Reorganized files

libsmallrna/libsmallrna/libsmallrna.pyx

@@ -267,7 +267,7 @@ def count_pimi(annot_info, write_queue):
 
 def find_matching_annot(annotations, seq):
     """Finds among annotations one to consider as the real one."""
-    warnings.warn("randomly deciding between several piRNA annotations")
+    warnings.warn("randomly deciding between several piRNA or miRNA annotations")
     return next(iter(annotations[0]))
 
 def count_pimis(annot_infos, write_queue):
@@ -316,6 +316,7 @@ def count_pimis(annot_infos, write_queue):
     return (pi_counter, mi_counter)
 
 
+# TODO: annotate TE and pseudogene siRNAs with TE > protein > pseudogene
 def count_si(annot_info, write_queue):
     """
     Returns a mixed dictionnary to count gene identifiers and annotation types.

small_RNA_seq_annotate.py

+small_RNA-seq/small_RNA_seq_annotate.py
\ No newline at end of file