How to use the cogent3.draw.linear.Box function in cogent3
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cogent3 / cogent3 / cogent3 / draw / linear.py View on Github 
showLabel=True, closed=False),
'operon': BluntArrow(False, colors.royalblue,
showLabel=True, closed=False),
# regulation
'attenuator': Box(False, colors.red),
'enhancer': Box(True, colors.green),
'CAAT_signal': Diamond(True, colors.blue),
'TATA_signal': Diamond(True, colors.teal),
'promoter': Box(False, colors.seagreen),
'GC_signal': Box(True, colors.purple),
'protein_bind': Box(True, colors.orange),
'misc_binding': Box(False, colors.black),
'-10_signal': Diamond(True, colors.blue),
'-35_signal': Diamond(True, colors.teal),
'terminator': Diamond(True, colors.red),
'misc_signal': Box(False, colors.maroon),
'rep_origin': Box(True, colors.linen),
'RBS': Diamond(True, colors.navy),
# repeats
'repeat_region': Box(True, colors.brown),
'repeat_unit': Arrow(True, colors.brown),
'LTR': Box(False, colors.black),
'satellite': Box(False, colors.brown),
'stem_loop': Box(False, colors.dimgray),
'misc_structure': Box(False, colors.darkslategray),
# rna genes
'rRNA': Arrow(False, colors.darkorchid, showLabel=True),
'scRNA': Arrow(False, colors.darkslateblue, showLabel=True),
'snRNA': Arrow(False, colors.darkviolet, showLabel=True),
'snoRNA': Arrow(False, colors.darkviolet, showLabel=True),
'tRNA': Arrow(False, colors.darkturquoise, showLabel=True),
# sequence'transit_peptide': Box(True, colors.navy),
'polyA_signal': Box(True, colors.lightgreen),
'polyA_site': Diamond(True, colors.lightgreen),
'gene': BluntArrow(False, colors.blue,
showLabel=True, closed=False),
'operon': BluntArrow(False, colors.royalblue,
showLabel=True, closed=False),
# regulation
'attenuator': Box(False, colors.red),
'enhancer': Box(True, colors.green),
'CAAT_signal': Diamond(True, colors.blue),
'TATA_signal': Diamond(True, colors.teal),
'promoter': Box(False, colors.seagreen),
'GC_signal': Box(True, colors.purple),
'protein_bind': Box(True, colors.orange),
'misc_binding': Box(False, colors.black),
'-10_signal': Diamond(True, colors.blue),
'-35_signal': Diamond(True, colors.teal),
'terminator': Diamond(True, colors.red),
'misc_signal': Box(False, colors.maroon),
'rep_origin': Box(True, colors.linen),
'RBS': Diamond(True, colors.navy),
# repeats
'repeat_region': Box(True, colors.brown),
'repeat_unit': Arrow(True, colors.brown),
'LTR': Box(False, colors.black),
'satellite': Box(False, colors.brown),
'stem_loop': Box(False, colors.dimgray),
'misc_structure': Box(False, colors.darkslategray),
# rna genes
'rRNA': Arrow(False, colors.darkorchid, showLabel=True),
'scRNA': Arrow(False, colors.darkslateblue, showLabel=True),'CDS': Box(True, colors.blue),
'mat_peptide': Box(True, colors.blue),
'sig_peptide': Box(True, colors.navy),
'transit_peptide': Box(True, colors.navy),
'polyA_signal': Box(True, colors.lightgreen),
'polyA_site': Diamond(True, colors.lightgreen),
'gene': BluntArrow(False, colors.blue,
showLabel=True, closed=False),
'operon': BluntArrow(False, colors.royalblue,
showLabel=True, closed=False),
# regulation
'attenuator': Box(False, colors.red),
'enhancer': Box(True, colors.green),
'CAAT_signal': Diamond(True, colors.blue),
'TATA_signal': Diamond(True, colors.teal),
'promoter': Box(False, colors.seagreen),
'GC_signal': Box(True, colors.purple),
