<s> """<STR_LIT>""" <EOL> class SgeOptions ( object ) : <EOL> """<STR_LIT>""" <EOL> def __init__ ( self , unique_id , use_sge = False , max_sge_jobs = <NUM_LIT> , <EOL> blasr_nproc = <NUM_LIT> , gcon_nproc = <NUM_LIT:8> , quiver_nproc = <NUM_LIT:8> , sge_env_name = '<STR_LIT>' , sge_queue = None ) : <EOL> self . unique_id = unique_id <EOL> self . use_sge = use_sge <EOL> self . max_sge_jobs = max_sge_jobs <EOL> self . blasr_nproc = blasr_nproc <EOL> self . gcon_nproc = gcon_nproc <EOL> self . quiver_nproc = quiver_nproc <EOL> self . sge_env_name = sge_env_name <EOL> self . sge_queue = sge_queue <EOL> def __str__ ( self ) : <EOL> return "<STR_LIT>" . format ( i = self . unique_id ) + "<STR_LIT>" . format ( u = self . use_sge ) + "<STR_LIT>" . format ( j = self . max_sge_jobs ) + "<STR_LIT>" . format ( n = self . blasr_nproc ) + "<STR_LIT>" . format ( n = self . gcon_nproc ) + "<STR_LIT>" . format ( t = self . quiver_nproc ) + "<STR_LIT>" . format ( self . sge_env_name ) + "<STR_LIT>" . format ( self . sge_queue ) <EOL> def cmd_str ( self , show_blasr_nproc = False , show_gcon_nproc = False , <EOL> show_quiver_nproc = False , show_sge_env_name = False , show_sge_queue = False ) : <EOL> """<STR_LIT>""" <EOL> cmd = "<STR_LIT>" <EOL> if self . use_sge is True : <EOL> cmd += "<STR_LIT>" <EOL> cmd += "<STR_LIT>" . format ( n = self . max_sge_jobs ) <EOL> cmd += "<STR_LIT>" . format ( n = self . unique_id ) <EOL> if show_blasr_nproc is True and self . blasr_nproc is not None : <EOL> cmd += "<STR_LIT>" . format ( n = self . blasr_nproc ) <EOL> if show_gcon_nproc is True and self . gcon_nproc is not None : <EOL> cmd += "<STR_LIT>" . format ( n = self . gcon_nproc ) <EOL> if show_quiver_nproc is True and self . quiver_nproc is not None : <EOL> cmd += "<STR_LIT>" . format ( n = self . quiver_nproc ) <EOL> if show_sge_env_name : <EOL> cmd += "<STR_LIT>" . format ( self . sge_env_name ) <EOL> if show_sge_queue and self . sge_queue is not None : <EOL> cmd += "<STR_LIT>" . format ( self . sge_queue ) <EOL> return cmd <EOL> class IceOptions ( object ) : <EOL> """<STR_LIT>""" <EOL> def __init__ ( self , flnc_reads_per_split = <NUM_LIT> , <EOL> ece_penalty = <NUM_LIT:1> , ece_min_len = <NUM_LIT:20> , bestn = <NUM_LIT> , quiver = False , use_finer_qv = False , targeted_isoseq = False ) : <EOL> self . cDNA_size = "<STR_LIT>" <EOL> self . ece_penalty = int ( ece_penalty ) <EOL> self . ece_min_len = int ( ece_min_len ) <EOL> self . bestn = int ( bestn ) <EOL> self . quiver = quiver <EOL> self . flnc_reads_per_split = int ( flnc_reads_per_split ) <EOL> self . use_finer_qv = use_finer_qv <EOL> self . targeted_isoseq = targeted_isoseq <EOL> @ classmethod <EOL> def cDNA_sizeBins ( cls ) : <EOL> """<STR_LIT>""" <EOL> return ( "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" ) <EOL> @ property <EOL> def maxScore ( self ) : <EOL> """<STR_LIT>""" <EOL> if self . cDNA_size