Tab Delimited Input
The CGView application and applet can read feature information from a tab delimited file. The file consists of the following lines:
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The # character followed by the name of the sequence. Optional.
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The % character followed by the length of the sequence. Required.
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The ! character followed by tab-separated names of the columns in your data file. Required.
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The tab-separated feature data in the same order as the named columns. Required.
The following column names and values are required:
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strand - whether the feature is on the forward or reverse strand.
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slot - an integer between 1 and 6 indicating which of the concentric feature rings should hold the feature.
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start - an integer between 1 and the length of the sequence.
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stop - an integer between 1 and the length of the sequence. The stop value should be greater than or equal to the start value regardless of the strand, unless the feature crosses the sequence start/end boundary.
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type - text indicating the type of feature. The following types are recognized: origin_of_replication, promoter, terminator, regulatory_sequence, unique_restriction_site, restriction_site, open_reading_frame, gene, predicted_gene, sequence_similarity, score, score_II, primer. The feature type determines how the feature is colored, and whether it is drawn as an arrow or an arc.
The following column names and values are optional:
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opacity - a real number between 0 and 1 indicating the opacity of the feature, with 1 being completely opaque. The default value is 1.
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thickness - a real number between 0 and 1 indicating what proportion of the slot thickness is occupied by the feature, with 1 being all the thickness. The default value is 1.
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radius - a real number between 0 and 1 indicating where in the slot the feature should be placed, with 1 being at the edge of the slot furthest from the center of the backbone circle. This value only has an effect when the thickness attribute is set to a value less than 1. Default value is 0.
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label - a text label for the feature. Shorter labels are better, because they are more likely to fit on the canvas.
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mouseover - text to appear at the bottom of the CGView applet, when the mouse pointer is placed over the feature label.
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hyperlink - a URL to access when the feature label is clicked. When creating an input file for use with the CGView applet, full URLs must be supplied (http://somesite.com/html/top.html as opposed to top.html for example).
If you include optional columns in your data file, any missing values under the optional columns should be marked using a dash (-) character.
An example input file is example_2_features.tab. Note that the multiple tabs can be used to separate values. However, the order of the values must match the order of the column names.
Citing CGView:
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Stothard P, Wishart DS. Circular genome visualization and exploration
using CGView. Bioinformatics 21:537-539.
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