Module Import alias alias alias ImportFrom alias ImportFrom alias alias Import alias FunctionDef arguments args defaults body Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Str keyword Str keyword Str Assign NameStore Call AttributeLoad NameLoad attr Return NameLoad decorator_list Assign NameStore Call NameLoad If AttributeLoad NameLoad attr body Assign NameStore Str Assign NameStore AttributeLoad NameLoad attr If AttributeLoad NameLoad attr body Assign NameStore Str Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr If NameLoad body Assign NameStore ListLoad Str orelse Assign NameStore ListLoad Str Str Assign NameStore Call NameLoad FunctionDef arguments args NameParam defaults body For TupleStore NameStore NameStore Call NameLoad NameLoad body Assign NameStore SubscriptLoad NameLoad Index NameLoad Print SubscriptLoad NameLoad Index NameLoad Assign SubscriptStore NameLoad Index SubscriptLoad NameLoad Index NameLoad Call NameLoad keyword NameLoad keyword SubscriptLoad NameLoad Index NameLoad keyword NameLoad keyword NameLoad keyword SubscriptLoad NameLoad Index NameLoad keyword NameLoad keyword NameLoad keyword NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults ListLoad Str body Expr Str With Call NameLoad NameLoad Str NameStore body Print NameLoad Str For NameStore Call AttributeLoad NameLoad attr body If AttributeLoad NameLoad attr body Assign NameStore SubscriptLoad NameLoad Index NameLoad orelse Assign NameStore AttributeLoad SubscriptLoad NameLoad Index NameLoad attr For NameStore Call AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr For NameStore NameLoad body For TupleStore NameStore NameStore Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr body Print NameLoad BinOpMod Str TupleLoad NameLoad NameLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults ListLoad Str body With Call NameLoad NameLoad Str NameStore body Print NameLoad Str For NameStore Call AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr Assign NameStore Str For NameStore NameLoad body For TupleStore NameStore NameStore Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr body Print NameLoad BinOpMod Str TupleLoad NameLoad NameLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore Call NameLoad With Call NameLoad NameLoad NameStore body For NameStore NameLoad body If CompareEq SubscriptLoad NameLoad Index Num Str body Continue Assign NameStore Call AttributeLoad SubscriptLoad NameLoad Slice Num attr Str Assign NameStore SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad Call AttributeLoad SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Index Num attr Str Index Num attr Str Index Num Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Num Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Num Assign NameStore SubscriptLoad NameLoad Index Num For NameStore Call AttributeLoad NameLoad attr body If UnaryOpNot Call AttributeLoad NameLoad attr NameLoad body Assign SubscriptStore NameLoad Index NameLoad Dict Assign NameStore Call NameLoad NameLoad NameLoad SubscriptLoad AttributeLoad SubscriptLoad NameLoad Index NameLoad attr Index NameLoad If CompareEq NameLoad Str body Assign AttributeStore NameLoad attr DictComp BinOpMult NameLoad Num NameLoad comprehension TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Assign AttributeStore NameLoad attr NameLoad Assign SubscriptStore SubscriptLoad NameLoad Index NameLoad Index NameLoad NameLoad Return NameLoad decorator_list Assign NameStore Call NameLoad NameLoad If AttributeLoad NameLoad attr body Assign NameStore Call NameLoad NameLoad AttributeLoad NameLoad attr If NameLoad body Expr Call NameLoad NameLoad NameLoad NameLoad orelse Expr Call NameLoad NameLoad NameLoad NameLoad Assign NameStore BinOpAdd Str NameLoad Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr
N/A N/A sys subprocess argparse smRtools * collections OrderedDict defaultdict N/A os Parser N/A N/A N/A N/A N/A the_parser N/A N/A argparse ArgumentParser N/A N/A N/A the_parser add_argument --output_size_distribution action store type str help size distribution dataframe N/A N/A N/A the_parser add_argument --reference_fasta action store type str help output file N/A N/A N/A the_parser add_argument --reference_bowtie_index action store help paths to indexed or fasta references N/A N/A N/A the_parser add_argument --input nargs + help paths to multiple input files N/A N/A N/A the_parser add_argument --ext nargs + help input file type N/A N/A N/A the_parser add_argument --label nargs + help labels of multiple input