not in IceOptions . cDNA_sizeBins ( ) : <EOL> raise ValueError ( "<STR_LIT>" . <EOL> format ( cs = self . cDNA_size ) ) <EOL> d = { "<STR_LIT>" : - <NUM_LIT:1000> , "<STR_LIT>" : - <NUM_LIT> , "<STR_LIT>" : - <NUM_LIT> , <EOL> "<STR_LIT>" : - <NUM_LIT> , "<STR_LIT>" : - <NUM_LIT> } <EOL> return d [ self . cDNA_size ] <EOL> @ property <EOL> def minLength ( self ) : <EOL> """<STR_LIT>""" <EOL> if self . cDNA_size not in IceOptions . cDNA_sizeBins ( ) : <EOL> raise ValueError ( "<STR_LIT>" . <EOL> format ( cs = self . cDNA_size ) ) <EOL> d = { "<STR_LIT>" : <NUM_LIT> , "<STR_LIT>" : <NUM_LIT> , "<STR_LIT>" : <NUM_LIT> , <EOL> "<STR_LIT>" : <NUM_LIT> , "<STR_LIT>" : <NUM_LIT> } <EOL> return d [ self . cDNA_size ] <EOL> def __str__ ( self ) : <EOL> return "<STR_LIT>" . format ( sz = self . cDNA_size ) + "<STR_LIT>" . format ( ms = self . maxScore ) + "<STR_LIT>" . format ( ep = self . ece_penalty ) + "<STR_LIT>" . format ( eml = self . ece_min_len ) + "<STR_LIT>" . format ( bsn = self . bestn ) + "<STR_LIT>" . format ( quiver = self . quiver ) + "<STR_LIT>" . format ( n = self . flnc_reads_per_split ) + "<STR_LIT>" . format ( qv = self . use_finer_qv ) <EOL> class IceQuiverHQLQOptions ( object ) : <EOL> """<STR_LIT>""" <EOL> def __init__ ( self , qv_trim_5 = <NUM_LIT:200> , qv_trim_3 = <NUM_LIT:50> , hq_quiver_min_accuracy = <NUM_LIT> , <EOL> hq_isoforms_fa = None , hq_isoforms_fq = None , <EOL> lq_isoforms_fa = None , lq_isoforms_fq = None ) : <EOL> self . qv_trim_5 = int ( qv_trim_5 ) <EOL> self . qv_trim_3 = int ( qv_trim_3 ) <EOL> self . hq_quiver_min_accuracy = float ( hq_quiver_min_accuracy ) <EOL> self . hq_isoforms_fa = hq_isoforms_fa <EOL> self . hq_isoforms_fq = hq_isoforms_fq <EOL> self . lq_isoforms_fa = lq_isoforms_fa <EOL> self . lq_isoforms_fq = lq_isoforms_fq <EOL> def __str__ ( self ) : <EOL> return "<STR_LIT>" . format ( n = self . qv_trim_5 ) + "<STR_LIT>" . format ( n = self . qv_trim_3 ) + "<STR_LIT>" . format ( n = self . hq_quiver_min_accuracy ) + "<STR_LIT>" . format ( fa = self . hq_isoforms_fa ) + "<STR_LIT>" . format ( fq = self . hq_isoforms_fq ) + "<STR_LIT>" . format ( fa = self . lq_isoforms_fa ) + "<STR_LIT>" . format ( fq = self . lq_isoforms_fq ) <EOL> def cmd_str ( self ) : <EOL> """<STR_LIT>""" <EOL> cmd = "<STR_LIT>" . format ( n = self . hq_quiver_min_accuracy ) + "<STR_LIT>" . format ( n = self . qv_trim_5 ) + "<STR_LIT>" . format ( n = self . qv_trim_3 ) <EOL> if self . hq_isoforms_fa is not None : <EOL> cmd += "<STR_LIT>" . format ( f = self . hq_isoforms_fa ) <EOL> if self . hq_isoforms_fq is not None : <EOL> cmd += "<STR_LIT>" . format ( f = self . hq_isoforms_fq ) <EOL> if self . lq_isoforms_fa is not None : <EOL> cmd += "<STR_LIT>" . format ( f = self . lq_isoforms_fa ) <EOL> if self . lq_isoforms_fq is not None : <EOL> cmd += "<STR_LIT>" . format ( f = self . lq_isoforms_fq ) <EOL> return cmd </s>
