Module Expr Str Import alias identifier Import alias ImportFrom alias ImportFrom alias ImportFrom alias alias ImportFrom alias alias ImportFrom alias alias Assign NameStore Call AttributeLoad Str attr NameLoad Str FunctionDef arguments args defaults body Assign NameStore TupleLoad TupleLoad Str Str Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad BinOpAdd AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Str keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr keyword Num Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareLt Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign NameStore BinOpDiv Call NameLoad SubscriptLoad NameLoad Index Num Num Assign NameStore SubscriptLoad NameLoad Slice Num For NameStore NameLoad body Assert Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad Str attr NameLoad Assign NameStore BinOpAdd Call NameLoad Str Str AugAssignAdd NameStore BinOpAdd Call NameLoad Str Str AugAssignAdd NameStore Str AugAssignAdd NameStore BinOpAdd BinOpAdd Str Call AttributeLoad Str attr Call AttributeLoad NameLoad attr Str Assign NameStore Call NameLoad NameLoad Assign NameStore ListLoad Assign NameStore Num For TupleStore NameStore NameStore NameLoad body Assign NameStore AttributeLoad NameLoad attr If CompareEq NameLoad Num body Continue AugAssignAdd NameStore Num Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Str Str Assign NameStore Call AttributeLoad Str attr NameLoad Assign NameStore Call NameLoad GeneratorExp Call NameLoad ListLoad NameLoad comprehension NameStore NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad AugAssignAdd NameStore BinOpAdd BinOpAdd Str Call AttributeLoad Str attr Call NameLoad NameLoad NameLoad keyword Str Str Assign NameStore ListLoad TupleLoad Str NameLoad TupleLoad Str Num TupleLoad Str AttributeLoad NameLoad attr TupleLoad Str Num TupleLoad Str Num TupleLoad Str AttributeLoad NameLoad attr AugAssignAdd NameStore BinOpAdd BinOpAdd Str Call AttributeLoad Str attr Call NameLoad NameLoad NameLoad keyword Str Str Assign NameStore Str Expr Call NameLoad NameLoad NameLoad keyword NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad Assign NameStore Str Expr Call NameLoad NameLoad NameLoad decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A N/A 
Subroutines to aid MERACULOUS assembly.
 N/A os.path op N/A sys jcvi.formats.fastq readlen jcvi.formats.base write_file jcvi.assembly.base FastqNamings get_libs jcvi.utils.table comment_banner load_csv jcvi.apps.base OptionParser ActionDispatcher N/A header N/A N/A 
lib_seq [ wildcard ][ prefix ][ insAvg ][ insSdev ][ avgReadLen ][
hasInnieArtifact ][ isRevComped ][ useForContigging ][ scaffRound ][
useForGapClosing ][ 5pWiggleRoom ][3pWiggleRoom]
 translate None []
 main N/A N/A N/A N/A N/A actions N/A N/A prepare prepare meraculous input N/A p N/A ActionDispatcher actions N/A N/A N/A p dispatch N/A globals N/A prepare N/A N/A args N/A N/A N/A 
    %prog prepare genomesize *.fastq

    Prepare MERACULOUS configuation file. Genome size should be entered in Mb.
     N/A p N/A OptionParser N/A N/A prepare __doc__ FastqNamings N/A N/A N/A p add_option -K default 51 type int help K-mer size N/A N/A N/A p set_cpus cpus 32 N/A N/A opts args N/A N/A p parse_args args N/A N/A N/A len args 2 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A genomesize N/A N/A float N/A args N/A 0 1000 N/A fnames N/A args N/A 1 N/A x fnames N/A N/A N/A N/A op exists x N/A N/A File `{0}` not found. format x N/A s N/A N/A comment_banner Meraculous params file N/A s N/A N/A comment_banner Basic parameters N/A s # Describe the libraries ( one line per library )
 N/A s N/A N/A #  N/A N/A join N/A N/A header split N/A libs N/A get_libs fnames N/A lib_seqs N/A N/A rank 0 N/A N/A lib fs libs N/A N/A size N/A lib size N/A N/A size 0 N/A N/A N/A rank 1 N/A library_name N/A lib library_name N/A name N/A N/A library_name replace - N/A wildcard N/A N/A {0}*.1.*,{0}*.2.* format library_name N/A rl N/A max N/A N/A readlen N/A x N/A x fs N/A lib_seq N/A N/A lib get_lib_seq wildcard name rl rank N/A N/A N/A lib_seqs append lib_seq N/A s N/A N/A N/A N/A join N/A load_csv None lib_seqs sep N/A params N/A N/A genome_size genomesize N/A is_diploid 0 N/A mer_size N/A opts K N/A num_prefix_blocks 1 N/A no_read_validation 0 N/A local_num_procs N/A opts cpus N/A s N/A N/A N/A N/A join N/A load_csv None params sep N/A cfgfile meraculous.config N/A N/A write_file cfgfile s tee True N/A s N/A N/A ~/export/meraculous/bin/run_meraculous.sh -c {0} format cfgfile N/A runsh run.sh N/A N/A write_file runsh s N/A N/A N/A __name__ __main__ N/A N/A N/A main