Chris Friedline cfriedline
cfriedline
/ diginorm_renamer.ipynb
Created
October 28, 2013 20:30
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| def run_diginorm_renamer(args): | |
| from Bio.SeqIO.QualityIO import FastqGeneralIterator | |
| infile, outfile = args | |
| with open(outfile, "w") as o: | |
| for i, (name, seq, qual) in enumerate(FastqGeneralIterator(open(infile))): | |
| add = 1 | |
| if i % 2 != 0: | |
| add = 2 | |
| o.write("@%s_%d\n%s\n+\n%s\n" % (name, add, seq, qual)) | |
| if i % 100000 == 0: |
cfriedline
/ gist:7138580
Last active
December 26, 2015 10:39
Poor man's IPython notebook manager, now that there's multidir. Put this into a new notebook, assumes that all notebooks are under a common directory, albeit in their own directories. Should help (me) with git.
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| manager_name = 'Manager.ipynb' | |
| import os | |
| from IPython.display import FileLink, FileLinks, display, HTML, display_html | |
| notebooks = !find . | grep .ipynb$ | grep -v checkpoint | |
| notebooks = sorted(notebooks) | |
| root_dir = [os.path.dirname(os.path.abspath(x)) for x in notebooks if manager_name in x] | |
| paths = [] | |
| for n in notebooks: | |
| u = os.path.abspath(n).replace(root_dir[0], '/notebooks') | |
| display_html(HTML('<li><a href=%s target=_new>%s' % (u, u))) |
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