Module Expr Str Import alias Import alias Import alias ImportFrom alias Assign NameStore Call NameLoad keyword Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Str Str keyword NameLoad ClassDef bases AttributeLoad NameLoad attr body FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Str Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Str Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Str Expr Call AttributeLoad AttributeLoad AttributeLoad NameLoad attr attr attr NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Str Str decorator_list decorator_list If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr
N/A N/A 
Tests for gtfutils / tobed
 N/A unittest N/A StringIO N/A ngsutils.gtf.tobed ngsutils.gtf GTF N/A gtf N/A GTF fileobj N/A N/A StringIO StringIO N/A N/A chr1|test|exon|1001|1100|0|+|.|gene_id "foo1"; transcript_id "bar1"; isoform_id "iso1"
chr1|test|exon|1201|1300|0|+|.|gene_id "foo1"; transcript_id "bar1"; isoform_id "iso1"
chr1|test|exon|1401|1500|0|+|.|gene_id "foo1"; transcript_id "bar1"; isoform_id "iso1"
chr1|test|CDS|1051|1447|0|+|1|gene_id "foo1"; transcript_id "bar1"; isoform_id "iso1"
chr1|test|start_codon|1051|1053|0|+|.|gene_id "foo1"; transcript_id "bar1"; isoform_id "iso1"
chr1|test|stop_codon|1448|1450|0|+|.|gene_id "foo1"; transcript_id "bar1"; isoform_id "iso1"
chr1|test|exon|1001|1100|0|+|.|gene_id "foo2"; transcript_id "bar2"; isoform_id "iso1"
chr1|test|exon|1401|1500|0|+|.|gene_id "foo2"; transcript_id "bar2"; isoform_id "iso1"
chr1|test|CDS|1051|1447|0|+|1|gene_id "foo2"; transcript_id "bar2"; isoform_id "iso1"
chr1|test|start_codon|1051|1053|0|+|.|gene_id "foo2"; transcript_id "bar2"; isoform_id "iso1"
chr1|test|stop_codon|1448|1450|0|+|.|gene_id "foo2"; transcript_id "bar2"; isoform_id "iso1"
 replace | quiet True GTFTest N/A N/A unittest TestCase N/A testGeneToBed N/A N/A self N/A N/A N/A out N/A N/A StringIO StringIO N/A N/A N/A N/A N/A ngsutils gtf tobed gtf_genes_tobed gtf out out N/A N/A N/A self assertEquals N/A N/A N/A N/A out getvalue replace | chr1|1000|1500|foo1|0|+
 N/A testExonToBed N/A N/A self N/A N/A N/A out N/A N/A StringIO StringIO N/A N/A N/A N/A N/A ngsutils gtf tobed gtf_exons_tobed gtf out out N/A N/A N/A self assertEquals N/A N/A N/A N/A out getvalue replace | chr1|1000|1100|foo1.1|0|+
chr1|1200|1300|foo1.2|0|+
chr1|1400|1500|foo1.3|0|+
 N/A testRegionToBed N/A N/A self N/A N/A N/A out N/A N/A StringIO StringIO N/A N/A N/A N/A N/A ngsutils gtf tobed gtf_regions_tobed gtf out out N/A N/A N/A self assertEquals N/A N/A N/A N/A out getvalue replace | chr1|1000|1100|foo1.const.1|2|+
chr1|1200|1300|foo1.alt.2|1|+
chr1|1400|1500|foo1.const.3|2|+
 N/A N/A N/A N/A __name__ __main__ N/A N/A N/A N/A unittest main