transform_index.left_join(1, tid_gid, 1)
gid_cnctype = transform_index.get_col('gid', 'index')
gid_cnctype = gid_cnctype.de_redundency()
gid_cnctype = gid_cnctype.key_by('gid', 'index')
coding = gid_cnctype.eget('union', '_index=coding')
noncoding = gid_cnctype.eget('union', '_index=noncoding')
ambiguity = gid_cnctype.eget('union', '_index=coding,noncoding',
'_index=noncoding,coding')
exon_number = gtf.getExon()
transform_index.left_join(1, exon_number, 1)
transform_index = transform_index.get_row_by_func(check_lncRNA)
all_gids = de_redundency(tid_gid.getCol('gid'))
C = coding.getCol('gid')
print "Novel coding genes:", len(C)
N = noncoding.getCol('gid')
AM = ambiguity.getCol('gid')
print "Ambiguous genes:", len(AM)
lnc = de_redundency(transform_index.getCol('gid'))
lnc = intersect_array(N, lnc)
print "Novel lincRNA genes:", len(lnc)
discard = sub_array(all_gids, C)
discard = sub_array(discard, AM)
gid_cnctype=transform_index.get_col('gid','index')
gid_cnctype=gid_cnctype.de_redundency()
gid_cnctype=gid_cnctype.key_by('gid','index')
coding=gid_cnctype.eget('union','_index=coding')
noncoding=gid_cnctype.eget('union','_index=noncoding')
ambiguity=gid_cnctype.eget('union','_index=coding,noncoding','_index=noncoding,coding')
exon_number=gtf.getExon()
transform_index.left_join(1,exon_number,1)
transform_index=transform_index.get_row_by_func(check_lncRNA)
all_gids=de_redundency(tid_gid.getCol('gid'))
C=coding.getCol('gid')
print "Novel coding genes:",len(C)
N=noncoding.getCol('gid')
AM=ambiguity.getCol('gid')
print "Ambiguous genes:",len(AM)
lnc=de_redundency(transform_index.getCol('gid'))
lnc=intersect_array(N,lnc)
print "Novel lincRNA genes:",len(lnc)
discard=sub_array(all_gids,C)