'protein_bind': Box(True, colors.orange),
'misc_binding': Box(False, colors.black),
'-10_signal': Diamond(True, colors.blue),
'-35_signal': Diamond(True, colors.teal),
'terminator': Diamond(True, colors.red),
'misc_signal': Box(False, colors.maroon),
'rep_origin': Box(True, colors.linen),
'RBS': Diamond(True, colors.navy),
# repeats
'repeat_region': Box(True, colors.brown),
'repeat_unit': Arrow(True, colors.brown),
'LTR': Box(False, colors.black),
'satellite': Box(False, colors.brown),
'stem_loop': Box(False, colors.dimgray),
'misc_structure': Box(False, colors.darkslategray),'sig_peptide': Box(True, colors.navy),
'transit_peptide': Box(True, colors.navy),
'polyA_signal': Box(True, colors.lightgreen),
'polyA_site': Diamond(True, colors.lightgreen),
'gene': BluntArrow(False, colors.blue,
showLabel=True, closed=False),
'operon': BluntArrow(False, colors.royalblue,
showLabel=True, closed=False),
# regulation
'attenuator': Box(False, colors.red),
'enhancer': Box(True, colors.green),
'CAAT_signal': Diamond(True, colors.blue),
'TATA_signal': Diamond(True, colors.teal),
'promoter': Box(False, colors.seagreen),
'GC_signal': Box(True, colors.purple),
'protein_bind': Box(True, colors.orange),
'misc_binding': Box(False, colors.black),
'-10_signal': Diamond(True, colors.blue),
'-35_signal': Diamond(True, colors.teal),
'terminator': Diamond(True, colors.red),
'misc_signal': Box(False, colors.maroon),
'rep_origin': Box(True, colors.linen),
'RBS': Diamond(True, colors.navy),
# repeats
'repeat_region': Box(True, colors.brown),
'repeat_unit': Arrow(True, colors.brown),
'LTR': Box(False, colors.black),
'satellite': Box(False, colors.brown),
'stem_loop': Box(False, colors.dimgray),
'misc_structure': Box(False, colors.darkslategray),
# rna genes
'rRNA': Arrow(False, colors.darkorchid, showLabel=True),'repeat_unit': Arrow(True, colors.brown),
'LTR': Box(False, colors.black),
'satellite': Box(False, colors.brown),
'stem_loop': Box(False, colors.dimgray),
'misc_structure': Box(False, colors.darkslategray),
# rna genes
'rRNA': Arrow(False, colors.darkorchid, showLabel=True),
'scRNA': Arrow(False, colors.darkslateblue, showLabel=True),
'snRNA': Arrow(False, colors.darkviolet, showLabel=True),
'snoRNA': Arrow(False, colors.darkviolet, showLabel=True),
'tRNA': Arrow(False, colors.darkturquoise, showLabel=True),
# sequence
'source': Box(False, colors.black, showLabel=True),
'misc_recomb': Box(False, colors.black, showLabel=True),
'variation': Diamond(True, colors.violet, showLabel=True),
'domain': Box(False, colors.darkorange, showLabel=True),
'bluediamond': Diamond(True, colors.blue),
'reddiamond': Diamond(True, colors.red),
'misc_feature': Box(True, colors.darkorange, showLabel=True),
'old_sequence': Box(False, colors.darkslategray),
'unsure': Diamond(False, colors.crimson, min_width=2,),
'misc_difference': Diamond(False, colors.darkorange),
'conflict': Box(False, colors.darkorange),
'modified_base': Diamond(True, colors.black),
'primer_bind': Arrow(False, colors.green, showLabel=True),
'STS': Box(False, colors.black),
'gap': Box(True, colors.gray),
# graphs
'blueline': Line(False, colors.blue),
'redline': Line(False, colors.red),
# other'TATA_signal': Diamond(True, colors.teal),
'promoter': Box(False, colors.seagreen),
'GC_signal': Box(True, colors.purple),
'protein_bind': Box(True, colors.orange),
'misc_binding': Box(False, colors.black),
