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> |
|---|---|
| date | Wed, 12 Aug 2015 09:27:45 +0100 |
| parents | |
| children | 628f82e72d72 |
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| 2:b6fd86c539ea | 3:8e1efafa6277 |
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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 |