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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 8964641b04ef
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13:8a87a2c44d09 14:628f82e72d72
8 -------- 8 --------
9 Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM). 9 Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM).
10 10
11 Parameters 11 Parameters
12 .......... 12 ..........
13
13 1. Ribo-Seq alignment file (Sorted BAM file) 14 1. Ribo-Seq alignment file (Sorted BAM file)
15 ++++++++++++++++++++++++++++++++++++++++++++
16 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
17 file should be sorted. This can be done using one of the following methods.
14 18
15 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM 19 1. RiboGalaxy_ -> Sort Data -> Sort BAM dataset.
16 file should be sorted. This can be done using one of the following methods. 20 2. ``samtools sort input.bam inputsorted``
17
18 1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
19 2. ``samtools sort input.bam inputsorted``
20 21
21 2. Transcriptome (FASTA) 22 2. Transcriptome (FASTA)
22 23 ++++++++++++++++++++++++
23 A FASTA format file with sequences of the transcripts. 24 A FASTA format file with sequences of the transcripts.
24 25
25 3. Name of the transcript to plot (Text) 26 3. Name of the transcript to plot (Text)
26 27 ++++++++++++++++++++++++++++++++++++++++
27 The name of the transcript to plot **should** match the name in the transcriptome (FASTA) 28 The name of the transcript to plot **should** match the name in the transcriptome (FASTA)
28 and the Ribo-Seq/RNA-Seq alignment (BAM). 29 and the Ribo-Seq/RNA-Seq alignment (BAM).
29 30
30 4. RNA coverage [optional] (Sorted BAM file) 31 4. RNA coverage [optional] (Sorted BAM file)
31 32 ++++++++++++++++++++++++++++++++++++++++++++
32 If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage. 33 If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage.
33 34
34 5. Read lengths to consider [Optional] (Integer - 0 or greater) 35 5. Read lengths to consider [Optional] (Integer - 0 or greater)
35 36 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
36 If this option is provided, only Ribo-Seq data of the given length is considered. 37 If this option is provided, only Ribo-Seq data of the given length is considered.
37 38
38 6. Offset [optional] (Integer - 0 or greater) 39 6. Offset [optional] (Integer - 0 or greater)
39 40 +++++++++++++++++++++++++++++++++++++++++++++
40 If this option is provided, this offset is added to the read alignment positions. 41 If this option is provided, this offset is added to the read alignment positions.
41 42
42 Output 43 Output
43 ...... 44 ......
44 1. Plots (PNG and SVG) 45 1. Plots (PNG and SVG)
46 ++++++++++++++++++++++
47 Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue)
45 48
46 Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue) 49 RNA coverage as a gray background (if the RNA coverage option was selected).
47 50
48 RNA coverage as a gray background (if the RNA coverage option was selected). 51 The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames.
49 52
50 The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames. 53 The color codes are start (white) and stop (dark gray).
51 54
52 The color codes are start (white) and stop (dark gray). 55 .. image:: ../images/riboplot.png
53 56
54 .. image:: ../images/riboplot.png 57 2. RiboSeq read counts (CSV)
55 58 ++++++++++++++++++++++++++++
56 2. RiboSeq read counts in 3 frames for each position in the transcript (CSV) 59 In 3 frames for each position in the transcript.
57 60
58 61
59 Command line 62 Command line
60 ............ 63 ............
61 ``riboplot`` can also be run on the command line. The usage is :: 64 ``riboplot`` can also be run on the command line. The usage is ::
62 65
63 usage: python riboplot.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT 66 usage: riboplot [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT
64 [-n RNA_FILE] [-l INTEGER] [-s INTEGER] [-m HTML_FILE] 67 [-n RNA_FILE] [-l INTEGER] [-s INTEGER] [-m HTML_FILE]
65 [-o OUTPUT_PATH] [-d] 68 [-o OUTPUT_PATH] [-d]
66 69
67 Plot and output read counts for a single transcript 70 Plot and output read counts for a single transcript
68 71
103 Output read counts for all transcripts in an alignment. 106 Output read counts for all transcripts in an alignment.
104 107
105 Parameters 108 Parameters
106 .......... 109 ..........
107 1. Ribo-Seq alignment file (Sorted BAM file) 110 1. Ribo-Seq alignment file (Sorted BAM file)
111 ++++++++++++++++++++++++++++++++++++++++++++
112 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
113 file should be sorted. This can be done using one of the following methods.
108 114
109 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM 115 1. RiboGalaxy_ -> Sort Data -> Sort BAM dataset.
110 file should be sorted. This can be done using one of the following methods. 116 2. ``samtools sort input.bam inputsorted``
111
112 1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
113 2. ``samtools sort input.bam inputsorted``
114 117
115 2. Transcriptome (FASTA) 118 2. Transcriptome (FASTA)
116 119 ++++++++++++++++++++++++
117 A FASTA format file with sequences of the transcripts. 120 A FASTA format file with sequences of the transcripts.
118 121
119 3. Read lengths to consider [optional] (Integer - 0 or greater) 122 3. Read lengths to consider [optional] (Integer - 0 or greater)
120 123 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
121 If this option is provided, only Ribo-Seq data of the given length is considered. 124 If this option is provided, only Ribo-Seq data of the given length is considered.
122 125
123 4. Offset [optional] (Integer - 0 or greater) 126 4. Offset [optional] (Integer - 0 or greater)
124 127 +++++++++++++++++++++++++++++++++++++++++++++
125 If this option is provided, this offset is added to the read alignment positions. 128 If this option is provided, this offset is added to the read alignment positions.
126 129
127 Output 130 Output
128 ...... 131 ......
129 Read counts for all transcripts in the alignment (ZIP) 132 Read counts for all transcripts in the alignment (ZIP)
130 133 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
131 The output file ``ribocount_output.zip`` should first be uncompressed. This will generate 134 The output file ``ribocount_output.zip`` should first be uncompressed. This will generate
132 a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount. 135 a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount.
133 136
134 Total reads for each transcript will be displayed in a table along with the name of the transcript and a link 137 Total reads for each transcript will be displayed in a table along with the name of the transcript and a link
135 to the CSV file containing the read counts in 3 frames for each position in the transcript. 138 to the CSV file containing the read counts in 3 frames for each position in the transcript.
138 141
139 Command line 142 Command line
140 ............ 143 ............
141 ``ribocount`` can also be run on the command line. The usage is :: 144 ``ribocount`` can also be run on the command line. The usage is ::
142 145
143 usage: python ribocount.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER] 146 usage: ribocount [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER]
144 [-s INTEGER] [-m HTML_FILE] [-o OUTPUT_PATH] [-d] 147 [-s INTEGER] [-m HTML_FILE] [-o OUTPUT_PATH] [-d]
145 148
146 Output read counts for all transcripts 149 Output read counts for all transcripts
147 150
148 optional arguments: 151 optional arguments:
170 Ribo-Seq alignment file in BAM format 173 Ribo-Seq alignment file in BAM format
171 174
172 -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA 175 -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA
173 FASTA format file of the transcriptome 176 FASTA format file of the transcriptome
174 177
178 .. links
179 .. _RiboGalaxy: http://ribogalaxy.ucc.ie
180