files N/A N/A N/A the_parser add_argument --normalization_factor nargs + type float help Normalization factor for input file N/A N/A N/A the_parser add_argument --gff type str help GFF containing regions of interest N/A N/A N/A the_parser add_argument --minquery type int help Minimum readsize N/A N/A N/A the_parser add_argument --maxquery type int help Maximum readsize N/A N/A N/A the_parser add_argument --rcode type str help R script N/A N/A N/A the_parser add_argument --global_size action store_true help if specified, size distribution is calcilated for the sum of all items N/A N/A N/A the_parser add_argument --collapse action store_true help if specified, forward and reverse reads are collapsed N/A args N/A N/A the_parser parse_args N/A args N/A N/A args N/A Parser N/A N/A args reference_fasta N/A N/A genomeRefFormat fastaSource N/A genomeRefFile N/A args reference_fasta N/A N/A args reference_bowtie_index N/A N/A genomeRefFormat bowtieIndex N/A genomeRefFile N/A args reference_bowtie_index N/A size_distribution_file N/A args output_size_distribution N/A minquery N/A args minquery N/A maxquery N/A args maxquery N/A Rcode N/A args rcode N/A filePath N/A args input N/A fileExt N/A args ext N/A fileLabel N/A args label N/A normalization_factor N/A args normalization_factor N/A global_size N/A args global_size N/A collapse N/A args collapse N/A collapse N/A N/A pol N/A both N/A N/A pol N/A F R N/A MasterListOfGenomes N/A OrderedDict process_samples N/A N/A filePath N/A N/A N/A N/A i filePath N/A enumerate filePath N/A N/A norm N/A normalization_factor N/A i N/A N/A fileLabel N/A i N/A N/A MasterListOfGenomes N/A N/A fileLabel N/A i N/A HandleSmRNAwindows alignmentFile filePath alignmentFileFormat N/A fileExt N/A i genomeRefFile genomeRefFile genomeRefFormat genomeRefFormat biosample N/A fileLabel N/A i size_inf minquery size_sup maxquery norm norm N/A MasterListOfGenomes N/A write_size_distribution_dataframe N/A N/A readDict size_distribution_file pol N/A N/A both N/A N/A refactored on 7-9-2014 N/A N/A open size_distribution_file w size_distrib N/A N/A size_distrib gene	polarity	size	count	sample N/A sample N/A N/A readDict keys N/A N/A N/A args gff N/A N/A dict N/A readDict N/A sample N/A N/A dict N/A N/A readDict N/A sample instanceDict N/A gene N/A N/A dict keys N/A N/A histogram N/A N/A N/A dict N/A gene size_histogram N/A polarity pol N/A N/A N/A size count N/A N/A N/A histogram N/A polarity iteritems N/A N/A size_distrib N/A %s	%s	%s	%s	%s N/A gene polarity size count sample N/A write_size_distribution_dataframe_global N/A N/A readDict size_distribution_file pol N/A N/A both N/A N/A N/A open size_distribution_file w size_distrib N/A N/A size_distrib gene	polarity	size	count	sample N/A sample N/A N/A readDict keys N/A N/A histogram N/A N/A N/A readDict N/A sample size_histogram N/A gene sample N/A polarity pol N/A N/A N/A size count N/A N/A N/A histogram N/A polarity iteritems N/A N/A size_distrib N/A %s	%s	%s	%s	%s N/A gene polarity size count sample N/A gff_item_subinstances N/A N/A readDict gff3 N/A N/A N/A GFFinstanceDict N/A OrderedDict N/A N/A open gff3 gff N/A N/A line gff N/A N/A N/A N/A line N/A 0 # N/A N/A N/A gff_fields N/A N/A N/A line N/A -1 split N/A chrom N/A gff_fields N/A 0 N/A gff_name N/A N/A N/A N/A N/A N/A N/A gff_fields N/A -1 split Name= N/A -1 split ; N/A 0 N/A item_upstream_coordinate N/A int N/A gff_fields N/A 3 N/A item_downstream_coordinate N/A int N/A gff_fields N/A 4 N/A item_polarity N/A gff_fields N/A 6 N/A sample N/A N/A readDict keys N/A N/A N/A N/A N/A GFFinstanceDict has_key sample N/A N/A N/A GFFinstanceDict N/A sample N/A N/A subinstance N/A extractsubinstance item_upstream_coordinate item_downstream_coordinate N/A N/A N/A readDict N/A sample instanceDict N/A chrom N/A N/A item_polarity - N/A N/A N/A subinstance readDict N/A N/A key -1 value N/A N/A key value N/A N/A N/A subinstance readDict iteritems N/A N/A subinstance gene gff_name N/A N/A N/A GFFinstanceDict N/A sample N/A gff_name subinstance N/A GFFinstanceDict N/A N/A MasterListOfGenomes N/A process_samples filePath N/A N/A args gff N/A N/A MasterListOfGenomes N/A gff_item_subinstances MasterListOfGenomes N/A args gff N/A global_size N/A N/A N/A write_size_distribution_dataframe_global MasterListOfGenomes size_distribution_file pol N/A N/A N/A write_size_distribution_dataframe MasterListOfGenomes size_distribution_file pol N/A R_command N/A Rscript  Rcode N/A process N/A N/A subprocess Popen N/A N/A R_command split N/A N/A N/A process wait