Example Gallery

In [1]:

# !pip install pygenomeviz
# !apt install ncbi-blast+ mummer mmseqs2

# !pip install pygenomeviz # !apt install ncbi-blast+ mummer mmseqs2

Yersinia phage¶

In [2]:

from pygenomeviz import GenomeViz
from pygenomeviz.parser import Genbank
from pygenomeviz.utils import load_example_genbank_dataset
from pygenomeviz.align import Blast, AlignCoord

gbk_files = load_example_genbank_dataset("yersinia_phage")
gbk_list = list(map(Genbank, gbk_files))

gv = GenomeViz(track_align_type="center")
gv.set_scale_bar()

# Plot CDS features
for gbk in gbk_list:
    track = gv.add_feature_track(gbk.name, gbk.get_seqid2size(), align_label=False)
    for seqid, features in gbk.get_seqid2features("CDS").items():
        segment = track.get_segment(seqid)
        segment.add_features(features, plotstyle="bigarrow", fc="limegreen", lw=0.5)

# Run BLAST alignment & filter by user-defined threshold
align_coords = Blast(gbk_list, seqtype="protein").run()
align_coords = AlignCoord.filter(align_coords, length_thr=100, identity_thr=30)

# Plot BLAST alignment links
if len(align_coords) > 0:
    min_ident = int(min([ac.identity for ac in align_coords if ac.identity]))
    color, inverted_color = "grey", "red"
    for ac in align_coords:
        gv.add_link(ac.query_link, ac.ref_link, color=color, inverted_color=inverted_color, v=ac.identity, vmin=min_ident)
    gv.set_colorbar([color, inverted_color], vmin=min_ident)

fig = gv.plotfig()
# gv.savefig("result.png")
# gv.savefig_html("result.html")

from pygenomeviz import GenomeViz from pygenomeviz.parser import Genbank from pygenomeviz.utils import load_example_genbank_dataset from pygenomeviz.align import Blast, AlignCoord gbk_files = load_example_genbank_dataset("yersinia_phage") gbk_list = list(map(Genbank, gbk_files)) gv = GenomeViz(track_align_type="center") gv.set_scale_bar() # Plot CDS features for gbk in gbk_list: track = gv.add_feature_track(gbk.name, gbk.get_seqid2size(), align_label=False) for seqid, features in gbk.get_seqid2features("CDS").items(): segment = track.get_segment(seqid) segment.add_features(features, plotstyle="bigarrow", fc="limegreen", lw=0.5) # Run BLAST alignment & filter by user-defined threshold align_coords = Blast(gbk_list, seqtype="protein").run() align_coords = AlignCoord.filter(align_coords, length_thr=100, identity_thr=30) # Plot BLAST alignment links if len(align_coords) > 0: min_ident = int(min([ac.identity for ac in align_coords if ac.identity])) color, inverted_color = "grey", "red" for ac in align_coords: gv.add_link(ac.query_link, ac.ref_link, color=color, inverted_color=inverted_color, v=ac.identity, vmin=min_ident) gv.set_colorbar([color, inverted_color], vmin=min_ident) fig = gv.plotfig() # gv.savefig("result.png") # gv.savefig_html("result.html")

Enterobacteria phage¶

In [3]:

from pygenomeviz import GenomeViz
from pygenomeviz.parser import Genbank
from pygenomeviz.utils import load_example_genbank_dataset
from pygenomeviz.align import MMseqs

gbk_files = load_example_genbank_dataset("enterobacteria_phage")
gbk_list = list(map(Genbank, gbk_files))

gv = GenomeViz(fig_track_height=0.8, feature_track_ratio=0.4)
gv.set_scale_xticks()

# Plot CDS features
for gbk in gbk_list:
    track = gv.add_feature_track(gbk.name, gbk.get_seqid2size(), align_label=False)
    for seqid, features in gbk.get_seqid2features("CDS").items():
        segment = track.get_segment(seqid)
        segment.add_features(features, fc="skyblue", lw=0.5)

