Mercurial > repos > vimalkumarvelayudhan > riboplot
comparison 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
author | Vimalkumar Velayudhan <vimal@biotechcoder.com> |
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date | Wed, 12 Aug 2015 09:27:45 +0100 |
parents | |
children | 628f82e72d72 |
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1 Outline | |
2 ------- | |
3 Log information by default | |
4 Errors to stderr | |
5 | |
6 | |
7 Arguments | |
8 --------- | |
9 -b ribo_file | |
10 -f transcriptome_fasta | |
11 -t transcript_name | |
12 -n rna_file | |
13 -l read_length | |
14 -s read_offset | |
15 -m html_file | |
16 -o output_path | |
17 -d debug | |
18 | |
19 Tests | |
20 ----- | |
21 | |
22 Check arguments | |
23 ............... | |
24 * BAM file valid (should be indexed for fetch to work) | |
25 * FASTA file should be valid | |
26 * Transcript name should exist in both BAM and FASTA (riboplot: yes, ribocount: no). | |
27 * If RNA file is provided, bedtools should exist in PATH | |
28 * Read length should be a valid integer (must exist in BAM) | |
29 * Read offset - positive integer (can't exceed ?) | |
30 * Should be possible to get codon positions. | |
31 | |
32 | |
33 Notes | |
34 ----- | |
35 * No way to check if input BAM is RNA-Seq/Ribo-Seq (plot will still be generated in either case) | |
36 * No way to check if BAM is sorted | |
37 | |
38 |