view docs/todo.rst @ 8:844eb8c36f32

Add help section in xml and update usage documentation

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
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* 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