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• Changing the x-axis of seqlogo figures in matlab

  - by JudoWill

  I'm making a large number of seqlogos programatically. They are hundreds of columns wide and so running a seqlogo normally creates letters that are too thin to see. I've noticed that I only care about a few of these columns (not necessarily consecutive columns) ... most are noise but some are highly conserved. I use something like this snippet: conserve_cell = seqlogo(wide_seqs, 'displaylogo', false); high_bit_cols = any(conserve_cell{2}>1.0,1); [~, handle] = seqlogo(wide_seqs(:,high_bit_cols )); Although when I do this I lose the information about which columns the data came from. Normally I would just change the x-axis of the seqlogo. However, seqlogo's are some sort of crazy java-based object and calls like: set(handle, 'xticklabel', num2str(find(high_bit_cols))) don't work. Any help would be greatly appreciated. Thanks, Will

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• Joining the previous and next sentence using python

  - by JudoWill

  I'm trying to join a set of sentences contained in a list. I have a function which determines whether a sentence in worth saving. However, in order to keep the context of the sentence I need to also keep the sentence before and after it. In the edge cases, where its either the first or last sentence then, I'll just keep the sentence and its only neighbor. An example is best: ex_paragraph = ['The quick brown fox jumps over the fence.', 'Where there is another red fox.', 'They run off together.', 'They live hapily ever after.'] t1 = lambda x: x.startswith('Where') t2 = lambda x: x'startswith('The ') The result for t1 should be: ['The quick brown fox jumps over the fence. Where there is another red fox. They run off together.'] The result for t2 should be: ['The quick brown fox jumps over the fence. Where there is another red fox.'] My solution is: def YieldContext(sent_list, cont_fun): def JoinSent(sent_list, ind): if ind == 0: return sent_list[ind]+sent_list[ind+1] elif ind == len(sent_list)-1: return sent_list[ind-1]+sent_list[ind] else: return ' '.join(sent_list[ind-1:ind+1]) for sent, sentnum in izip(sent_list, count(0)): if cont_fun(sent): yield JoinSent(sent_list, sent_num) Does anyone know a "cleaner" or more pythonic way to do something like this. The if-elif-else seems a little forced. Thanks, Will PS. I'm obviously doing this with a more complicated "context-function" but this is just for a simple example.

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• How can I load a sql "dump" file into sql alchemy

  - by JudoWill

  I have a large sql dump file ... with multiple CREATE TABLE and INSERT INTO statements. Is there any way to load these all into a SQLAlchemy sqlite database at once. I plan to use the introspected ORM from sqlsoup after I've created the tables. However, when I use the engine.execute() method it complains: sqlite3.Warning: You can only execute one statement at a time. Is there a way to work around this issue. Perhaps splitting the file with a regexp or some kind of parser, but I don't know enough SQL to get all of the cases for the regexp. Any help would be greatly appreciated. Will EDIT: Since this seems important ... The dump file was created with a MySQL database and so it has quite a few commands/syntax that sqlite3 does not understand correctly.

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• Removing python and then re-installing on Mac OSX

  - by JudoWill

  I was wondering if anyone had tips on how to completely remove a python installation form Mac OSX (10.5.8) ... including virtual environments and its related binaries. Over the past few years I've completely messed up the installed site-packages, virtual-environments, etc. and the only way I can see to fix it is to just uninstall everything and re-install. I'd like to completely re-do everything and use virtualenv, pip, etc. from the beginning. On the other hand if anyone knows a way to do this without removing python and re-installing I'd be happy to here about it. Thanks, Will

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