linux · science –
As I’ve been working to get some results done for my Ph.D. thesis, I’ve stumbled across the problem of having different data obtained through different software. Even if it’s just a matter of text files, the fields are all different and even if dealing with the same data, trying to infer relationships is a pain.
Therefore I decided to create a small database to host the data of my work and query it accordingly. I didn’t want to run a database server, so I settled for SQLite, a lightweight file-driven database, I don’t handle enormous amount of data so it should be ok. Up to now I’ve inserted parts of the Entrez Gene database. First of all I downloaded the gene_info.gz from NCBI’s FTP, which contains data such as gene name, gene symbol, and so on. Then it was a matter of filtering out non-human entries, and to do so I wrote a small script called taxon_filter.py:
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anime –
It seems I can’t quite keep up with the episodes given my limited spare time (considering also I have the second book of The S.T.E.A.L. Saga to take care of), so here I am with a recap of the last two episodes of Maho Shojo Lyrical Nanoha StrikerS.
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linux –
[code lang=”bash”]
lb@hardin:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 7.04
Release: 7.04
Codename: feisty
[/code]
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linux –
I just read on Slashdot that the famous RMS has now sung something against the prisoners in Guantanamo Bay (no link, I’m not giving it hits). All this while being in Cuba, for all heavens, that’s not even remotely a democracy. I don’t deny the fact that that place may have been ground for abuses, but I find it hypocritical that RMS did that in a place where people are imprisoned on a whim and human rights are not upheld constantly.
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linux · science –
I’ve again seen how useful and powerful Python can be. The other day I had to prepare an Excel spreadsheet (sadly) which among other things needed to contain links to the GeneCards database for each gene listed. There were more than 2900 genes listed, so adding links by hand would have been suicidal.
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anime –
Ok, I so _tried to keep separate posts for each series I watched. But there are _so many, it’s impossible to keep up! (including also my limited time to write). I’ll just present them in reduced form here, along with a few comments.
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science –
This post sums up my frustration in trying to use Python for my daily work. Like Perl and Ruby, it has its own Bio version to deal with biological data. However, the current implementation leaves a lot to be desired. A lot of stuff that doesn’t deal with sequence analysis, even for simple tasks such as fetching annotations from Entrez Gene, is missing (but present in Bioperl, for example). Also, documentation for some modules is lacking or non-existant (why keeping a parser for Affymetrix CEL files when there are no information on how to use it, let alone know which formats does it support?). Basically, maintenance is good for everything related to sequence analysis… the rest is somewhat in slumber.
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