'-10_signal': Diamond(True, colors.blue),
'-35_signal': Diamond(True, colors.teal),
'terminator': Diamond(True, colors.red),
'misc_signal': Box(False, colors.maroon),
'rep_origin': Box(True, colors.linen),
'RBS': Diamond(True, colors.navy),
# repeats
'repeat_region': Box(True, colors.brown),
'repeat_unit': Arrow(True, colors.brown),
'LTR': Box(False, colors.black),
'satellite': Box(False, colors.brown),
'stem_loop': Box(False, colors.dimgray),
'misc_structure': Box(False, colors.darkslategray),
# rna genes
'rRNA': Arrow(False, colors.darkorchid, showLabel=True),
'scRNA': Arrow(False, colors.darkslateblue, showLabel=True),
'snRNA': Arrow(False, colors.darkviolet, showLabel=True),
'snoRNA': Arrow(False, colors.darkviolet, showLabel=True),
'tRNA': Arrow(False, colors.darkturquoise, showLabel=True),
# sequence
'source': Box(False, colors.black, showLabel=True),
'misc_recomb': Box(False, colors.black, showLabel=True),
'variation': Diamond(True, colors.violet, showLabel=True),
'domain': Box(False, colors.darkorange, showLabel=True),
'bluediamond': Diamond(True, colors.blue),
'reddiamond': Diamond(True, colors.red),
'misc_feature': Box(True, colors.darkorange, showLabel=True),'mat_peptide': Box(True, colors.blue),
'sig_peptide': Box(True, colors.navy),
'transit_peptide': Box(True, colors.navy),
'polyA_signal': Box(True, colors.lightgreen),
'polyA_site': Diamond(True, colors.lightgreen),
'gene': BluntArrow(False, colors.blue,
showLabel=True, closed=False),
'operon': BluntArrow(False, colors.royalblue,
showLabel=True, closed=False),
# regulation
'attenuator': Box(False, colors.red),
'enhancer': Box(True, colors.green),
'CAAT_signal': Diamond(True, colors.blue),
'TATA_signal': Diamond(True, colors.teal),
'promoter': Box(False, colors.seagreen),
'GC_signal': Box(True, colors.purple),
'protein_bind': Box(True, colors.orange),
'misc_binding': Box(False, colors.black),
'-10_signal': Diamond(True, colors.blue),
'-35_signal': Diamond(True, colors.teal),
'terminator': Diamond(True, colors.red),
'misc_signal': Box(False, colors.maroon),
'rep_origin': Box(True, colors.linen),
'RBS': Diamond(True, colors.navy),
# repeats
'repeat_region': Box(True, colors.brown),
'repeat_unit': Arrow(True, colors.brown),
'LTR': Box(False, colors.black),
'satellite': Box(False, colors.brown),
'stem_loop': Box(False, colors.dimgray),
'misc_structure': Box(False, colors.darkslategray),
# rna genes'stem_loop': Box(False, colors.dimgray),
'misc_structure': Box(False, colors.darkslategray),
# rna genes
'rRNA': Arrow(False, colors.darkorchid, showLabel=True),
'scRNA': Arrow(False, colors.darkslateblue, showLabel=True),
'snRNA': Arrow(False, colors.darkviolet, showLabel=True),
'snoRNA': Arrow(False, colors.darkviolet, showLabel=True),
'tRNA': Arrow(False, colors.darkturquoise, showLabel=True),
# sequence
'source': Box(False, colors.black, showLabel=True),
'misc_recomb': Box(False, colors.black, showLabel=True),
'variation': Diamond(True, colors.violet, showLabel=True),
'domain': Box(False, colors.darkorange, showLabel=True),
'bluediamond': Diamond(True, colors.blue),
'reddiamond': Diamond(True, colors.red),
'misc_feature': Box(True, colors.darkorange, showLabel=True),
'old_sequence': Box(False, colors.darkslategray),
'unsure': Diamond(False, colors.crimson, min_width=2,),
'misc_difference': Diamond(False, colors.darkorange),
