[2] | 1 | <tool id="gtf2bedgraph" name="GTF-to-BEDGraph"> |
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| 2 | <description>converter</description> |
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| 3 | <command interpreter="python">gtf_to_bedgraph_converter.py $input $out_file1 $attribute_name</command> |
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| 4 | <inputs> |
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| 5 | <param format="gtf" name="input" type="data" label="Convert this query"/> |
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| 6 | <param name="attribute_name" type="text" label="Attribute to Use for Value"/> |
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| 7 | </inputs> |
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| 8 | <outputs> |
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| 9 | <data format="bedgraph" name="out_file1" /> |
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| 10 | </outputs> |
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| 11 | <tests> |
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| 12 | <test> |
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| 13 | <param name="input" value="gtf2bedgraph_in.gtf" ftype="gtf"/> |
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| 14 | <param name="attribute_name" value="FPKM"/> |
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| 15 | <output name="out_file1" file="gtf2bedgraph_out.bedgraph" ftype="bedgraph"/> |
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| 16 | </test> |
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| 17 | </tests> |
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| 18 | <help> |
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| 19 | |
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| 20 | **What it does** |
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| 21 | |
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| 22 | This tool converts data from GTF format to BEDGraph format (scroll down for format description). |
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| 23 | |
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| 24 | -------- |
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| 25 | |
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| 26 | **Example** |
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| 27 | |
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| 28 | The following data in GFF format:: |
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| 29 | |
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| 30 | chr22 GeneA enhancer 10000000 10001000 500 + . gene_id "GeneA"; transcript_id "TranscriptAlpha"; FPKM "2.75"; frac "1.000000"; |
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| 31 | chr22 GeneA promoter 10010000 10010100 900 + . gene_id "GeneA"; transcript_id "TranscriptsAlpha"; FPKM "2.25"; frac "1.000000"; |
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| 32 | |
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| 33 | using the attribute name 'FPKM' will be converted to BEDGraph (**note** that 1 is subtracted from the start coordinate):: |
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| 34 | |
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| 35 | |
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| 36 | chr22 9999999 10001000 2.75 |
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| 37 | chr22 10009999 10010100 2.25 |
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| 38 | |
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| 39 | ------ |
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| 40 | |
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| 41 | .. class:: infomark |
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| 42 | |
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| 43 | **About formats** |
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| 44 | |
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| 45 | **GTF format** Gene Transfer Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GTF lines have nine tab-separated fields:: |
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| 46 | |
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| 47 | 1. seqname - Must be a chromosome or scaffold. |
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| 48 | 2. source - The program that generated this feature. |
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| 49 | 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon". |
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| 50 | 4. start - The starting position of the feature in the sequence. The first base is numbered 1. |
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| 51 | 5. end - The ending position of the feature (inclusive). |
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| 52 | 6. score - A score between 0 and 1000. If there is no score value, enter ".". |
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| 53 | 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). |
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| 54 | 8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'. |
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| 55 | 9. group - The group field is a list of attributes. Each attribute consists of a type/value pair. Attributes must end in a semi-colon, and be separated from any following attribute by exactly one space. The attribute list must begin with the two mandatory attributes: (i) gene_id value - A globally unique identifier for the genomic source of the sequence and (ii) transcript_id value - A globally unique identifier for the predicted transcript. |
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| 56 | |
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| 57 | **BEDGraph format** |
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| 58 | |
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| 59 | The bedGraph format is line-oriented. Bedgraph data are preceeded by a track definition line, which adds a number of options for controlling the default display of this track. |
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| 60 | |
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| 61 | For the track definition line, all options are placed in a single line separated by spaces: |
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| 62 | track type=bedGraph name=track_label description=center_label |
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| 63 | visibility=display_mode color=r,g,b altColor=r,g,b |
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| 64 | priority=priority autoScale=on|off alwaysZero=on|off |
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| 65 | gridDefault=on|off maxHeightPixels=max:default:min |
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| 66 | graphType=bar|points viewLimits=lower:upper |
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| 67 | yLineMark=real-value yLineOnOff=on|off |
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| 68 | windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16 |
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| 69 | |
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| 70 | The track type is REQUIRED, and must be bedGraph: |
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| 71 | type=bedGraph |
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| 72 | |
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| 73 | Following the track definition line are the track data in four column BED format:: |
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| 74 | |
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| 75 | chromA chromStartA chromEndA dataValueA |
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| 76 | chromB chromStartB chromEndB dataValueB |
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| 77 | |
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| 78 | </help> |
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| 79 | </tool> |
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