yonatanf  committed cb518ba

FIX: fixed error is readme, and a few typos

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     from optparse import OptionParser
     kwargs = {}
     usage  = ('Compute pseudo p-vals from a set correlations obtained from shuffled data.\n' 
-              'Pseudo p-vals are the precentage of times a corrleation at least as extreme as the "real" one was observed in simulated datasets. \n'
+              'Pseudo p-vals are the percentage of times a correlation at least as extreme as the "real" one was observed in simulated datasets. \n'
               'p-values can be either two-sided (considering only the correlation magnitude) or one-sided (accounting for the sign of correlations).\n'
               'Files containing the simulated correlations should be named [prefix]_[num].txt. The naming prefix is the second input argument, and the total number of simulated sets is the third.\n'
               'Usage:   python real_cor_file sim_cor_file_prefix num_simulations [options]\n'
-              'Example: python example/basis_corr/cor_mat_sparcc.out example/pvals/sim_cor 5 -o pals.txt -t one_sided')
+              'Example: python example/basis_corr/cor_mat_sparcc.out example/pvals/sim_cor 5 -o pvals.txt -t one_sided')
     parser = OptionParser(usage)
     parser.add_option("-t", "--type", dest="type", type = 'str',
                       action="callback", callback= kwargs_callback, callback_kwargs = {'d':kwargs}, 
 The following will compute both one and two sided p-values.
-   python example/basis_corr/cor_sparcc.txt example/pvals/sim_cor 5 -o example/pvals/pvals_one_sided.txt -t 'one_sided'
-   python example/basis_corr/cor_sparcc.txt example/pvals/sim_cor 5 -o example/pvals/pvals_two_sided.txt -t 'two_sided'
+   python example/basis_corr/cor_sparcc.out example/pvals/sim_cor 5 -o example/pvals/pvals_one_sided.txt -t 'one_sided'
+   python example/basis_corr/cor_sparcc.out example/pvals/sim_cor 5 -o example/pvals/pvals_two_sided.txt -t 'two_sided'