41 lines
1.6 KiB
Markdown
41 lines
1.6 KiB
Markdown
---
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author: einar
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comments: true
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date: 2007-03-13 20:00:17+00:00
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layout: page
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slug: a-bed-file-builder
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title: A BED file builder
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wordpress_id: 196
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categories:
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- Linux
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- Science
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---
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As I anticipated, I can finally release this small script. Its purpose is to build [BED files](http://http//genome.ucsc.edu/goldenPath/help/customTrack.html#BED) out of tab-delimited text files. I made this because I had several files to make and moving columns left and right (not to mention writing a heading line for the [Genome Browser](http://genome.ucsc.edu)) was becoming annoying. Its use is fairly straightforward, as the help itself says:
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<!-- more -->
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`usage: make_bed_file.py [options] [destination]`
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`options:
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-h, --help show this help message and exit
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-i FILE, --input=FILE
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Use ranges from FILE
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-n NAME, --name=NAME Use NAME as BED track name
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-t TYPE, --tracks=TYPE
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Format other annotation tracks according to TYPE
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(default: pack)
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-v TYPE, --visibility=TYPE
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Set visibility of the BED track to TYPE
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(default: full)
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-d DISPLAY, --display=DISPLAY
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Select specific annotation tracks
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(comma-delimited list; default: all)`
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The input file format is rather simple as well:
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Chromosome | Identifier | Start Position | End position | Score
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The score column is optional. The file must be tab-delimited. If you want to change the format of the file, have a look at the ncbi class inside the source. The result is a BED file with chromosome, position, name and score.
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[Get the script]({{ site.url }}/files/make_bed_file.py) and make it executable. If you have any problems, please report.
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