Please download:

Count lines in files or in standard input

import sys

def counter(source):
    count = 0
    for line in source:
        count += 1
    return count

filenames = sys.argv[1:]
if len(filenames) == 0:
    print 'STDIN', counter(sys.stdin)
else:
    for filename in filenames:
        reader = open(filename, 'r')
        count = counter(reader)
        print filename, count

Count marlins in each file in turn

# Count marlins in each data file.
for filename in $*
do
   grep marlin $filename |\
   wc -l
done

Count by date

echo '# count-by-date.sh' $*
grep -h -v '#' $* | \
grep -v Species | \
cut -d ',' -f 1 | \
sort | \
uniq -c

Count marlins using Python

my_file = file('fish.txt', 'r')
sum = 0
for line in my_file:
    if 'marlin' in line:
        date, species, count = line.split(',')
        sum += int(count)
print sum

Information: Since 1998, Software Carpentry has taught scientists and engineers the skills and tools they need to use computing more productively. Thanks to a grant from the Sloan Foundation, we are running a two-day boot camp Utah State University, followed by an optional 4-8 weeks of self-paced online learning. The boot camp covers the core skills a researcher needs to know in order to be productive in a small team:

• Using the shell to do more in less time
• Using version control to manage and share information
• Basic Python programming
• How (and how much) to test programs
• Working with relational databas

The online follow-up goes into these topics in more detail, and also touch on program design and construction, matrix programming, using spreadsheets in a disciplined way, data management, and software development lifecycles.

In collaboration with Ethan White's lab in the Department of Biology we will be offering the boot camp at Utah State on the weekend of April 14th and 15th. The boot camp is free, you just need to bring a laptop and commit to spending 2 days learning about how to be a better scientific programmer. Space is limited and signups are on a first come first serve basis.

For more information, please see http://software-carpentry.org, or contact us by email at . You can also feel free to email Ethan (ethan.white@usu.edu) with any questions.