diff --git a/CHANGELOG.txt b/CHANGELOG.txt index 15c05c35..67e9dea4 100644 --- a/CHANGELOG.txt +++ b/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) diff --git a/bin/reademption b/bin/reademption index 6f9b8b33..20979630 100755 --- a/bin/reademption +++ b/bin/reademption @@ -9,7 +9,7 @@ __author__ = "Konrad Foerstner " __copyright__ = "2011-2014 by Konrad Foerstner " __license__ = "ISC license" __email__ = "konrad@foerstner.org" -__version__ = "0.2.5" +__version__ = "0.2.6" def main(): parser = argparse.ArgumentParser() diff --git a/docs/source/conf.py b/docs/source/conf.py index 2ba3e339..8e3e7368 100644 --- a/docs/source/conf.py +++ b/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. diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst index fdf5f0b5..6b2866d9 100644 --- a/docs/source/troubleshooting.rst +++ b/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. diff --git a/reademptionlib/deseq.py b/reademptionlib/deseq.py index ed91ce7e..770cf1c3 100644 --- a/reademptionlib/deseq.py +++ b/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" diff --git a/setup.py b/setup.py index 415a1629..d5b951b8 100644 --- a/setup.py +++ b/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='konrad@foerstner.org',