reset pathings for PyPI upload

MANIFEST.in

@@ -1,9 +1 @@
-include README.md
-include LICENSE
-include models/human_T_alpha/*
-include models/human_T_beta/*
-include models/mouse_T_beta/*
-include models/human_B_heavy/*
-include expanded_alphabet_files/example_expanded_amino_acid_alphabet.txt
-include results/
-include data/
+recursive-include olga/default_models/ *

compute_single_sequence_pgen.py → build/lib/olga/compute_single_sequence_pgen.py

@@ -136,7 +136,7 @@
 from olga.utils import nt2aa
 from optparse import OptionParser
 
-def main(argv):
+def main():
     """Compute Pgen of a single sequence."""
 
 
@@ -172,17 +172,13 @@ def main(argv):
         print 'Exiting...'
         return -1
 
-    try:
-        main_folder = __file__.rsplit('/', 1)[-2]
-    except IndexError: #In current folder, called from within python.
-        main_folder = '.'
+    main_folder = os.path.dirname(__file__)
 
     default_models = {}
-
-    default_models['humanTCRA'] = [main_folder + '/models/human_T_alpha/',  'VJ']
-    default_models['humanTCRB'] = [main_folder + '/models/human_T_beta/', 'VDJ']
-    default_models['mouseTCRB'] = [main_folder + '/models/mouse_T_beta/', 'VDJ']
-    default_models['humanIGH'] = [main_folder + '/models/human_B_heavy/', 'VDJ']
+    default_models['humanTCRA'] = [os.path.join(main_folder, 'default_models', 'human_T_alpha'),  'VJ']
+    default_models['humanTCRB'] = [os.path.join(main_folder, 'default_models', 'human_T_beta'), 'VDJ']
+    default_models['mouseTCRB'] = [os.path.join(main_folder, 'default_models', 'mouse_T_beta'), 'VDJ']
+    default_models['humanIGH'] = [os.path.join(main_folder, 'default_models', 'human_B_heavy'), 'VDJ']
 
     num_models_specified = sum([1 for x in default_models.keys() + ['vj_model_folder', 'vdj_model_folder'] if getattr(options, x)])
 
@@ -193,10 +189,10 @@ def main(argv):
             recomb_type = default_models[d_model][1]
         except IndexError:
             if options.vdj_model_folder: #custom VDJ model specified
-                model_folder = options.vdj_model_folder.rstrip('/') + '/'
+                model_folder = options.vdj_model_folder
                 recomb_type = 'VDJ'
             elif options.vj_model_folder: #custom VJ model specified
-                model_folder = options.vj_model_folder.rstrip('/') + '/'
+                model_folder = options.vj_model_folder
                 recomb_type = 'VJ'
     elif num_models_specified == 0:
         print 'Need to indicate generative model.'
@@ -213,10 +209,10 @@ def main(argv):
         print 'Exiting...'
         return -1
 
-    params_file_name = model_folder + 'model_params.txt'
-    marginals_file_name = model_folder + 'model_marginals.txt'
-    V_anchor_pos_file = model_folder + 'V_gene_CDR3_anchors.csv'
-    J_anchor_pos_file = model_folder + 'J_gene_CDR3_anchors.csv'
+    params_file_name = os.path.join(model_folder,'model_params.txt')
+    marginals_file_name = os.path.join(model_folder,'model_marginals.txt')
+    V_anchor_pos_file = os.path.join(model_folder,'V_gene_CDR3_anchors.csv')
+    J_anchor_pos_file = os.path.join(model_folder,'J_gene_CDR3_anchors.csv')
 
     for x in [params_file_name, marginals_file_name, V_anchor_pos_file, J_anchor_pos_file]:
         if not os.path.isfile(x):
@@ -359,4 +355,4 @@ def main(argv):
 
     print ''
 
-if __name__ == '__main__': main(sys.argv)
+if __name__ == '__main__': main()

models/human_T_alpha/J_gene_CDR3_anchors.csv → build/lib/olga/default_models/human_T_alpha/J_gene_CDR3_anchors.csv

