Heather (and everyone),
On Oct 14, 2011, at 8:22 PM, Heather Lintz wrote:
> Hi Pythonistas,
>
> I am a Corvallis ghost member of your group. My name is Heather. I am also
> an ecologist working on climate change topics. I program all the time in
> MATLAB, and less often in R and Python. So far, I have only used Python to
> do some ArcGIS tasks using the ArcGIS library in Python (and some other
> basic libraries too). However, I now have a couple somewhat hefty new
> projects I would like to accomplish in Python. I was wondering if there is a
> good time/place to catch some of you and talk about some potential
> Python tutoring with these tasks in mind. I already have some experience
> with the language (for example, I posted some of my code below that I wrote
> awhile and forgot about). Is the monthly meet-up a good place for this?
> You seem to have agendas for those meetings perhaps?
>
> Here are the projects I have in mind that I would like to work on:
>
> 1. Code a statistical algorithm and divide and delegate computation tasks to
> multiple processors on a Linux system. The processors would each generate
> results and the results would be pooled for an optimization.
>
> 2. Import RNA Seq data generated from the Illumina High Seq 2000 and learn
> how to manipulate INSANELY large bioinformatics/genomics data sets. I
> especially like
> to do statistics on such data (things that I normally do in MATLAB).
> But this time it would be treating the INSANELY LARGE AMOUNT of data as a
> matrix to manipulate it, etc. in Python.
>
> I'd like to come up twice a month for Python 'tutoring' to get these
> projects accomplished and learn Python better. There's nothing like wisdom
> from other programmers to help. Would this interest any of you? Can you
> recommend someone in your group that is great at
> scientific-python-programming-teaching challenges?
>
> Many thanks,
> Heather
>
>
> P.s. Here's my previous dinky Python code that I already forgot about. It's
> the max of my ability.
>
> ########################
> # Import system modules
> ########################
>
> import sys, string, os, arcgisscripting, copy, glob, linecache, csv from
> quantile import quantile
>
> # Create the Geoprocessor
> gp = arcgisscripting.create()
> gp.overwriteoutput = 1
>
> ####################################################################
> #READ DATA FROM EACH ASC FILE AND CALCULATE QUANTILES FROM EACH FILE
> ####################################################################
>
> q1=[]
> q2=[]
> q3=[]
>
> os.chdir(ascDIR)
> runlist=os.listdir(ascDIR)
> print repr(runlist)
> print len(runlist)
> for file in runlist:
> print repr(file)
> gq=[]
> x=open(file,'r')
> for i in xrange(6):
> x.readline()
> z= x.readline()
> while z != '':
> z=z.strip().split()
> for num in z:
> num=float(num)
> if num > -1:
> gq.append(num)
> z= x.readline()
> a=quantile(gq, .25, qtype = 7, issorted = False)
> #print a
> b=quantile(gq, .5, qtype = 7, issorted = False)
> c=quantile(gq, .75, qtype = 7, issorted = False)
> q1.append(a)
> q2.append(b)
> q3.append(c)
> print len(q1), len(q2), len(q3)
>
> outfile = open("outfile.txt", "w")
> for i in xrange(len(q1)):
> outfile.write("%12.3e%12.3e%12.3e\n" % (q1[i], q2[i], q3[i]))
> outfile.close()
>
> outfile = open("outfilezones.txt", "w")
> for i in xrange(len(q1)):
> outfile.write(runlist)
> outfile.close()
>
>
>
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This is a really awesome question.
There are a few hack-nights around town that aren't oriented around a specific
language that you could attend. Check: http://calagator.org/
I'm not aware of a regular Python tutoring/workshop style meeting (maybe
someone else is). However, I would be very interested in participating in and
helping to organize such a meeting.
As for your particular problem, I haven't done any scientific computing, but I
can share my experience using Python for web development. Maybe there is some
technology crossover (message queues, or even just your database layer? Oops, I
dunno, I'm not a scientist!).
Anyway, "large bioinformatics/genomics data"? Sounds awesome!
Best,
Andrew
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