# Run MMseqs RBH search
align_coords = MMseqs(gbk_list).run()

# Plot MMseqs RBH search links
if len(align_coords) > 0:
    min_ident = int(min([ac.identity for ac in align_coords if ac.identity]))
    color, inverted_color = "chocolate", "limegreen"
    for ac in align_coords:
        gv.add_link(ac.query_link, ac.ref_link, color=color, inverted_color=inverted_color, v=ac.identity, vmin=min_ident, curve=True)
    gv.set_colorbar([color, inverted_color], vmin=min_ident)

fig = gv.plotfig()

from pygenomeviz import GenomeViz from pygenomeviz.parser import Genbank from pygenomeviz.utils import load_example_genbank_dataset from pygenomeviz.align import MMseqs gbk_files = load_example_genbank_dataset("enterobacteria_phage") gbk_list = list(map(Genbank, gbk_files)) gv = GenomeViz(fig_track_height=0.8, feature_track_ratio=0.4) gv.set_scale_xticks() # Plot CDS features for gbk in gbk_list: track = gv.add_feature_track(gbk.name, gbk.get_seqid2size(), align_label=False) for seqid, features in gbk.get_seqid2features("CDS").items(): segment = track.get_segment(seqid) segment.add_features(features, fc="skyblue", lw=0.5) # Run MMseqs RBH search align_coords = MMseqs(gbk_list).run() # Plot MMseqs RBH search links if len(align_coords) > 0: min_ident = int(min([ac.identity for ac in align_coords if ac.identity])) color, inverted_color = "chocolate", "limegreen" for ac in align_coords: gv.add_link(ac.query_link, ac.ref_link, color=color, inverted_color=inverted_color, v=ac.identity, vmin=min_ident, curve=True) gv.set_colorbar([color, inverted_color], vmin=min_ident) fig = gv.plotfig()

Acinetobacter phage¶

In [4]:

from pygenomeviz import GenomeViz
from pygenomeviz.parser import Genbank
from pygenomeviz.utils import load_example_genbank_dataset
from pygenomeviz.align import MMseqs

gbk_files = load_example_genbank_dataset("acinetobacter_phage")
gbk_list = list(map(Genbank, gbk_files))

gv = GenomeViz(fig_track_height=0.8, feature_track_ratio=0.4)
gv.set_scale_xticks()

# Plot CDS features
for gbk in gbk_list:
    track = gv.add_feature_track(gbk.name, gbk.get_seqid2size(), align_label=False)
    for seqid, features in gbk.get_seqid2features("CDS").items():
        segment = track.get_segment(seqid)
        segment.add_features(features, fc="lightgreen", lw=0.2)

# Run MMseqs RBH search
align_coords = MMseqs(gbk_list).run()

# Plot MMseqs RBH search links
if len(align_coords) > 0:
    min_ident = int(min([ac.identity for ac in align_coords if ac.identity]))
    color, inverted_color = "skyblue", "salmon"
    for ac in align_coords:
        gv.add_link(ac.query_link, ac.ref_link, color=color, inverted_color=inverted_color, v=ac.identity, vmin=min_ident, curve=True)
    gv.set_colorbar([color, inverted_color], vmin=min_ident)

fig = gv.plotfig()

from pygenomeviz import GenomeViz from pygenomeviz.parser import Genbank from pygenomeviz.utils import load_example_genbank_dataset from pygenomeviz.align import MMseqs gbk_files = load_example_genbank_dataset("acinetobacter_phage") gbk_list = list(map(Genbank, gbk_files)) gv = GenomeViz(fig_track_height=0.8, feature_track_ratio=0.4) gv.set_scale_xticks() # Plot CDS features for gbk in gbk_list: track = gv.add_feature_track(gbk.name, gbk.get_seqid2size(), align_label=False) for seqid, features in gbk.get_seqid2features("CDS").items(): segment = track.get_segment(seqid) segment.add_features(features, fc="lightgreen", lw=0.2) # Run MMseqs RBH search align_coords = MMseqs(gbk_list).run() # Plot MMseqs RBH search links if len(align_coords) > 0: min_ident = int(min([ac.identity for ac in align_coords if ac.identity])) color, inverted_color = "skyblue", "salmon" for ac in align_coords: gv.add_link(ac.query_link, ac.ref_link, color=color, inverted_color=inverted_color, v=ac.identity, vmin=min_ident, curve=True) gv.set_colorbar([color, inverted_color], vmin=min_ident) fig = gv.plotfig()

