def umi_visualization(bams, chrom, start, end, output, coor):
doc = genomeview.Document(1000)
global umi_colors
umi_colors = {}
# genome
source = genomeview.FastaGenomeSource(REF_FA)
gv = genomeview.GenomeView(chrom, max(0, start), end, "+", source)
axis = genomeview.Axis()
gv.add_track(axis)
label_track = genomeview.track.TrackLabel('{}:{}-{}'.format(
chrom, start, end))
gv.tracks.insert(0, label_track)
for bam in bams:
# VCF/BAM track
name = bam.split('/')[-1]
if bam[-7:] == '.vcf.gz': # VCF track
variant_track = VCFTrack(bam, name, chrom, start, end)
gv.add_track(variant_track)
else: # bam track
track = genomeview.PairedEndBAMTrack(bam, name=name)
#track = genomeview.SingleEndBAMTrack(bam, name=name)
gv.add_track(track)
track.nuc_colors = {
"A": "blue",
"C": "orange",
"G": "green",
"T": "black",
"N": "gray"
}
track.quick_consensus = False
# format
global count, colors
count, frag_draw, umi_draw, umi_all, any_umi = stats_umi(
bam, chrom, start, end)
if len(coor.split(':')) == 3:
colors = ColorIter(umi_draw) # color generater
umi_ar = list(count.keys())
for umi in umi_ar:
umi_n = count[umi]
if umi_n > 1 and umi not in umi_colors:
umi_colors[umi] = colors.next_color()
track.color_fn = color_by_umi
track.include_read_fn = filter_by_umi # exculde reads out of
else:
colors = ColorIter(len(any_umi)) # color generater
for umi in any_umi:
umi_colors[umi] = colors.next_color()
track.include_read_fn = filter_by_coor # exculde reads out of
track.color_fn = color_by_umi
#track.color_fn = lambda x: "lightgray"
doc.elements.append(gv)
genomeview.save(doc, '{}.svg'.format(output))
def test_view_without_source():
import genomeview
doc = genomeview.Document(900)
view = genomeview.GenomeView("chr4", 96549060, 96549060+1000, "+")
doc.add_view(view)
bam_track_hg002 = genomeview.SingleEndBAMTrack("data/quick_consensus_test.bam", name="HG002")
bam_track_hg002.draw_mismatches = False
view.add_track(bam_track_hg002)
axis_track = genomeview.Axis()
view.add_track(axis_track)
genomeview.save(doc, "results/temp_without_source.svg")
with pytest.raises(AssertionError):
bam_track_hg002.draw_mismatches = True
genomeview.save(doc, "results/temp_without_source_error.svg")
import genomeview
dataset_paths = [
"data/pacbio.chr1.bam", "data/illumina.chr1.bam",
"/Users/nspies/Downloads/hg19.refseq.sorted.bed.gz"
]
reference = "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz"
chrom = "chr1"
start = 224368899
end = 224398899
doc = genomeview.visualize_data(dataset_paths, chrom, start, end, reference)
genomeview.save(doc, "example.svg")
# import genomeview.track
# chrom = "14"
# start = 66901400
# genome_path = "data/chr14.fa"
# doc = genomeview.Document(950)
# source = genomeview.FastaGenomeSource(genome_path)
# gv = genomeview.genomeview.GenomeView("bam", chrom, start, start+10000, "+", source)
# # Add the coordinate axis at the top
# axis = genomeview.axis.Axis("axis")
# gv.add_track(axis)
def test_bed():
file_paths = ["data/genes.sorted.bed.gz"]
doc = genomeview.visualize_data(file_paths, "chr3", 179500230, 179800230)
genomeview.save(doc, "results/bed_view.svg")
def test_bed2(which_bed):
file_paths = ["data/{}.bed".format(which_bed)]
doc = genomeview.visualize_data(file_paths, "chr3", 179500230, 179800230)
genomeview.save(doc, "results/{}_view.svg".format(which_bed))
def test_arrows(reference_path):
for i in [100, 1000, 2000, 5000]:
print(i)
doc = genomeview.visualize_data(["data/illumina.bam"], "chr4", 96549060, 96549060+i, reference_path)
genomeview.save(doc, "results/temp_{}.png".format(i))
def test_export_to_png(bam_doc):
genomeview.save(bam_doc, "results/temp.png")
def test_save_to_svg(bam_doc):
genomeview.save(bam_doc, "results/temp.svg")