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comparison docs/todo.rst @ 14:628f82e72d72

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Version as released on PyPI 0.1.0
author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Wed, 26 Aug 2015 16:37:10 +0100
parents 8e1efafa6277
children
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13:8a87a2c44d09 14:628f82e72d72
1 Outline 1 Todo
2 ------- 2 ----
3 Log information by default 3 * No way to check if input BAM is RNA-Seq/Ribo-Seq (plot will still be generated in either case).
4 Errors to stderr 4 * Check if BAM is sorted.
5 5
6 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