Module Expr Str Import alias Import alias identifier Import alias Import alias ImportFrom alias alias alias alias alias FunctionDef arguments args defaults body Assign NameStore TupleLoad TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str 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 ImportFrom alias ImportFrom alias Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore NameLoad Assign NameStore BinOpAdd NameLoad Str Assign NameStore BinOpAdd NameLoad Str If Call NameLoad TupleLoad NameLoad NameLoad TupleLoad NameLoad NameLoad body Assign NameStore Call AttributeLoad Str attr AttributeLoad NameLoad attr AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad NameLoad Expr Call NameLoad NameLoad Assign NameStore BinOpAdd SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Str If Call NameLoad NameLoad NameLoad body Assign NameStore Call AttributeLoad Str attr NameLoad Expr Call NameLoad NameLoad keyword NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad Assign NameStore BinOpAdd SubscriptLoad Call AttributeLoad NameLoad attr Str Num Index Num Str Assign NameStore Call NameLoad NameLoad Str Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Assign NameStore AttributeLoad NameLoad attr If CompareIn Str NameLoad body Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index Str Index Num orelse Assign NameStore SubscriptLoad SubscriptLoad NameLoad Index Str Index Num Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num If CompareNotIn NameLoad NameLoad body Continue Print NameLoad NameLoad If CompareEq AttributeLoad NameLoad attr Str body Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str keyword Str Expr Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad NameLoad attr keyword Num Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Str Assert Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad Str attr NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr AttributeLoad NameLoad attr If NameLoad body Assign NameStore Str If Call NameLoad NameLoad NameLoad body Assign NameStore Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad NameLoad Expr Call NameLoad NameLoad AugAssignAdd NameStore Call AttributeLoad Str attr NameLoad orelse AugAssignAdd NameStore Str Expr Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Str decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore NameStore NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore Str Expr Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Str Expr Call AttributeLoad NameLoad attr Str Expr Call NameLoad Call AttributeLoad Str attr NameLoad NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Str Expr Call NameLoad Call AttributeLoad Str attr NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore NameStore NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore Str Assign NameStore Call AttributeLoad NameLoad attr Expr Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad Str attr NameLoad NameLoad If Call AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad NameLoad NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad NameLoad Expr Call NameLoad Str Expr Call NameLoad Call AttributeLoad Str attr NameLoad Expr Call NameLoad Str If AttributeLoad NameLoad attr body Expr Call NameLoad Call AttributeLoad Str attr NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Call NameLoad Call AttributeLoad Str attr NameLoad decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A N/A 
Train ab initio gene predictors.
 N/A os N/A os.path op N/A sys N/A logging jcvi.apps.base OptionParser ActionDispatcher mkdir sh need_update main N/A N/A N/A N/A N/A actions N/A N/A pasa extract pasa training models N/A snap train snap model N/A augustus train augustus model N/A genemark train genemark model N/A p N/A ActionDispatcher actions N/A N/A N/A p dispatch N/A globals N/A pasa N/A N/A args N/A N/A N/A 
    %prog ${pasadb}.assemblies.fasta ${pasadb}.pasa_assemblies.gff3

    Wraps `pasa_asmbls_to_training_set.dbi`.
     jcvi.formats.base SetFile jcvi.formats.gff Gff N/A p N/A OptionParser N/A pasa __doc__ N/A N/A N/A p set_home pasa 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 N/A fastafile gffile args N/A transcodergff N/A fastafile .transdecoder.gff3 N/A transcodergenomegff N/A fastafile .transdecoder.genome.gff3 N/A N/A need_update N/A fastafile gffile N/A transcodergff transcodergenomegff N/A N/A cmd N/A N/A {0}/scripts/pasa_asmbls_to_training_set.dbi format N/A opts pasa_home N/A cmd N/A N/A  --pasa_transcripts_fasta {0} --pasa_transcripts_gff3 {1} format fastafile gffile N/A N/A sh cmd N/A completeids N/A N/A N/A N/A fastafile rsplit . 1 N/A 0 .complete.ids N/A N/A need_update transcodergff completeids N/A N/A cmd N/A N/A grep complete {0} | cut -f1 | sort -u format transcodergff N/A N/A sh cmd outfile completeids N/A complete N/A SetFile completeids N/A seen N/A set N/A completegff N/A N/A N/A N/A transcodergenomegff rsplit . 1 N/A 0 .complete.gff3 N/A fw N/A open completegff w N/A gff N/A Gff transcodergenomegff N/A g gff N/A N/A a N/A g attributes N/A N/A Parent a N/A N/A id N/A N/A a N/A Parent N/A 0 N/A N/A id N/A N/A a N/A ID N/A 0 N/A asmbl_id N/A N/A N/A id split | N/A 0 N/A N/A asmbl_id complete N/A N/A N/A fw g N/A N/A N/A g type gene N/A N/A N/A N/A seen add id N/A N/A N/A fw close N/A N/A N/A logging debug N/A N/A A total of {0} complete models extracted to `{1}`. format N/A len seen completegff N/A genemark N/A N/A args N/A N/A N/A 
    %prog genemark species fastafile

