convert to print_function

diff --git a/htsworkflow/pipelines/bustard.py b/htsworkflow/pipelines/bustard.py
index 99f231dd73e748a0c88b528f4489968ab20b8428..5df79c7fb80eb3afd5cba76f536e6c194a39d533 100644 (file)
--- a/htsworkflow/pipelines/bustard.py
+++ b/htsworkflow/pipelines/bustard.py
@@ -4,6 +4,8 @@ Extract configuration from Illumina Bustard Directory.
 This includes the version number, run date, bustard executable parameters, and
 phasing estimates.
 """
+from __future__ import print_function
+
 from copy import copy
 from datetime import date
 from glob import glob
@@ -289,7 +291,7 @@ class Bustard(object):
     time = property(_get_time, doc='return run time as seconds since epoch')
 
     def dump(self):
-        #print ElementTree.tostring(self.get_elements())
+        #print(ElementTree.tostring(self.get_elements()))
         ElementTree.dump(self.get_elements())
 
     def get_elements(self):
@@ -456,22 +458,22 @@ def main(cmdline):
     opts, args = parser.parse_args(cmdline)
 
     for bustard_dir in args:
-        print u'analyzing bustard directory: ' + unicode(bustard_dir)
+        print(u'analyzing bustard directory: ' + unicode(bustard_dir))
         bustard_object = bustard(bustard_dir)
         bustard_object.dump()
 
         bustard_object2 = Bustard(xml=bustard_object.get_elements())
-        print ('-------------------------------------')
+        print('-------------------------------------')
         bustard_object2.dump()
-        print ('=====================================')
+        print('=====================================')
         b1_tree = bustard_object.get_elements()
         b1 = ElementTree.tostring(b1_tree).split(os.linesep)
         b2_tree = bustard_object2.get_elements()
         b2 = ElementTree.tostring(b2_tree).split(os.linesep)
         for line1, line2 in zip(b1, b2):
             if b1 != b2:
-                print "b1: ", b1
-                print "b2: ", b2
+                print("b1: ", b1)
+                print("b2: ", b2)
 
 if __name__ == "__main__":
     main(sys.argv[1:])

diff --git a/htsworkflow/pipelines/eland.py b/htsworkflow/pipelines/eland.py
index a508a494c8c24900e8574c75f43c3616bf309814..acc805a889d3000ffbe4a1f73cedec2930e47bbf 100644 (file)
--- a/htsworkflow/pipelines/eland.py
+++ b/htsworkflow/pipelines/eland.py
@@ -1,6 +1,8 @@
 """
 Analyze ELAND files
 """
+from __future__ import print_function
+
 import collections
 from glob import glob
 import logging
@@ -895,7 +897,7 @@ def main(cmdline=None):
     for a in args:
         LOGGER.info("Starting scan of %s" % (a,))
         e = eland(a)
-        print ElementTree.tostring(e.get_elements())
+        print(ElementTree.tostring(e.get_elements()))
     return
 
 

diff --git a/htsworkflow/pipelines/firecrest.py b/htsworkflow/pipelines/firecrest.py
index 3519eb0123600ef99602cccb25210d119a62a073..11c1d4cb9f0642d8e5d9ffc556ca0e1c4c354435 100644 (file)
--- a/htsworkflow/pipelines/firecrest.py
+++ b/htsworkflow/pipelines/firecrest.py
@@ -9,6 +9,7 @@ fromxml
   Firecrest factory function initalized from an xml dump from
   the Firecrest object.
 """
+from __future__ import print_function
 
 from datetime import date
 from glob import glob
@@ -66,11 +67,11 @@ class Firecrest(object):
     def dump(self):
         """Report debugginf information
         """
-        print "Starting cycle:", self.start
-        print "Ending cycle:", self.stop
-        print "Firecrest version:", self.version
-        print "Run date:", self.date
-        print "user:", self.user
+        print("Starting cycle:", self.start)
+        print("Ending cycle:", self.stop)
+        print("Firecrest version:", self.version)
+        print("Run date:", self.date)
+        print("user:", self.user)
 
     def get_elements(self):
         """Return XML serialization structure.

diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py
index dd70fe262bbed816e0d0ed38c9ab793dca79281e..d1a40bdb408897a271ffaeb87f753f2aab468f61 100644 (file)
--- a/htsworkflow/pipelines/gerald.py
+++ b/htsworkflow/pipelines/gerald.py
@@ -1,5 +1,7 @@
 """Provide access to information stored in the GERALD directory.
 """
+from __future__ import print_function
+
 import collections
 from datetime import datetime, date
 import logging
@@ -59,10 +61,10 @@ class Alignment(object):
         """
         Debugging function, report current object
         """
-        print 'Software:'. self.__class__.__name__
-        print 'Alignment version:', self.version
-        print 'Run date:', self.date
-        print 'config.xml:', self.tree
+        print('Software:'. self.__class__.__name__)
+        print('Alignment version:', self.version)
+        print('Run date:', self.date)
+        print('config.xml:', self.tree)
         self.summary.dump()
 
     def get_elements(self, root_tag):

diff --git a/htsworkflow/pipelines/ipar.py b/htsworkflow/pipelines/ipar.py
index 6c3acbe19b50c8959b5deb011e36eb9cf7396212..46758ec141af2629838e439ce0747642d8f024e6 100644 (file)
--- a/htsworkflow/pipelines/ipar.py
+++ b/htsworkflow/pipelines/ipar.py
@@ -9,6 +9,8 @@ fromxml
     IPAR factory function initalized from an xml dump from
     the IPAR object.
 """
+from __future__ import print_function
+
 __docformat__ = "restructuredtext en"
 
 import datetime
@@ -159,7 +161,7 @@ class IPAR(object):
         """
         suffix_node = self.tree.find('RunParameters/CompressionSuffix')
         if suffix_node is None:
-          print "find compression suffix failed"
+          print("find compression suffix failed")
           return None
         suffix = suffix_node.text
         files = []
@@ -172,8 +174,8 @@ class IPAR(object):
         return files
 
     def dump(self):
-        print "Matrix:", self.matrix
-        print "Tree:", self.tree
+        print("Matrix:", self.matrix)
+        print("Tree:", self.tree)
 
     def get_elements(self):
         attribs = {'version': str(IPAR.XML_VERSION) }

diff --git a/htsworkflow/pipelines/srf.py b/htsworkflow/pipelines/srf.py
index 03b96b8f35b481fddfb7f41100ed0366c2ef473f..2663ee39bd6453a02b4c9043d096e41e152171a7 100644 (file)
--- a/htsworkflow/pipelines/srf.py
+++ b/htsworkflow/pipelines/srf.py
@@ -238,7 +238,6 @@ def main(cmdline=None):
         seq_cmds = make_srf_commands(opts.name, source, opts.lanes, opts.site_name, opts.destination, 0)
     else:
         raise ValueError('Unknown --format=%s' % (opts.format))
-    print seq_cmds
     srf.run_commands(args.source, seq_cmds, num_jobs)
 
 def make_parser():

diff --git a/htsworkflow/pipelines/summary.py b/htsworkflow/pipelines/summary.py
index 100b2c0edcf7fd8cae1f48f679b7f673cc8a1c75..1da11a39b416f8141ca9f97c485d9477ed5dfbcb 100644 (file)
--- a/htsworkflow/pipelines/summary.py
+++ b/htsworkflow/pipelines/summary.py
@@ -1,6 +1,8 @@
 """
 Analyze the Summary.htm file produced by GERALD
 """
+from __future__ import print_function
+
 import os
 import logging
 import re
@@ -67,7 +69,7 @@ class Summary(object):
         Debugging function, report current object
         """
         tree = self.get_elements()
-        print etree.tostring(tree)
+        print(etree.tostring(tree))
 
 class SummaryGA(Summary):
     def __init__(self, filename=None, xml=None):