Converting Ensembl ID to gene symbol

thomaster has asked for the wisdom of the Perl Monks concerning the following question:

Hello, I'm trying to simply convert an Ensembl ID to a uniprot gene symbol. I've been trying to find something for this but it's like finding a needle in a haystack. I think I should use $gene->external_name() from the BioMart API, but I'm not sure how to correctly incorporate this in my script (which modules to use, what elements are needed etc). I need this because I have hundreds of files with RNAseq data and for each file I remove the unexpressed genes. In the resulting list of expressed genes, there are a lot of pseudogenes, which I do not need. When I convert the Ensembl ID to gene name, the actual genes (with a gene symbol) can be easily extracted. I can do this conversion with biomart or some other tool but that's too much work for hunderds of files. That's why I need a simple function in my script to convert the ID in each line to gene symbol, and insert it in the next column. Does anyone have an idea how to do this? Thanks in advance.

Comment on Converting Ensembl ID to gene symbol

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Re: Converting Ensembl ID to gene symbol by choroba (Cardinal) on Feb 23, 2016 at 15:57 UTC
Most people here are not bioinformaticians. I have no idea what your're asking even after having solved 249 tasks at Rosalind.info. Can you show a sample of the input data, link to the API you want to use, and basically describe the task as you'd do it to a five years old? ($q=q:Sq=~/;[c](.)(.)/;chr(-\|\|-\|5+lengthSq)`"S\|oS2"`map{chr \|+ord }map{substrSq`S_+\|`\|}3E\|-\|`7**2-3:)=~y+S\|`+$1,++print+eval$q,q,a, [download]	[reply] [d/l]
Re: Converting Ensembl ID to gene symbol by FreeBeerReekingMonk (Deacon) on Feb 23, 2016 at 18:49 UTC
Maybe collect all your Ensembl ID's in a list, then use this webpage http://www.uniprot.org/uploadlists/ to upload your file, convert them to uniprot, then save the output. With this output, you can now process the conversion?	[reply]