Comments for Bioinfo Blog!

Comment on Come trasformare vim in un ambiente di sviluppo per python by Aron

Aron — Tue, 08 Sep 2009 12:13:33 +0000

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Comment on Come trasformare vim in un ambiente di sviluppo per python by Bill

Bill — Mon, 07 Sep 2009 03:12:16 +0000

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Comment on Come trasformare vim in un ambiente di sviluppo per python by Bill

Bill — Sat, 05 Sep 2009 09:28:39 +0000

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Comment on ruffus, a tool to write scientific pipelines in python by Paulo

Paulo — Thu, 18 Jun 2009 00:37:15 +0000

The patch seems fine.

Comment on ruffus, a tool to write scientific pipelines in python by admin

admin — Sun, 14 Jun 2009 12:41:46 +0000

Hi Thomas,
I don’t know for sure, but I think you can do anything you can do in python.

Probably you can use the glob.glob function, and then the @parallel decorator.

Anyway, the authors of the tool are around here, they reply quickly to bug reports, and the tool is open source; so if there is something which can be improved, I am pretty confident they will implement it.

Comment on a parser for KEGG pathways in python by Simon Cockell

Simon Cockell — Fri, 12 Jun 2009 20:39:50 +0000

I’ve suggested this in reply to your comment on my blog, but thought I’d leave it here too. Have you tried cElementTree, rather than ElementTree in your code? It is in the standard libraries (since 2.5), but is MUCH faster than ElementTree. It is also completely synonymous, so the only thing you’d have to change in your code is the import statement.
i.e.
import xml.etree.ElementTree as ET
becomes:
import xml.etree.cElementTree as ET

Comment on a parser for KEGG pathways in python by Simon Cockell | This week in links #1 | Fuzzier Logic

Simon Cockell | This week in links #1 | Fuzzier Logic — Fri, 12 Jun 2009 16:39:02 +0000

[...] Parsing KEGG in Python [...]

Comment on ruffus, a tool to write scientific pipelines in python by Thomas Mailund

Thomas Mailund — Fri, 12 Jun 2009 05:13:01 +0000

Sounds like something I should have a look at.

Is it possible to specify “wild card” files like in Make, do you know?

I mean, I have some pipelines where I produce files from my input, but the number of files depend on the input — essentially I split large input into smaller job for parallel processing — and I then need to process each file as a job.

In make (at least gmake) I can do something like

foo: *.suffix
process $?
touch foo

although with a bit of hacking to then collect the results in a single table afterwards…

Comment on a parser for KEGG pathways in python by João Rodrigues

João Rodrigues — Mon, 08 Jun 2009 23:16:05 +0000

Regarding SOAPpy and KEGG, I have used it in one of my projects behind an http proxy. Email me if you want to have a look at the code anaryin [at] gmail [dot] com

Nice idea with this parser, keep up the good work!

Comment on ruffus, a tool to write scientific pipelines in python by admin

admin — Fri, 05 Jun 2009 14:58:29 +0000

hi Paulo,
I see, I have the same issue in this computer.

Have you tried the patch posted in this bug report?
- http://code.google.com/p/ruffus/issues/detail?id=1