supported to run ROSE2 in python3 environment #67
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jdimatteo
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jdimatteo
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Overall changes look good to me -- thank you for taking the time to update this code to python3.
Are there any tests for ROSE2 that were run to ensure this doesn't break things or have significant negative effects on performance?
I'm very sorry that this wasn't reviewed sooner. Also, I'm not very familiar with the ROSE2 code. If you are interested in becoming a contributor on this repository to help maintenance of ROSE2, please let me know.
| import os | ||
| import subprocess | ||
| from string import join | ||
| # from string import join |
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Please delete code instead of commenting it out.
| pass | ||
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| from string import join, maketrans | ||
| # from string import join, maketrans |
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please delete code instead of commenting it out
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| # get the ID and convert to name | ||
| closestGene = startDict[allEnhancerGenes[distList.index(min(distList))]]['name'] | ||
| except: |
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Do you want this to fail silently? Or give some meaningful message to the user? Or catch a specific kind of error that you expect?
| idxStats= idxStats.communicate() | ||
| bamChromList = [line.split('\t')[0] for line in idxStats[0].split('\n')[0:-2]] | ||
| idxStats = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True, | ||
| universal_newlines=True).communicate()[0] |
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Generally it's not good practice to use shell=True, but probably for a small scientific pipeline this would be okay. Here is an example of not using shell=True: https://github.com/HPC-buildtest/buildtest-framework/blob/devel/buildtest/utils/command.py#L55
| marker = idfun(item) | ||
| # in old Python versions: | ||
| # if seen.has_key(marker) | ||
| # if marker in seen |
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Is this necessary to keep since it's commented out?
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@gauravj49 I suspect you'll need to rebase with master so that the fixes to the testing are present (and we can test your changes as well!) |
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Hi all,
Just want to make sure you're connected with Jost who has been maintaining
ROSE2 for our lab.
Thanks for all of the work on bamliquidator!
…-Charles
Charles Y. Lin
On Wed, Mar 18, 2020 at 12:16 PM Vanessasaurus ***@***.***> wrote:
@gauravj49 <https://github.com/gauravj49> I suspect you'll need to rebase
with master so that the fixes to the testing are present (and we can test
your changes as well!)
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