import numpy.matlib
import os.path
+import cPickle
-fixedParamQ = numpy.matlib.mat(
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- [ 0.69677236], [ 0.41673747], [ 0.564245 ], [ 0.37613432], [ 0.88805642],
- [ 0.69677236], [ 0.41673747], [ 0.564245 ], [ 0.37613432], [ 0.88805642],
- [ 0.69677236], [ 0.41673747], [ 0.564245 ], [ 0.37613432], [ 0.88805642],
- [ 0.88691608], [ 0.69476752], [ 0.81659504], [ 0.17801859], [ 0.71048235],
- [ 0.08188783], [ 0.54884803], [ 0.84039558], [ 0.6982093 ], [ 0.41686176],
- [ 0.38568873], [ 0.29401347], [ 0.12704074], [ 0.30640858], [ 0.89578031],
- [ 0.84621571], [ 0.11783439], [ 0.0944695 ], [ 0.34081575], [ 0.44157643],
- [ 0.77847185], [ 0.04283567], [ 0.45107823], [ 0.89789891], [ 0.41045519],
- [ 0.49073531], [ 0.29727627], [ 0.94711483], [ 0.24898204], [ 0.26181212],
- [ 0.71760957], [ 0.60326883], [ 0.80887576], [ 0.09448718], [ 0.88064525],
- [ 0.84317654], [ 0.48893703], [ 0.24847021], [ 0.84203596], [ 0.34104156],
- [ 0.75604701], [ 0.91703057], [ 0.69325475], [ 0.61276969], [ 0.16335226],
- [ 0.4684374 ], [ 0.16553371], [ 0.79594434], [ 0.6440283 ], [ 0.80922237],
- [ 0.5349296 ], [ 0.31924316], [ 0.10960695], [ 0.40151062], [ 0.50473641],
- [ 0.14812671], [ 0.73523169], [ 0.35141625], [ 0.80364238], [ 0.02128181],
- [ 0.0061226 ], [ 0.34541924], [ 0.07694485], [ 0.05551339], [ 0.23087636],
- [ 0.87016395], [ 0.31682377], [ 0.27375113], [ 0.72226332], [ 0.62914149],
- [ 0.59236012], [ 0.2070238 ], [ 0.52390942], [ 0.11894098], [ 0.55725917],
- [ 0.72706009], [ 0.087196 ], [ 0.04745082], [ 0.95636492], [ 0.31524576],
- [ 0.79685218], [ 0.80386771], [ 0.70942604], [ 0.82869417], [ 0.26906569],
- [ 0.51848039], [ 0.64169354], [ 0.07114973], [ 0.39249454], [ 0.07002803],
- [ 0.94667567], [ 0.02252752], [ 0.01039039], [ 0.5721312 ], [ 0.06065969],
- [ 0.88691608], [ 0.69476752], [ 0.81659504], [ 0.17801859], [ 0.71048235],
- [ 0.88691608], [ 0.69476752], [ 0.81659504], [ 0.17801859], [ 0.71048235],
- [ 0.08188783], [ 0.54884803], [ 0.84039558], [ 0.6982093 ], [ 0.41686176],
- [ 0.38568873], [ 0.29401347], [ 0.12704074], [ 0.30640858], [ 0.89578031],
- [ 0.84621571], [ 0.11783439], [ 0.0944695 ], [ 0.34081575], [ 0.44157643],
- [ 0.77847185], [ 0.04283567], [ 0.45107823], [ 0.89789891], [ 0.41045519],
- [ 0.49073531], [ 0.29727627], [ 0.94711483], [ 0.24898204], [ 0.26181212],
- [ 0.71760957], [ 0.60326883], [ 0.80887576], [ 0.09448718], [ 0.88064525],
- [ 0.84317654], [ 0.48893703], [ 0.24847021], [ 0.84203596], [ 0.34104156],
- [ 0.75604701], [ 0.91703057], [ 0.69325475], [ 0.61276969], [ 0.16335226],
- [ 0.4684374 ], [ 0.16553371], [ 0.79594434], [ 0.6440283 ], [ 0.80922237],
- [ 0.5349296 ], [ 0.31924316], [ 0.10960695], [ 0.40151062], [ 0.50473641],
- [ 0.14812671], [ 0.73523169], [ 0.35141625], [ 0.80364238], [ 0.02128181],
- [ 0.0061226 ], [ 0.34541924], [ 0.07694485], [ 0.05551339], [ 0.23087636],
- [ 0.87016395], [ 0.31682377], [ 0.27375113], [ 0.72226332], [ 0.62914149],
- [ 0.59236012], [ 0.2070238 ], [ 0.52390942], [ 0.11894098], [ 0.55725917],
- [ 0.72706009], [ 0.087196 ], [ 0.04745082], [ 0.95636492], [ 0.31524576],
- [ 0.79685218], [ 0.80386771], [ 0.70942604], [ 0.82869417], [ 0.26906569],
