Code for ESPERR (Evolutionary and Sequence Pattern Extraction through Reduced Representation)
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jxtx rp_score_maf.py: improve coordinate handling. Previously output posit…
…ion was the start of the window plus half the window size, which could become inaccurate for windows containing many reference gaps. This now actually calculates the genome position the center of the alignment window corresponds to. Also, skips windows with more than half gaps in the reference (this could result in scores being written for alignment windows corresponding to very small genome windows)
Latest commit dc87eca Mar 25, 2013
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rp Adding .hgignore Mar 8, 2013
test_data Renaming Jun 12, 2006
third_party/gill_pst Renaming Jun 12, 2006
.hgignore Adding .hgignore Mar 8, 2013
Makefile Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
README Update README Mar 8, 2013
ancestral_dists.py Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
atom_mapping_to_complete.py Another script. Jul 17, 2006
cv_precomputed_scores.py Renaming Jun 12, 2006
distribute_setup.py adding distribute_setup.py Mar 7, 2013
entropy_agglomeration.py Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
genome_windows.py Genome windowing script. Oct 26, 2006
maf_to_ints.py Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
make_mapping_from_clusters.py Adding some core scripts for ESPERR. Jul 7, 2006
random_alphabet.py Renaming Jun 12, 2006
rp_adapt.py Renaming Jun 12, 2006
rp_adapt_mc_mpi.py Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
rp_adapt_mc_ts.py Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
rp_adapt_mpi.py Renaming Jun 12, 2006
rp_combine_mappings.py Renaming Jun 12, 2006
rp_cv.py Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
rp_cv_multiclass.py Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
rp_cv_ts.py Renaming Jun 12, 2006
rp_dump_tree.py Renaming Jun 12, 2006
rp_make_mapping.py Renaming Jun 12, 2006
rp_prob_classify.py Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
rp_score.py Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
rp_score_bed_ints.py Renaming Jun 12, 2006
rp_score_maf.py rp_score_maf.py: improve coordinate handling. Previously output posit… Mar 25, 2013
rp_score_maf_BUGGED.py Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
rp_score_words.py Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
rp_train.py Updates for numpy and fixes for more modern Pyrex. Jul 31, 2009
rp_train_probs.py Renaming Jun 12, 2006
setup.py Import fix for doc_optparse Mar 8, 2013
test_standard_model.py Renaming Jun 12, 2006

README

Implementation of the ESPERR method for training classification  models 
on multiple alignments and creating scores (e.g. Regulatory Potential)