^^YcfgfhXaHY^O^c\tchr9.fa\t67717938\tR\t99\t72
 HWI-ST0787\t102\t{lane}\t1101\t1625\t1994\t{index}\t1\tAANAATGCTACAGAGACAAAACAAAACTGATATGAAAGTTGAGAATAAA\tB^BS\cccgegg[Q[QQQ[`egdgffbeggfgh^^YcfgfhXaHY^O^c\t3:4:3\t\t\t\t\t\t\t\t\t\t\tY
 """.format(lane=lane, index=index_seq)
     return body
 
-def ls_tree(root):
+def print_ls_tree(root):
+    """List tree contents, useful for debugging.
+    """
     for dirpath, dirnames, filenames in os.walk(root):
         for filename in filenames:
             print os.path.join(dirpath, filename)