- [ 0.51848039], [ 0.64169354], [ 0.07114973], [ 0.39249454], [ 0.07002803],
- [ 0.94667567], [ 0.02252752], [ 0.01039039], [ 0.5721312 ], [ 0.06065969],
- [ 0.88691608], [ 0.69476752], [ 0.81659504], [ 0.17801859], [ 0.71048235],
- [ 0.08188783], [ 0.54884803], [ 0.84039558], [ 0.6982093 ], [ 0.41686176],
- [ 0.38568873], [ 0.29401347], [ 0.12704074], [ 0.30640858], [ 0.89578031],
- [ 0.84621571], [ 0.11783439], [ 0.0944695 ], [ 0.34081575], [ 0.44157643],
- [ 0.84621571], [ 0.11783439], [ 0.0944695 ], [ 0.34081575], [ 0.44157643],
- [ 0.77847185], [ 0.04283567], [ 0.45107823], [ 0.89789891], [ 0.41045519],
- [ 0.49073531], [ 0.29727627], [ 0.94711483], [ 0.24898204], [ 0.26181212],
- [ 0.71760957], [ 0.60326883], [ 0.80887576], [ 0.09448718], [ 0.88064525],
- [ 0.84317654], [ 0.48893703], [ 0.24847021], [ 0.84203596], [ 0.34104156],
- [ 0.75604701], [ 0.91703057], [ 0.69325475], [ 0.61276969], [ 0.16335226],
- [ 0.4684374 ], [ 0.16553371], [ 0.79594434], [ 0.6440283 ], [ 0.80922237],
- [ 0.5349296 ], [ 0.31924316], [ 0.10960695], [ 0.40151062], [ 0.50473641],
- [ 0.14812671], [ 0.73523169], [ 0.35141625], [ 0.80364238], [ 0.02128181],
- [ 0.0061226 ], [ 0.34541924], [ 0.07694485], [ 0.05551339], [ 0.23087636],
- [ 0.87016395], [ 0.31682377], [ 0.27375113], [ 0.72226332], [ 0.62914149],
- [ 0.59236012], [ 0.2070238 ], [ 0.52390942], [ 0.11894098], [ 0.55725917],
- [ 0.72706009], [ 0.087196 ], [ 0.04745082], [ 0.95636492], [ 0.31524576],
- [ 0.79685218], [ 0.80386771], [ 0.70942604], [ 0.82869417], [ 0.26906569],
- [ 0.51848039], [ 0.64169354], [ 0.07114973], [ 0.39249454], [ 0.07002803],
- [ 0.94667567], [ 0.02252752], [ 0.01039039], [ 0.5721312 ], [ 0.06065969],
- [ 0.69422476], [ 0.4310939 ], [ 0.03069099], [ 0.35969779], [ 0.18047331],
- [ 0.4177651 ], [ 0.01360547], [ 0.29069319]
- ])
-
-fixedParam = numpy.matlib.mat([[ 0.62870709], [ 0.7012026 ], [ 0.60236784],
- [ 0.51316259], [ 0.20220814], [ 0.70324863], [ 0.37218684], [ 0.82178927],
- [ 0.60394866], [ 0.70371272], [ 0.07548074], [ 0.63412803], [ 0.97442266],
- [ 0.13216791], [ 0.71041168], [ 0.2093887 ], [ 0.35227344], [ 0.3405142 ],
- [ 0.69677236], [ 0.41673747], [ 0.564245 ], [ 0.37613432], [ 0.88805642],
- [ 0.88691608], [ 0.69476752], [ 0.81659504], [ 0.17801859], [ 0.71048235],
- [ 0.08188783], [ 0.54884803], [ 0.84039558], [ 0.6982093 ], [ 0.41686176],
- [ 0.38568873], [ 0.29401347], [ 0.12704074], [ 0.30640858], [ 0.89578031],
- [ 0.84621571], [ 0.11783439], [ 0.0944695 ], [ 0.34081575], [ 0.44157643],
- [ 0.77847185], [ 0.04283567], [ 0.45107823], [ 0.89789891], [ 0.41045519],
- [ 0.49073531], [ 0.29727627], [ 0.94711483], [ 0.24898204], [ 0.26181212],
- [ 0.71760957], [ 0.60326883], [ 0.80887576], [ 0.09448718], [ 0.88064525],
- [ 0.84317654], [ 0.48893703], [ 0.24847021], [ 0.84203596], [ 0.34104156],
- [ 0.75604701], [ 0.91703057], [ 0.69325475], [ 0.61276969], [ 0.16335226],
- [ 0.4684374 ], [ 0.16553371], [ 0.79594434], [ 0.6440283 ], [ 0.80922237],
- [ 0.5349296 ], [ 0.31924316], [ 0.10960695], [ 0.40151062], [ 0.50473641],
- [ 0.14812671], [ 0.73523169], [ 0.35141625], [ 0.80364238], [ 0.02128181],