    Train GENEMARK model given fastafile. GENEMARK self-trains so no trainig
    model gff file is needed.
     N/A p N/A OptionParser N/A genemark __doc__ N/A N/A N/A p add_option --junctions help Path to `junctions.bed` from Tophat2 N/A N/A N/A p set_home gmes 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 N/A species fastafile args N/A junctions N/A opts junctions N/A mhome N/A opts gmes_home N/A license N/A N/A op expanduser ~/.gm_key N/A N/A N/A op exists license N/A N/A License key ({0}) not found! format license N/A cmd N/A N/A {0}/gmes_petap.pl --sequence {1} format mhome fastafile N/A cmd N/A N/A  --cores {0} format N/A opts cpus N/A junctions N/A N/A intronsgff introns.gff N/A N/A need_update junctions intronsgff N/A N/A jcmd N/A N/A {0}/bet_to_gff.pl format mhome N/A jcmd N/A N/A  --bed {0} --gff {1} --label Tophat2 format junctions intronsgff N/A N/A sh jcmd N/A cmd N/A N/A  --ET {0} --et_score 10 format intronsgff N/A N/A cmd  --ES N/A N/A sh cmd N/A N/A N/A logging debug GENEMARK matrix written to `output/gmhmm.mod N/A snap N/A N/A args N/A N/A N/A 
    %prog snap species gffile fastafile

    Train SNAP model given gffile and fastafile. Whole procedure taken from:
    <http://gmod.org/wiki/MAKER_Tutorial_2012>
     N/A p N/A OptionParser N/A snap __doc__ N/A N/A N/A p set_home maker N/A N/A opts args N/A N/A p parse_args args N/A N/A N/A len args 3 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A species gffile fastafile args N/A mhome N/A opts maker_home N/A snapdir snap N/A N/A mkdir snapdir N/A cwd N/A N/A os getcwd N/A N/A N/A os chdir snapdir N/A newgffile training.gff3 N/A N/A N/A logging debug Construct GFF file combined with sequence ... N/A N/A sh N/A N/A cat ../{0} > {1} format gffile newgffile N/A N/A sh N/A N/A echo "##FASTA" >> {0} format newgffile N/A N/A sh N/A N/A cat ../{0} >> {1} format fastafile newgffile N/A N/A N/A logging debug Make models ... N/A N/A sh N/A N/A {0}/src/bin/maker2zff training.gff3 format mhome N/A N/A sh N/A N/A {0}/exe/snap/fathom -categorize 1000 genome.ann genome.dna format mhome N/A N/A sh N/A N/A {0}/exe/snap/fathom -export 1000 -plus uni.ann uni.dna format mhome N/A N/A sh N/A N/A {0}/exe/snap/forge export.ann export.dna format mhome N/A N/A sh N/A N/A {0}/exe/snap/hmm-assembler.pl {1} . > {1}.hmm format mhome species N/A N/A N/A os chdir cwd N/A N/A N/A logging debug N/A N/A SNAP matrix written to `{0}/{1}.hmm` format snapdir species N/A augustus N/A N/A args N/A N/A N/A 
    %prog augustus species gffile fastafile

    Train AUGUSTUS model given gffile and fastafile. Whole procedure taken from:
    <http://www.molecularevolution.org/molevolfiles/exercises/augustus/training.html>
     N/A p N/A OptionParser N/A snap __doc__ N/A N/A N/A p add_option --autotrain default False action store_true help Run autoAugTrain.pl to iteratively train AUGUSTUS N/A N/A N/A p set_home augustus N/A N/A opts args N/A N/A p parse_args args N/A N/A N/A len args 3 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A species gffile fastafile args N/A mhome N/A opts augustus_home N/A augdir augustus N/A cwd N/A N/A os getcwd N/A N/A mkdir augdir N/A N/A N/A os chdir augdir N/A target N/A N/A {0}/config/species/{1} format mhome species N/A N/A N/A op exists target N/A N/A N/A N/A logging debug N/A N/A Removing existing target `{0}` format target N/A N/A sh N/A N/A rm -rf {0} format target N/A N/A sh N/A N/A {0}/scripts/new_species.pl --species={1} format mhome species N/A N/A sh N/A N/A {0}/scripts/gff2gbSmallDNA.pl ../{1} ../{2} 1000 raw.gb format mhome gffile fastafile N/A N/A sh N/A N/A {0}/bin/etraining --species={1} raw.gb 2> train.err format mhome species N/A N/A sh cat train.err | perl -pe 's/.*in sequence (\S+): .*/$1/' > badgenes.lst N/A N/A sh N/A N/A {0}/scripts/filterGenes.pl badgenes.lst raw.gb > training.gb format mhome N/A N/A sh grep -c LOCUS raw.gb training.gb N/A N/A opts autotrain N/A N/A N/A sh N/A N/A rm -rf {0} format target N/A N/A sh N/A N/A {0}/scripts/autoAugTrain.pl --trainingset=training.gb --species={1} format mhome species N/A N/A N/A os chdir cwd N/A N/A sh N/A N/A cp -r {0} augustus/ format target N/A N/A N/A __name__ __main__ N/A N/A N/A main