'conflict': Box(False, colors.darkorange),
'modified_base': Diamond(True, colors.black),
'primer_bind': Arrow(False, colors.green, showLabel=True),
'STS': Box(False, colors.black),
'gap': Box(True, colors.gray),
# graphs
'blueline': Line(False, colors.blue),
'redline': Line(False, colors.red),
# other# repeats
'repeat_region': Box(True, colors.brown),
'repeat_unit': Arrow(True, colors.brown),
'LTR': Box(False, colors.black),
'satellite': Box(False, colors.brown),
'stem_loop': Box(False, colors.dimgray),
'misc_structure': Box(False, colors.darkslategray),
# rna genes
'rRNA': Arrow(False, colors.darkorchid, showLabel=True),
'scRNA': Arrow(False, colors.darkslateblue, showLabel=True),
'snRNA': Arrow(False, colors.darkviolet, showLabel=True),
'snoRNA': Arrow(False, colors.darkviolet, showLabel=True),
'tRNA': Arrow(False, colors.darkturquoise, showLabel=True),
# sequence
'source': Box(False, colors.black, showLabel=True),
'misc_recomb': Box(False, colors.black, showLabel=True),
'variation': Diamond(True, colors.violet, showLabel=True),
'domain': Box(False, colors.darkorange, showLabel=True),
'bluediamond': Diamond(True, colors.blue),
'reddiamond': Diamond(True, colors.red),
'misc_feature': Box(True, colors.darkorange, showLabel=True),
'old_sequence': Box(False, colors.darkslategray),
'unsure': Diamond(False, colors.crimson, min_width=2,),
'misc_difference': Diamond(False, colors.darkorange),
'conflict': Box(False, colors.darkorange),
'modified_base': Diamond(True, colors.black),
'primer_bind': Arrow(False, colors.green, showLabel=True),
'STS': Box(False, colors.black),
'gap': Box(True, colors.gray),
# graphs
'blueline': Line(False, colors.blue),
'redline': Line(False, colors.red),def _makeFeatureStyles(self):
return {
# gene structure
'misc_RNA': Box(True, colors.lightcyan),
'precursor_RNA': Box(True, colors.lightcyan),
'prim_transcript': Box(True, colors.lightcyan),
"3'clip": Box(True, colors.lightcyan),
"5'clip": Box(True, colors.lightcyan),
'mRNA': Box(True, colors.cyan),
'exon': Box(True, colors.cyan),
'intron': Box(False, colors.cyan, closed=False),
"3'UTR": Box(True, colors.cyan),
"5'UTR": Box(True, colors.cyan),
'CDS': Box(True, colors.blue),
'mat_peptide': Box(True, colors.blue),
'sig_peptide': Box(True, colors.navy),
'transit_peptide': Box(True, colors.navy),
'polyA_signal': Box(True, colors.lightgreen),
'polyA_site': Diamond(True, colors.lightgreen),
'gene': BluntArrow(False, colors.blue,
showLabel=True, closed=False),
'operon': BluntArrow(False, colors.royalblue,cogent3
COmparative GENomics Toolkit 3: genomic sequence analysis within notebooks or on compute systems with 1000s of CPUs.
Package Health Score
81 / 100Popular cogent3 functions
- cogent3.app.evo.model
- cogent3.core.alignment.ArrayAlignment
- cogent3.core.location.Span
- cogent3.core.tree.TreeNode
- cogent3.DNA
- cogent3.DNA.make_seq
- cogent3.draw.linear.Box
- cogent3.evolve.models.get_model
- cogent3.evolve.substitution_model.TimeReversibleNucleotide
- cogent3.load_aligned_seqs
- cogent3.make_aligned_seqs
- cogent3.make_tree
- cogent3.maths.stats.number.CategoryCounter
- cogent3.parse.tree.DndParser
- cogent3.util.dict2d.Dict2D
- cogent3.util.dict_array.DictArrayTemplate
- cogent3.util.misc.get_object_provenance
- cogent3.util.table.Table
- cogent3.util.union_dict.UnionDict
- cogent3.util.unit_test.TestCase