diff docs/todo.rst @ 3:8e1efafa6277

Updated version * Bugfix: blue lines in some plots (bar colors were not set correctly) * Cookiecutter template * Additional unit tests * Add plot legend

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/todo.rst	Wed Aug 12 09:27:45 2015 +0100
@@ -0,0 +1,38 @@
+Outline
+-------
+Log information by default
+Errors to stderr
+
+
+Arguments
+---------
+-b ribo_file
+-f transcriptome_fasta 
+-t transcript_name
+-n rna_file
+-l read_length
+-s read_offset
+-m html_file
+-o output_path
+-d debug
+
+Tests
+-----
+
+Check arguments
+...............
+* BAM file valid (should be indexed for fetch to work)
+* FASTA file should be valid
+* Transcript name should exist in both BAM and FASTA (riboplot: yes, ribocount: no).
+* If RNA file is provided, bedtools should exist in PATH
+* Read length should be a valid integer (must exist in BAM)
+* Read offset - positive integer (can't exceed ?)
+* Should be possible to get codon positions.
+
+
+Notes
+-----
+* No way to check if input BAM is RNA-Seq/Ribo-Seq (plot will still be generated in either case)
+* No way to check if BAM is sorted
+
+