Merge branch 'dev'

CHANGELOG.txt

@@ -1,3 +1,6 @@
+v0.2.6 (2014-04-10)
+- Fix error with newer R
+- Add error/solution for older DESeq2 version
 v0.2.5 (2014-04-05)
 - Add troubleshooting page to docs
 v0.2.4 (2014-04-05)

bin/reademption

@@ -9,7 +9,7 @@ __author__ = "Konrad Foerstner <[email protected]>"
 __copyright__ = "2011-2014 by Konrad Foerstner <[email protected]>"
 __license__ = "ISC license"
 __email__ = "[email protected]"
-__version__ = "0.2.5"
+__version__ = "0.2.6"
 
 def main():
     parser = argparse.ArgumentParser()

docs/source/conf.py

@@ -50,7 +50,7 @@
 # The short X.Y version.
 version = '0.2'
 # The full version, including alpha/beta/rc tags.
-release = '0.2.5'
+release = '0.2.6'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/troubleshooting.rst

@@ -1,7 +1,7 @@
 Troubleshooting
 ===============
 
-Pickling Error
+Pickling error
 --------------
 
 Problem
@@ -18,3 +18,21 @@ Solution
 ~~~~~~~~
 
 Switch to Python 3.3 or higher. The newer versions can handle this.
+
+DESeq2 unused argument error
+----------------------------
+
+Problem
+~~~~~~~
+
+Whenn running ``deseq`` you get an error similar to this:
+::
+   Error in results(dds, contrast = c("condition", "XXX", "YYY")) : 
+     unused argument (contrast = c("condition", "XXX", "YYY"))
+   Execution halted
+   Apparently DESeq did not generate the file "deseq_comp_XXX_vs_YYY.csv". Extension stopped.
+
+Solution
+~~~~~~~~
+
+Get a newer version of DESeq2. Version 1.2.10 and higher should work.

reademptionlib/deseq.py

@@ -41,8 +41,8 @@ def create_deseq_script_file(self):
         conditions = [libs_to_conditions[lib] for lib in libs]
         condition_str = ", ".join(["'%s'" % cond for cond in conditions])
         file_content = self._deseq_script_template() % (
-            self._gene_wise_quanti_combined_path, self._first_data_column,
-            libs_str, condition_str)
+            self._gene_wise_quanti_combined_path, self._first_data_column-1, 
+            len(libs),self._first_data_column, libs_str, condition_str)
         file_content += self._comparison_call_strings(conditions)
         deseq_fh = open(self._deseq_script_path, "w")
         deseq_fh.write(file_content)
@@ -112,7 +112,7 @@ def _deseq_script_template(self):
         return (
             "library('DESeq2')\n"
             "rawCountTable <- read.table('%s', skip=1, sep='\\t', "
-            "quote='', comment.char='')\n"
+            "quote='', comment.char='', colClasses=c(rep('character',%s), rep('numeric',%s)))\n"
             "countTable <- round(rawCountTable[,%s:length(names("
             "rawCountTable))])\n"
             "libs <- c(%s)\n"

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='READemption',
-    version='0.2.5',
+    version='0.2.6',
     packages=['reademptionlib', 'tests'],
     author='Konrad U. Förstner',
     author_email='[email protected]',