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annotate docs/todo.rst @ 5:cef780bcce01

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Remove include directives in rsti (docs). Replaced with links instead
author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Wed, 12 Aug 2015 09:53:06 +0100
parents 8e1efafa6277
children 628f82e72d72
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1 Outline
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2 -------
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3 Log information by default
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4 Errors to stderr
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5
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7 Arguments
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8 ---------
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9 -b ribo_file
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10 -f transcriptome_fasta
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11 -t transcript_name
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12 -n rna_file
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13 -l read_length
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14 -s read_offset
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15 -m html_file
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16 -o output_path
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17 -d debug
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19 Tests
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20 -----
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22 Check arguments
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23 ...............
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24 * BAM file valid (should be indexed for fetch to work)
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25 * FASTA file should be valid
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26 * Transcript name should exist in both BAM and FASTA (riboplot: yes, ribocount: no).
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27 * If RNA file is provided, bedtools should exist in PATH
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28 * Read length should be a valid integer (must exist in BAM)
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29 * Read offset - positive integer (can't exceed ?)
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30 * Should be possible to get codon positions.
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33 Notes
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34 -----
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35 * No way to check if input BAM is RNA-Seq/Ribo-Seq (plot will still be generated in either case)
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36 * No way to check if BAM is sorted
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