Mycoplasma mycoides¶

In [5]:

from pygenomeviz import GenomeViz
from pygenomeviz.parser import Genbank
from pygenomeviz.utils import load_example_genbank_dataset, is_pseudo_feature
from pygenomeviz.align import MUMmer

gbk_files = load_example_genbank_dataset("mycoplasma_mycoides")
gbk_list = list(map(Genbank, gbk_files))

gv = GenomeViz()
gv.set_scale_bar()

# Plot CDS, rRNA features for each contig to tracks
for gbk in gbk_list:
    track = gv.add_feature_track(gbk.name, gbk.get_seqid2size(), align_label=False)
    for seqid, features in gbk.get_seqid2features(None).items():
        segment = track.get_segment(seqid)
        for feature in features:
            if feature.type == "CDS":
                # CDS: blue, CDS(pseudo): grey
                color = "grey" if is_pseudo_feature(feature) else "blue"
                segment.add_features(feature, fc=color)
            elif feature.type == "rRNA":
                # rRNA: lime
                segment.add_features(feature, fc="lime")

# Run MUMmer alignment
align_coords = MUMmer(gbk_list).run()

# Plot MUMmer alignment links
if len(align_coords) > 0:
    min_ident = int(min([ac.identity for ac in align_coords if ac.identity]))
    color, inverted_color = "grey", "red"
    for ac in align_coords:
        gv.add_link(ac.query_link, ac.ref_link, color=color, inverted_color=inverted_color, v=ac.identity, vmin=min_ident)
    gv.set_colorbar([color, inverted_color], vmin=min_ident)

fig = gv.plotfig()

from pygenomeviz import GenomeViz from pygenomeviz.parser import Genbank from pygenomeviz.utils import load_example_genbank_dataset, is_pseudo_feature from pygenomeviz.align import MUMmer gbk_files = load_example_genbank_dataset("mycoplasma_mycoides") gbk_list = list(map(Genbank, gbk_files)) gv = GenomeViz() gv.set_scale_bar() # Plot CDS, rRNA features for each contig to tracks for gbk in gbk_list: track = gv.add_feature_track(gbk.name, gbk.get_seqid2size(), align_label=False) for seqid, features in gbk.get_seqid2features(None).items(): segment = track.get_segment(seqid) for feature in features: if feature.type == "CDS": # CDS: blue, CDS(pseudo): grey color = "grey" if is_pseudo_feature(feature) else "blue" segment.add_features(feature, fc=color) elif feature.type == "rRNA": # rRNA: lime segment.add_features(feature, fc="lime") # Run MUMmer alignment align_coords = MUMmer(gbk_list).run() # Plot MUMmer alignment links if len(align_coords) > 0: min_ident = int(min([ac.identity for ac in align_coords if ac.identity])) color, inverted_color = "grey", "red" for ac in align_coords: gv.add_link(ac.query_link, ac.ref_link, color=color, inverted_color=inverted_color, v=ac.identity, vmin=min_ident) gv.set_colorbar([color, inverted_color], vmin=min_ident) fig = gv.plotfig()

Escherichia coli¶

In [1]:

from pygenomeviz import GenomeViz
from pygenomeviz.align import MUMmer
from pygenomeviz.parser import Genbank
from pygenomeviz.utils import load_example_genbank_dataset, ColorCycler
ColorCycler.set_cmap("Set2")

gbk_files = load_example_genbank_dataset("escherichia_coli")
gbk_list = list(map(Genbank, gbk_files))

gv = GenomeViz(fig_track_height=0.8, feature_track_ratio=0.05)
gv.set_scale_xticks(ymargin=3.0)

# Plot chromosomes
for gbk in gbk_list:
    color = ColorCycler()
    track = gv.add_feature_track(gbk.name, gbk.get_seqid2size(), space=0.01, label_kws=dict(color=color))
    for segment in track.segments:
        segment.add_feature(segment.start, segment.end, plotstyle="bigrbox", fc=color, lw=0.5)

