Luca Beltrame
64b24842b8
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22 lines
1.2 KiB
Markdown
22 lines
1.2 KiB
Markdown
---
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author: einar
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categories:
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- General
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- Linux
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- Science
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comments: true
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date: "2006-11-25T09:06:10Z"
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header:
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image_fullwidth: banner_other.jpg
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slug: a-simple-annotator
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title: 'A simple annotator '
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omit_header_text: true
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disable_share: true
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wordpress_id: 132
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---
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In the past two days I've written a simple annotator program, that given an input list of RefSeq genes, automatically determines the relevant Entrez Gene IDs and annotates them using the flat files provided by the [NCBI](http://www.ncbi.nlm.nih.gov). A direct conversion was not possible due to limitations in Biopython's parsers, but I managed to use the GenBank parser to identify and extract the references to the Gene IDs (and putting them in a list).
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Once that had been done, I created a series of dictionaries when reading the annotation file, for data such as gene name, symbol, chromosome and cytoband. Using the list I already obtained, it was easy to create a new file with the required fields.
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During this process I learnt somewhat more about how to play with iterators to skip headings and so on. The code is not yet sufficiently generic, but once I finish toying with it, I may publish it for "general" (assuming anyone would use it) consumption, under GPL v2.
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