replace loop variable in system shell command of ipython

Question

I would like to iterate through a list (of sample names) and repeat the same command for each sample using the system shell command of ipython ("!"). I have done this previously with no problem but keep getting a SyntaxError under this specific code. If you know what is wrong please let me know - thank you!

Here is the sample code (in reality there are more samples):

samples = ["ERR007200", "ERR007204", "ERR007208"]
def remove_ambMap():
    !samtools view -q 20 -b home/pathToFile/{samp}.realn.bam | samtools sort - {samp}
for samp in samples:
    remove_ambMap()

Note that samtools is a program that is in the $PATH and that if I perform the command specifying the path of the file it works - sorry this will not be reproducible as you need to have the program installed and these are massive genomic files - I am hoping someone might be able to spot what is wrong!

Can you post the SyntaxError? The same code (replacing samtools with various bash built-ins) works for me. — jedwards
– jedwards, Commented Mar 9, 2015 at 20:44
Sure @jedwards: !samtools view -q 20 -b /home/tmsmith/data/expEvo/RGA/RGAbams/Bais/{samp}.realn.bam | samtools sort - {samp} ^ SyntaxError: invalid syntax — ONeillMB1
– ONeillMB1, Commented Mar 9, 2015 at 20:47
I've had it work for other programs in the past, perhaps it is just something specific to this program — ONeillMB1
– ONeillMB1, Commented Mar 9, 2015 at 20:48

Antti Haapala · Accepted Answer · 2015-03-09 20:59:27Z

1

For this kind of task you'd use to use the subprocess module; the easiest would be to use the call method with shell=True:

from subprocess import call

def remove_ambMap(samp):
    call('samtools view -q 20 -b home/pathToFile/{samp}.realn.bam '
         '| samtools sort - {samp}'.format(samp=samp), shell=True)

for samp in samples:
    remove_ambMap(samp)

answered Mar 9, 2015 at 20:59

Antti Haapala

135k23 gold badges297 silver badges349 bronze badges

Sign up to request clarification or add additional context in comments.

1 Comment

ONeillMB1 Over a year ago

Thank you! I was just wondering if taking out the ipython dependencies would solve the problem and it appears to do so.

Collectives™ on Stack Overflow

replace loop variable in system shell command of ipython

1 Answer 1

1 Comment

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

1 Comment

Your Answer

Sign up or log in

Post as a guest

Related