# HG changeset patch # User Vimalkumar Velayudhan # Date 1439803678 -3600 # Node ID 844eb8c36f32696cd3af04946f898baa64beabf1 # Parent 096c6bbf4a04a1693026c5b06fcd840295919566 Add help section in xml and update usage documentation diff -r 096c6bbf4a04 -r 844eb8c36f32 docs/conf.py --- a/docs/conf.py Thu Aug 13 15:03:20 2015 +0100 +++ b/docs/conf.py Mon Aug 17 10:27:58 2015 +0100 @@ -118,8 +118,8 @@ # documentation. #html_theme_options = {} html_theme_options = { - 'font_family': '"Open Sans", Ubuntu, sans-serif', - 'head_font_family': '"Open Sans", Ubuntu, sans-serif', + 'font_family': '"Source Sans Pro", Ubuntu, sans-serif', + 'head_font_family': 'Cabin, Ubuntu, sans-serif', 'code_font_family': '"Source Code Pro", "Ubuntu Mono", monospace', 'code_font_size': '0.8em', 'pre_bg': '#f9f9f9', 'note_bg': '#e6f7ff', 'note_border': '#ccefff', diff -r 096c6bbf4a04 -r 844eb8c36f32 docs/usage.rst --- a/docs/usage.rst Thu Aug 13 15:03:20 2015 +0100 +++ b/docs/usage.rst Mon Aug 17 10:27:58 2015 +0100 @@ -8,9 +8,165 @@ Parameters .......... -1. Ribo-Seq alignment file (sorted BAM) - A bowtie 1 +1. Ribo-Seq alignment file (Sorted BAM file) + + A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM + file should be sorted. This can be done using one of the following methods. + + 1. RiboGalaxy -> Sort Data -> Sort BAM dataset. + 2. ``samtools sort input.bam inputsorted`` + +2. Transcriptome (FASTA) + + A FASTA format file with sequences of the transcripts. + +3. Name of the transcript to plot (Text) + + The name of the transcript to plot **should** match the name in the transcriptome (FASTA) + and the Ribo-Seq/RNA-Seq alignment (BAM). + +4. RNA coverage [optional] (Sorted BAM file) + + If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage. + +5. Read lengths to consider [Optional] (Integer - 0 or greater) + + If this option is provided, only Ribo-Seq data of the given length is considered. + +6. Offset [optional] (Integer - 0 or greater) + + If this option is provided, this offset is added to the read alignment positions. + +Output +...... +1. Plots (PNG and SVG) + + Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue) + + RNA coverage as a gray background (if the RNA coverage option was selected). + + The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames. + + The color codes are start (white) and stop (dark gray). + + .. image:: ../images/riboplot.png + +2. RiboSeq read counts in 3 frames for each position in the transcript (CSV) + + +Command line +............ +``riboplot`` can also be run on the command line. The usage is :: + + usage: python riboplot.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT + [-n RNA_FILE] [-l INTEGER] [-s INTEGER] [-m HTML_FILE] + [-o OUTPUT_PATH] [-d] + + Plot and output read counts for a single transcript + + optional arguments: + -h, --help + show this help message and exit + + -n RNA_FILE, --rna_file RNA_FILE + RNA-Seq alignment file (BAM) + + -l INTEGER, --read_length INTEGER + Read length to consider (default: None) + + -s INTEGER, --read_offset INTEGER + Read offset (default: 0) + + -m HTML_FILE, --html_file HTML_FILE + Output file for results (HTML) + + -o OUTPUT_PATH, --output_path OUTPUT_PATH + Files are saved in this directory + + -d, --debug + Flag. Produce debug output + + required arguments: + -b RIBO_FILE, --ribo_file RIBO_FILE + Ribo-Seq alignment file in BAM format + + -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA + FASTA format file of the transcriptome + + -t TEXT, --transcript_name TEXT + Transcript name RiboCount --------- +Output read counts for all transcripts in an alignment. +Parameters +.......... +1. Ribo-Seq alignment file (Sorted BAM file) + + A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM + file should be sorted. This can be done using one of the following methods. + + 1. RiboGalaxy -> Sort Data -> Sort BAM dataset. + 2. ``samtools sort input.bam inputsorted`` + +2. Transcriptome (FASTA) + + A FASTA format file with sequences of the transcripts. + +3. Read lengths to consider [optional] (Integer - 0 or greater) + + If this option is provided, only Ribo-Seq data of the given length is considered. + +4. Offset [optional] (Integer - 0 or greater) + + If this option is provided, this offset is added to the read alignment positions. + +Output +...... +Read counts for all transcripts in the alignment (ZIP) + +The output file ``ribocount_output.zip`` should first be uncompressed. This will generate +a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount. + +Total reads for each transcript will be displayed in a table along with the name of the transcript and a link +to the CSV file containing the read counts in 3 frames for each position in the transcript. + +.. image:: ../images/ribocount.png + +Command line +............ +``ribocount`` can also be run on the command line. The usage is :: + + usage: python ribocount.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER] + [-s INTEGER] [-m HTML_FILE] [-o OUTPUT_PATH] [-d] + + Output read counts for all transcripts + + optional arguments: + + -h, --help show this help message and exit + + -l INTEGER, --read_length INTEGER + Read length to consider (default: None) + + -s INTEGER, --read_offset INTEGER + Read offset (default: 0) + + -m HTML_FILE, --html_file HTML_FILE + + Output file for results (HTML) + + -o OUTPUT_PATH, --output_path OUTPUT_PATH + Files are saved in this directory + + -d, --debug Flag. Produce debug output + + required arguments: + + -b RIBO_FILE, --ribo_file RIBO_FILE + Ribo-Seq alignment file in BAM format + + -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA + FASTA format file of the transcriptome + diff -r 096c6bbf4a04 -r 844eb8c36f32 ribocount.xml --- a/ribocount.xml Thu Aug 13 15:03:20 2015 +0100 +++ b/ribocount.xml Mon Aug 17 10:27:58 2015 +0100 @@ -26,5 +26,47 @@ +**RiboCount** + +Output read counts for all transcripts in an alignment. + +---- + +**Parameters** + +1. Ribo-Seq alignment file (Sorted BAM file) + + A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM + file should be sorted. This can be done using one of the following methods. + + 1. RiboGalaxy -> Sort Data -> Sort BAM dataset. + 2. ``samtools sort input.bam inputsorted`` + +2. Transcriptome (FASTA) + + A FASTA format file with sequences of the transcripts. + +3. Read lengths to consider [optional] (Integer - 0 or greater) + + If this option is provided, only Ribo-Seq data of the given length is considered. + +4. Offset [optional] (Integer - 0 or greater) + + If this option is provided, this offset is added to the read alignment positions. + +---- + +**Output** + +Read counts for all transcripts in the alignment (ZIP) + +The output file ``ribocount_output.zip`` should first be uncompressed. This will generate +a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount. + +Total reads for each transcript will be displayed in a table along with the name of the transcript and a link +to the CSV file containing the read counts in 3 frames for each position in the transcript. + +.. image:: images/ribocount.png + diff -r 096c6bbf4a04 -r 844eb8c36f32 riboplot.xml --- a/riboplot.xml Thu Aug 13 15:03:20 2015 +0100 +++ b/riboplot.xml Mon Aug 17 10:27:58 2015 +0100 @@ -50,5 +50,60 @@ +**RiboPlot** + +Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM). + +---- + +**Parameters** + +1. Ribo-Seq alignment file (Sorted BAM file) + + A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM + file should be sorted. This can be done using one of the following methods. + + 1. RiboGalaxy -> Sort Data -> Sort BAM dataset. + 2. ``samtools sort input.bam inputsorted`` + +2. Transcriptome (FASTA) + + A FASTA format file with sequences of the transcripts. + +3. Name of the transcript to plot (Text) + + The name of the transcript to plot **should** match the name in the transcriptome (FASTA) + and the Ribo-Seq/RNA-Seq alignment (BAM). + +4. RNA coverage [optional] (Sorted BAM file) + + If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage. + +5. Read lengths to consider [Optional] (Integer - 0 or greater) + + If this option is provided, only Ribo-Seq data of the given length is considered. + +6. Offset [optional] (Integer - 0 or greater) + + If this option is provided, this offset is added to the read alignment positions. + +---- + +**Output** + +1. Plots (PNG and SVG) + + Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue) + + RNA coverage as a gray background (if the RNA coverage option was selected). + + The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames. + + The color codes are start (white) and stop (dark gray). + + .. image:: images/riboplot.png + +2. RiboSeq read counts in 3 frames for each position in the transcript (CSV) +