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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