@@ -1,68 +1,68 @@
-gene,anchor_index,function
-TRAJ1*01,28,ORF
-TRAJ10*01,30,F
-TRAJ11*01,26,F
-TRAJ12*01,26,F
-TRAJ13*01,29,F
-TRAJ13*02,29,F
-TRAJ14*01,18,F
-TRAJ15*01,26,F
-TRAJ15*02,26,F
-TRAJ16*01,26,F
-TRAJ17*01,29,F
-TRAJ18*01,32,F
-TRAJ19*01,26,ORF
-TRAJ2*01,32,ORF
-TRAJ20*01,23,F
-TRAJ21*01,21,F
-TRAJ22*01,29,F
-TRAJ23*01,29,F
-TRAJ23*02,29,F
-TRAJ24*01,29,F
-TRAJ24*02,29,F
-TRAJ25*01,26,ORF
-TRAJ26*01,26,F
-TRAJ27*01,25,F
-TRAJ28*01,32,F
-TRAJ29*01,26,F
-TRAJ3*01,28,F
-TRAJ30*01,23,F
-TRAJ31*01,22,F
-TRAJ32*01,32,F
-TRAJ32*02,26,(F)
-TRAJ33*01,23,F
-TRAJ34*01,24,F
-TRAJ35*01,25,ORF
-TRAJ36*01,25,F
-TRAJ37*01,28,F
-TRAJ37*02,28,(F)
-TRAJ38*01,28,F
-TRAJ39*01,29,F
-TRAJ4*01,29,F
-TRAJ40*01,27,F
-TRAJ41*01,28,F
-TRAJ42*01,32,F
-TRAJ43*01,20,F
-TRAJ44*01,29,F
-TRAJ45*01,32,F
-TRAJ46*01,29,F
-TRAJ47*01,23,F
-TRAJ47*02,23,(F)
-TRAJ48*01,29,F
-TRAJ49*01,22,F
-TRAJ5*01,26,F
-TRAJ50*01,26,F
-TRAJ51*01,29,P
-TRAJ52*01,35,F
-TRAJ53*01,32,F
-TRAJ54*01,26,F
-TRAJ55*01,23,P
-TRAJ56*01,28,F
-TRAJ57*01,29,F
-TRAJ58*01,29,ORF
-TRAJ59*01,26,ORF
-TRAJ6*01,28,F
-TRAJ60*01,23,P
-TRAJ61*01,26,ORF
-TRAJ7*01,25,F
-TRAJ8*01,26,F
+gene,anchor_index,function
+TRAJ1*01,28,ORF
+TRAJ10*01,30,F
+TRAJ11*01,26,F
+TRAJ12*01,26,F
+TRAJ13*01,29,F
+TRAJ13*02,29,F
+TRAJ14*01,18,F
+TRAJ15*01,26,F
+TRAJ15*02,26,F
+TRAJ16*01,26,F
+TRAJ17*01,29,F
+TRAJ18*01,32,F
+TRAJ19*01,26,ORF
+TRAJ2*01,32,ORF
+TRAJ20*01,23,F
+TRAJ21*01,21,F
+TRAJ22*01,29,F
+TRAJ23*01,29,F
+TRAJ23*02,29,F
+TRAJ24*01,29,F
+TRAJ24*02,29,F
+TRAJ25*01,26,ORF
+TRAJ26*01,26,F
+TRAJ27*01,25,F
+TRAJ28*01,32,F
+TRAJ29*01,26,F
+TRAJ3*01,28,F
+TRAJ30*01,23,F
+TRAJ31*01,22,F
+TRAJ32*01,32,F
+TRAJ32*02,26,(F)
+TRAJ33*01,23,F
+TRAJ34*01,24,F
+TRAJ35*01,25,ORF
+TRAJ36*01,25,F
+TRAJ37*01,28,F
+TRAJ37*02,28,(F)
+TRAJ38*01,28,F
+TRAJ39*01,29,F
+TRAJ4*01,29,F
+TRAJ40*01,27,F
+TRAJ41*01,28,F
+TRAJ42*01,32,F
+TRAJ43*01,20,F
+TRAJ44*01,29,F
+TRAJ45*01,32,F
+TRAJ46*01,29,F
+TRAJ47*01,23,F
+TRAJ47*02,23,(F)
+TRAJ48*01,29,F
+TRAJ49*01,22,F
+TRAJ5*01,26,F
+TRAJ50*01,26,F
+TRAJ51*01,29,P
+TRAJ52*01,35,F
+TRAJ53*01,32,F
+TRAJ54*01,26,F
+TRAJ55*01,23,P
+TRAJ56*01,28,F
+TRAJ57*01,29,F
+TRAJ58*01,29,ORF
+TRAJ59*01,26,ORF
+TRAJ6*01,28,F
+TRAJ60*01,23,P
+TRAJ61*01,26,ORF
+TRAJ7*01,25,F
+TRAJ8*01,26,F

models/human_T_beta/J_gene_CDR3_anchors.csv → build/lib/olga/default_models/human_T_beta/J_gene_CDR3_anchors.csv

@@ -1,14 +1,14 @@
-gene,anchor_index,function
-TRBJ1-1*01,17,F
-TRBJ1-2*01,17,F
-TRBJ1-3*01,19,F
-TRBJ1-4*01,20,F
-TRBJ1-5*01,19,F
-TRBJ1-6*01,22,F
-TRBJ2-1*01,19,F
-TRBJ2-2*01,20,F
-TRBJ2-3*01,18,F
-TRBJ2-4*01,19,F
-TRBJ2-5*01,17,F
-TRBJ2-6*01,22,F
+gene,anchor_index,function
+TRBJ1-1*01,17,F
+TRBJ1-2*01,17,F
+TRBJ1-3*01,19,F
+TRBJ1-4*01,20,F
+TRBJ1-5*01,19,F
+TRBJ1-6*01,22,F
+TRBJ2-1*01,19,F
+TRBJ2-2*01,20,F
+TRBJ2-3*01,18,F
+TRBJ2-4*01,19,F
+TRBJ2-5*01,17,F
+TRBJ2-6*01,22,F
 TRBJ2-7*01,16,F