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content/post/2007-03-13-a-bed-file-builder.markdown

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+---
+author: einar
+categories:
+- Linux
+- Science
+comments: true
+date: "2007-03-13T20:00:17Z"
+header:
+  image_fullwidth: banner_other.jpg
+slug: a-bed-file-builder
+title: A BED file builder
+disable_share: true
+wordpress_id: 196
+---
+
+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:
+
+<!--more-->
+
+`usage: make_bed_file.py [options] [destination]`
+
+`options:
+-h, --help            show this help message and exit
+-i FILE, --input=FILE
+Use ranges from FILE
+-n NAME, --name=NAME  Use NAME as BED track name
+-t TYPE, --tracks=TYPE
+Format other annotation tracks according to TYPE
+(default: pack)
+-v TYPE, --visibility=TYPE
+Set visibility of the BED track to TYPE
+(default: full)
+-d DISPLAY, --display=DISPLAY
+Select specific annotation tracks
+(comma-delimited list; default: all)`
+
+The input file format is rather simple as well:
+
+Chromosome | Identifier | Start Position | End position | Score
+
+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.
+
+[Get the script]({{ site.url }}/files/make_bed_file.py) and make it executable. If you have any problems, please report.