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Add help section in xml and update usage documentation
author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Mon, 17 Aug 2015 10:27:58 +0100
parents 096c6bbf4a04
children 8964641b04ef
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1 ========
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2 Usage
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3 ========
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4
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5 RiboPlot
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6 --------
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7 Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM).
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8
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9 Parameters
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10 ..........
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11 1. Ribo-Seq alignment file (Sorted BAM file)
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12
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13 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
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14 file should be sorted. This can be done using one of the following methods.
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15
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16 1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
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17 2. ``samtools sort input.bam inputsorted``
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18
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19 2. Transcriptome (FASTA)
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20
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21 A FASTA format file with sequences of the transcripts.
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22
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23 3. Name of the transcript to plot (Text)
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24
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25 The name of the transcript to plot **should** match the name in the transcriptome (FASTA)
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26 and the Ribo-Seq/RNA-Seq alignment (BAM).
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27
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28 4. RNA coverage [optional] (Sorted BAM file)
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29
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30 If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage.
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31
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32 5. Read lengths to consider [Optional] (Integer - 0 or greater)
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33
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34 If this option is provided, only Ribo-Seq data of the given length is considered.
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35
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36 6. Offset [optional] (Integer - 0 or greater)
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37
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38 If this option is provided, this offset is added to the read alignment positions.
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39
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40 Output
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41 ......
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42 1. Plots (PNG and SVG)
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43
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44 Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue)
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45
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46 RNA coverage as a gray background (if the RNA coverage option was selected).
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47
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48 The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames.
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49
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50 The color codes are start (white) and stop (dark gray).
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51
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52 .. image:: ../images/riboplot.png
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53
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54 2. RiboSeq read counts in 3 frames for each position in the transcript (CSV)
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55
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56
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57 Command line
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58 ............
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59 ``riboplot`` can also be run on the command line. The usage is ::
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60
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61 usage: python riboplot.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT
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62 [-n RNA_FILE] [-l INTEGER] [-s INTEGER] [-m HTML_FILE]
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63 [-o OUTPUT_PATH] [-d]
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64
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65 Plot and output read counts for a single transcript
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66
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67 optional arguments:
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68 -h, --help
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69 show this help message and exit
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70
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71 -n RNA_FILE, --rna_file RNA_FILE
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72 RNA-Seq alignment file (BAM)
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73
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74 -l INTEGER, --read_length INTEGER
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75 Read length to consider (default: None)
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76
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77 -s INTEGER, --read_offset INTEGER
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78 Read offset (default: 0)
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79
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80 -m HTML_FILE, --html_file HTML_FILE
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81 Output file for results (HTML)
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82
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83 -o OUTPUT_PATH, --output_path OUTPUT_PATH
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84 Files are saved in this directory
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85
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86 -d, --debug
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87 Flag. Produce debug output
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88
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89 required arguments:
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90 -b RIBO_FILE, --ribo_file RIBO_FILE
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91 Ribo-Seq alignment file in BAM format
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92
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93 -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA
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94 FASTA format file of the transcriptome
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95
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96 -t TEXT, --transcript_name TEXT
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97 Transcript name
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98
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99 RiboCount
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100 ---------
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101 Output read counts for all transcripts in an alignment.
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102
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103 Parameters
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104 ..........
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105 1. Ribo-Seq alignment file (Sorted BAM file)
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106
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107 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
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108 file should be sorted. This can be done using one of the following methods.
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109
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110 1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
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111 2. ``samtools sort input.bam inputsorted``
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112
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113 2. Transcriptome (FASTA)
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114
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115 A FASTA format file with sequences of the transcripts.
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116
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117 3. Read lengths to consider [optional] (Integer - 0 or greater)
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118
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119 If this option is provided, only Ribo-Seq data of the given length is considered.
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120
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121 4. Offset [optional] (Integer - 0 or greater)
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122
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123 If this option is provided, this offset is added to the read alignment positions.
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124
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125 Output
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126 ......
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127 Read counts for all transcripts in the alignment (ZIP)
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128
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129 The output file ``ribocount_output.zip`` should first be uncompressed. This will generate
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130 a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount.
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131
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132 Total reads for each transcript will be displayed in a table along with the name of the transcript and a link
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133 to the CSV file containing the read counts in 3 frames for each position in the transcript.
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134
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135 .. image:: ../images/ribocount.png
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136
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137 Command line
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138 ............
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139 ``ribocount`` can also be run on the command line. The usage is ::
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140
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141 usage: python ribocount.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER]
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142 [-s INTEGER] [-m HTML_FILE] [-o OUTPUT_PATH] [-d]
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143
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144 Output read counts for all transcripts
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145
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146 optional arguments:
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147
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148 -h, --help show this help message and exit
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149
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150 -l INTEGER, --read_length INTEGER
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151 Read length to consider (default: None)
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152
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153 -s INTEGER, --read_offset INTEGER
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154 Read offset (default: 0)
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155
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156 -m HTML_FILE, --html_file HTML_FILE
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157
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158 Output file for results (HTML)
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159
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160 -o OUTPUT_PATH, --output_path OUTPUT_PATH
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161 Files are saved in this directory
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162
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163 -d, --debug Flag. Produce debug output
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164
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165 required arguments:
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166
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167 -b RIBO_FILE, --ribo_file RIBO_FILE
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168 Ribo-Seq alignment file in BAM format
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169
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170 -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA
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171 FASTA format file of the transcriptome
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172