Documentation and #18

jeffhsu3 · Jan 20, 2015 · 296c061 · 296c061
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diff --git a/doc/source/aei.rst b/doc/source/aei.rst
@@ -4,14 +4,20 @@
 Running Aellic Expression Imbalance
 *********************
 
-Running aellic expression imbalance analysis on RNA-Sequencing data. 
+Running aellic expression imbalance analysis on RNA-Sequencing data.  Returns 
+a pandas dataframe pickled to a file specified by OUTPUT.
 
-python AEI_2.py genotype_data file_to_sample_mapping.txt -o OUTPUT
+.. code-block
+    python genda_path/scripts/aei_count.py genotype_data file_to_sample_mapping.txt -o OUTPUT
 
 file_to_sample_mapping.txt should have the following tab-delimited format.
 
+.. code-block
 sample_name    path_to_file
 Sample_1    /proj/data/sample_1.bam
 
+genotype_data is a file specificying which SNPs to count at in the 1000G VCF 
+type format.
+
 At the moment the script has a lot of limitations.  Tested on STAR and tophat
-aligned data.
+aligned bams.
diff --git a/genda/stats/aei_count_samples.pyx b/genda/stats/aei_count_samples.pyx
@@ -11,6 +11,8 @@ from . import *
 
 STUFF = 'hi'
 
+# Not correctly implemented yet
+
 @cython.boundscheck(False)
 cpdef aei_count_samples(np.ndarray[dtype_t, ndim=2] geno,
         np.ndarray geno_columns,