<s> """<STR_LIT>""" <EOL> import os . path as op <EOL> import sys <EOL> from jcvi . formats . fastq import readlen <EOL> from jcvi . formats . base import write_file <EOL> from jcvi . assembly . base import FastqNamings , get_libs <EOL> from jcvi . utils . table import comment_banner , load_csv <EOL> from jcvi . apps . base import OptionParser , ActionDispatcher <EOL> header = """<STR_LIT>""" . translate ( None , "<STR_LIT>" ) <EOL> def main ( ) : <EOL> actions = ( <EOL> ( '<STR_LIT>' , '<STR_LIT>' ) , <EOL> ) <EOL> p = ActionDispatcher ( actions ) <EOL> p . dispatch ( globals ( ) ) <EOL> def prepare ( args ) : <EOL> """<STR_LIT>""" <EOL> p = OptionParser ( prepare . __doc__ + FastqNamings ) <EOL> p . add_option ( "<STR_LIT>" , default = <NUM_LIT> , type = "<STR_LIT:int>" , help = "<STR_LIT>" ) <EOL> p . set_cpus ( cpus = <NUM_LIT:32> ) <EOL> opts , args = p . parse_args ( args ) <EOL> if len ( args ) < <NUM_LIT:2> : <EOL> sys . exit ( not p . print_help ( ) ) <EOL> genomesize = float ( args [ <NUM_LIT:0> ] ) / <NUM_LIT:1000> <EOL> fnames = args [ <NUM_LIT:1> : ] <EOL> for x in fnames : <EOL> assert op . exists ( x ) , "<STR_LIT>" . format ( x ) <EOL> s = comment_banner ( "<STR_LIT>" ) + "<STR_LIT:\n>" <EOL> s += comment_banner ( "<STR_LIT>" ) + "<STR_LIT:\n>" <EOL> s += "<STR_LIT>" <EOL> s += "<STR_LIT>" + "<STR_LIT:U+0020>" . join ( header . split ( ) ) + "<STR_LIT:\n>" <EOL> libs = get_libs ( fnames ) <EOL> lib_seqs = [ ] <EOL> rank = <NUM_LIT:0> <EOL> for lib , fs in libs : <EOL> size = lib . size <EOL> if size == <NUM_LIT:0> : <EOL> continue <EOL> rank += <NUM_LIT:1> <EOL> library_name = lib . library_name <EOL> name = library_name . replace ( "<STR_LIT:->" , "<STR_LIT>" ) <EOL> wildcard = "<STR_LIT>" . format ( library_name ) <EOL> rl = max ( readlen ( [ x ] ) for x in fs ) <EOL> lib_seq = lib . get_lib_seq ( wildcard , name , rl , rank ) <EOL> lib_seqs . append ( lib_seq ) <EOL> s += "<STR_LIT:\n>" + "<STR_LIT:\n>" . join ( load_csv ( None , lib_seqs , sep = "<STR_LIT:U+0020>" ) ) + "<STR_LIT:\n>" <EOL> params = [ ( "<STR_LIT>" , genomesize ) , <EOL> ( "<STR_LIT>" , <NUM_LIT:0> ) , <EOL> ( "<STR_LIT>" , opts . K ) , <EOL> ( "<STR_LIT>" , <NUM_LIT:1> ) , <EOL> ( "<STR_LIT>" , <NUM_LIT:0> ) , <EOL> ( "<STR_LIT>" , opts . cpus ) ] <EOL> s += "<STR_LIT:\n>" + "<STR_LIT:\n>" . join ( load_csv ( None , params , sep = "<STR_LIT:U+0020>" ) ) + "<STR_LIT:\n>" <EOL> cfgfile = "<STR_LIT>" <EOL> write_file ( cfgfile , s , tee = True ) <EOL> s = "<STR_LIT>" . format ( cfgfile ) <EOL> runsh = "<STR_LIT>" <EOL> write_file ( runsh , s ) <EOL> if __name__ == '<STR_LIT:__main__>' : <EOL> main ( ) </s>