- [ 0.0061226 ], [ 0.34541924], [ 0.07694485], [ 0.05551339], [ 0.23087636],
- [ 0.87016395], [ 0.31682377], [ 0.27375113], [ 0.72226332], [ 0.62914149],
- [ 0.59236012], [ 0.2070238 ], [ 0.52390942], [ 0.11894098], [ 0.55725917],
- [ 0.72706009], [ 0.087196 ], [ 0.04745082], [ 0.95636492], [ 0.31524576],
- [ 0.79685218], [ 0.80386771], [ 0.70942604], [ 0.82869417], [ 0.26906569],
- [ 0.51848039], [ 0.64169354], [ 0.07114973], [ 0.39249454], [ 0.07002803],
- [ 0.94667567], [ 0.02252752], [ 0.01039039], [ 0.5721312 ], [ 0.06065969],
- [ 0.69422476], [ 0.4310939 ], [ 0.03069099], [ 0.35969779], [ 0.18047331],
- [ 0.4177651 ], [ 0.01360547], [ 0.29069319]])
+###############################################################################
+#
+# Load a random but fixed initial parameter vector this makes debugging easier
+#
+###############################################################################
-#fixedParamQ = numpy.matlib.mat(range(1300))
-#fixedParamQ = fixedParamQ.reshape((1300,1))
+fixedParamQ = cPickle.load(open('/fml/ag-raetsch/home/fabio/svn/projects/QPalma/scripts/randInitParam.pickle'))
###########################################################
#
# The parameters for the QPalma algorithm
#
#
-
C = 1
+
+
###############################################################################
#
# CHOOSING THE MODE
#mode = 'normal'
mode = 'using_quality_scores'
-
-
###############################################################################
#
# When using quality scores our scoring function is defined as
joinp = os.path.join
-tmp_dir = '/fml/ag-raetsch/home/fabio/tmp/solexa_tmp'
-
-data_path = '/fml/ag-raetsch/share/projects/qpalma/solexa'
+tmp_dir = '/fml/ag-raetsch/home/fabio/tmp/solexa_tmp'
+data_path = '/fml/ag-raetsch/share/projects/qpalma/solexa'
-dna_filename = joinp(data_path,'allGenes.pickle')
-est_filename = joinp(data_path,'remapped_solexa_data/map_best_hit.18.unambig')
-
-remapped_path = joinp(data_path,'remapped_solexa_data')
-annot_path = joinp(data_path,'annotation_data')
original_path = joinp(data_path,'original_solexa_data')
+annot_path = joinp(data_path,'annotation_data')
+remapped_path = joinp(data_path,'remapped_solexa_data')
-joinp(annot_path,'TAIR7_GFF3_genes_Chr1.gff_v1')
+dna_flat_fn = joinp(data_path,'allGenes.pickle')
+gff_fn = joinp(annot_path,'TAIR7_GFF3_genes_Chr1.gff_v1')
+filtered_fn = joinp(data_path,'filteredReads_1_recent')
+remapped_fn = joinp(remapped_path,'map_best_hit.18.unambig')
+dataset_fn = '/fml/ag-raetsch/home/fabio/svn/projects/QPalma/scripts/chr1_dataset.pickle'
-data_filename = ''
###############################################################################
#
# SANITY CHECKS
assert numLengthSuppPoints > 1
assert numQualSuppPoints > 1
-assert os.path.exists(dna_filename), 'DNA data does not exist!'
-assert os.path.exists(est_filename), 'EST/Reads data does not exist!'
-#assert os.path.exists(tair7_seq_filename), 'Sequence data does not exist!'
-
+assert os.path.exists(dna_flat_fn), 'DNA data does not exist!'
+assert os.path.exists(gff_fn), 'EST/Reads data does not exist!'
+assert os.path.exists(filtered_fn), 'EST/Reads data does not exist!'
+assert os.path.exists(remapped_fn), 'EST/Reads data does not exist!'