# Run MUMmer alignment
align_coords = MUMmer(gbk_list).run()

# Plot MUMmer alignment links
if len(align_coords) > 0:
    min_ident = int(min([ac.identity for ac in align_coords if ac.identity]))
    color, inverted_color = "olive", "purple"
    for ac in align_coords:
        gv.add_link(ac.query_link, ac.ref_link, color=color, inverted_color=inverted_color, v=ac.identity, vmin=min_ident)
    gv.set_colorbar([color, inverted_color], vmin=min_ident)

fig = gv.plotfig()

from pygenomeviz import GenomeViz from pygenomeviz.align import MUMmer from pygenomeviz.parser import Genbank from pygenomeviz.utils import load_example_genbank_dataset, ColorCycler ColorCycler.set_cmap("Set2") gbk_files = load_example_genbank_dataset("escherichia_coli") gbk_list = list(map(Genbank, gbk_files)) gv = GenomeViz(fig_track_height=0.8, feature_track_ratio=0.05) gv.set_scale_xticks(ymargin=3.0) # Plot chromosomes for gbk in gbk_list: color = ColorCycler() track = gv.add_feature_track(gbk.name, gbk.get_seqid2size(), space=0.01, label_kws=dict(color=color)) for segment in track.segments: segment.add_feature(segment.start, segment.end, plotstyle="bigrbox", fc=color, lw=0.5) # Run MUMmer alignment align_coords = MUMmer(gbk_list).run() # Plot MUMmer alignment links if len(align_coords) > 0: min_ident = int(min([ac.identity for ac in align_coords if ac.identity])) color, inverted_color = "olive", "purple" for ac in align_coords: gv.add_link(ac.query_link, ac.ref_link, color=color, inverted_color=inverted_color, v=ac.identity, vmin=min_ident) gv.set_colorbar([color, inverted_color], vmin=min_ident) fig = gv.plotfig()

Saccharomyces¶

In [2]:

from pygenomeviz import GenomeViz
from pygenomeviz.align import MUMmer
from pygenomeviz.parser import Genbank
from pygenomeviz.utils import load_example_genbank_dataset, ColorCycler
ColorCycler.set_cmap("tab10")

gbk_files = load_example_genbank_dataset("saccharomyces")
gbk_list = list(map(Genbank, gbk_files))

gv = GenomeViz(feature_track_ratio=0.1)
gv.set_scale_bar(ymargin=2.0)

# Plot chromosomes
for gbk in gbk_list:
    color = ColorCycler()
    track = gv.add_feature_track(gbk.name, gbk.get_seqid2size(), space=0.01, label_kws=dict(color=color))
    track.set_label(track.name.replace("_", "\n"))
    for segment in track.segments:
        segment.add_feature(segment.start, segment.end, plotstyle="bigrbox", fc=color, lw=0.5)

# Run MUMmer alignment
align_coords = MUMmer(gbk_list).run()

# Plot MUMmer alignment links
if len(align_coords) > 0:
    for ac in align_coords:
        gv.add_link(ac.query_link, ac.ref_link, color="grey", inverted_color="red", curve=True, filter_length=1000)

fig = gv.plotfig()

from pygenomeviz import GenomeViz from pygenomeviz.align import MUMmer from pygenomeviz.parser import Genbank from pygenomeviz.utils import load_example_genbank_dataset, ColorCycler ColorCycler.set_cmap("tab10") gbk_files = load_example_genbank_dataset("saccharomyces") gbk_list = list(map(Genbank, gbk_files)) gv = GenomeViz(feature_track_ratio=0.1) gv.set_scale_bar(ymargin=2.0) # Plot chromosomes for gbk in gbk_list: color = ColorCycler() track = gv.add_feature_track(gbk.name, gbk.get_seqid2size(), space=0.01, label_kws=dict(color=color)) track.set_label(track.name.replace("_", "\n")) for segment in track.segments: segment.add_feature(segment.start, segment.end, plotstyle="bigrbox", fc=color, lw=0.5) # Run MUMmer alignment align_coords = MUMmer(gbk_list).run() # Plot MUMmer alignment links if len(align_coords) > 0: for ac in align_coords: gv.add_link(ac.query_link, ac.ref_link, color="grey", inverted_color="red", curve=True, filter_length=1000) fig = gv.plotfig()