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Publication-quality bioinformatics figures - phylogenetic trees, genome browsers, iTOL datasets, and data presentation
npx skill4agent add delphine-l/claude_global bioinformatics-visualizationDATASET_BINARY
SEPARATOR TAB
DATASET_LABEL CLR Technology
COLOR #ff0000
LEGEND_TITLE Sequencing Technology
LEGEND_SHAPES 2
LEGEND_COLORS #ff0000
LEGEND_LABELS CLR (PacBio)
FIELD_SHAPES 2
FIELD_COLORS #ff0000
FIELD_LABELS CLR
DATA
Species_name_1 1
Species_name_2 0
Species_name_3 1species<tab>0_or_1# Convert scientific names to tree format with case normalization
df['species_tree'] = df['scientific_name'].str.replace(' ', '_')
# Fix uppercase after underscore (Alca_Torda -> Alca_torda)
df['species_tree'] = df['species_tree'].str.replace(
r'_([A-Z])',
lambda m: '_' + m.group(1).lower(),
regex=True
)# Always validate species compatibility
import re
# Extract species from tree
with open('tree.nwk') as f:
tree_content = f.read()
tree_species = set(re.findall(r'([A-Z][a-z]+_[a-z]+)', tree_content))
# Check config species
config_species = set(df['species_tree'])
missing = config_species - tree_species
if missing:
print(f"Species in config but not in tree: {missing}")#ffffcc#b10026