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genbank_viewer.py
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genbank_viewer.py
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from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio.Seq import Seq
from Bio import Alphabet
from Bio import SeqIO
import matplotlib
import matplotlib.pyplot as plt
import seaborn as sns
import sys
import math
#matplotlib.rcParams['pgf.preamble'] = [r'\usepackage{hyperref}']
template = {'legend.numpoints': 1, 'axes.axisbelow': True, 'font.sans-serif': [u'Arial', u'Liberation Sans', u'Bitstream Vera Sans', u'sans-serif'], 'axes.labelcolor': '.15', 'ytick.major.size': 0.05, 'axes.grid': False, 'ytick.minor.size': 0.0, 'legend.scatterpoints': 1, 'axes.edgecolor': "black", 'grid.color': 'white', 'legend.frameon': False, 'ytick.color': '.15', 'xtick.major.size': 2.0, 'figure.facecolor': "#EAEAF2", 'xtick.color': '.15', 'xtick.minor.size': 3.0, 'font.family': [u'sans-serif'], 'xtick.direction': u'out', 'lines.solid_capstyle': u'round', 'grid.linestyle': u'-', 'image.cmap': u'Greys', 'axes.facecolor': "white", 'text.color': '.15', 'ytick.direction': u'out', 'axes.linewidth': 0.5}
sns.set_context("poster", font_scale=1.0, rc={"lines.linewidth": 2.0})
#sns.set_style(template)
class GenbView(object):
def __init__(self,gb,fig):
self.gb = gb
self.ax = None
self.fig = fig
self.width = 0.025
self.url_list = []
def make_parameter_list(self, start_pos, end_pos):
self.arrows_parameters = []
self.start_pos = start_pos
self.end_pos = end_pos
partial_gb = self.extract(start_pos, end_pos, make_file = False)
self.length = end_pos - start_pos
self.hl = (end_pos-start_pos) * 0.01
ypos = 1.00 # height of arrow positio
num = 0
e_num = 0
box = [[0] * 10001]
pre_box_start = 0
pre_box_end = -1
for i, afeat in enumerate(partial_gb.features):
parameter_dict = {}
if afeat.location.start < start_pos:
start = start_pos
elif "region" in afeat.qualifiers.keys() and len(afeat.qualifiers["region"]) == 1:
start = int(afeat.qualifiers["region"][0].split(":")[0])
else:
start = afeat.location.start
if afeat.location.end > end_pos:
end = end_pos
elif "region" in afeat.qualifiers.keys() and len(afeat.qualifiers["region"]) == 1:
end = int(afeat.qualifiers["region"][0].split(":")[1])
else:
end = afeat.location.end
if afeat.type != "gene" and afeat.type != "mRNA" and afeat.type != "exon" and afeat.type != "source":
if afeat.strand == 1:
xpos = start - start_pos
tdx = end - start
dx = end - start - self.hl
if afeat.type == "CDS":
edgecolor = "#C481A1"
direction = "right"
else:
edgecolor = "#C9BD74"
direction = "right"
if dx < 0:
dx = self.hl
else:
xpos = end - start_pos
tdx = start - end
dx = start - end + self.hl
if afeat.type == "CDS":
edgecolor = "#74AFB9"
direction = "left"
else:
edgecolor = "#C9BD74"
direction = "left"
if dx > 0:
dx = -1.0 * self.hl
if "note" in afeat.qualifiers.keys() and "SPADE" in afeat.qualifiers["note"][0]:
pass
else:
if "old_locus_tag" in afeat.qualifiers.keys():
locus_tag = afeat.qualifiers["old_locus_tag"][0]
elif "locus_tag" in afeat.qualifiers.keys():
locus_tag = afeat.qualifiers["locus_tag"][0]
else:
locus_tag = "-"
if "product" in afeat.qualifiers.keys() and 4.5 * len(afeat.qualifiers["product"][0]) < 346 * (1.0 * abs(dx) / self.length):
txt_annotation = afeat.qualifiers["product"][0]
elif "gene" in afeat.qualifiers.keys() and 4.5 * len(afeat.qualifiers["gene"][0]) < 346 * (1.0 * abs(dx) / self.length):
txt_annotation = afeat.qualifiers["gene"][0]
if "locus_tag" in afeat.qualifiers.keys() and 4.5 * len(afeat.qualifiers["locus_tag"][0]) < 346 * (1.0 * abs(dx) / self.length):
txt_annotation = afeat.qualifiers["locus_tag"][0]
elif "old_locus_tag" in afeat.qualifiers.keys() and 4.5 * len(afeat.qualifiers["old_locus_tag"][0]) < 346 * (1.0 * abs(dx) / self.length):
txt_annotation = afeat.qualifiers["old_locus_tag"][0]
elif "rpt_family" in afeat.qualifiers.keys() and 4.5 * len(afeat.qualifiers["rpt_family"][0]) < 346 * (1.0 * abs(dx) / self.length):
txt_annotation = afeat.qualifiers["rpt_family"][0]
else:
txt_annotation = afeat.type
hl = self.hl
#if abs(dx) + abs(self.hl) == end_pos - start_pos:
# dx = 10 * dx
# if afeat.strand == 1:
# xpos = xpos-100
# if afeat.strand == -1:
# xpos = xpos+100
#if afeat.strand == 1 and xpos == 0:
# xpos = xpos-100
# dx = dx+100
#if afeat.strand == -1 and xpos == end_pos-start_pos:
# xpos = xpos+100
# dx = dx-100
if afeat.strand == -1 and xpos + dx - self.hl <= 0.1:
dx = dx-self.hl
hl = 0
parameter_dict["start"] = hl
parameter_dict["start"] = start
parameter_dict["end"] = end
parameter_dict["xpos"] = xpos
parameter_dict["dx"] = dx
parameter_dict["edgecolor"] = edgecolor
parameter_dict["direction"] = direction
parameter_dict["facecolor"] = "#FFFFEF"
parameter_dict["annotation"] = txt_annotation
flag = 0
box_start = int(10000 * (xpos) * 1.0/self.length)
box_end = int(math.ceil(10000 * (xpos+tdx) * 1.0/self.length))
box_start,box_end = sorted([box_start,box_end])
for j in range(len(box)):
if box[j][box_start] == 0:
box[j][box_start:box_end] = [1] * (box_end - box_start)
ypos = 1.0 - 0.03 * j
flag = 1
break
else:
pass
if flag == 0:
ypos = 1.0 - 0.03 * (j + 1)
box.append([0] * 10001)
box[-1][box_end:box_start] = [1] * (box_end - box_start)
pre_box_start = box_start
pre_box_end = box_end
parameter_dict["ypos"] = ypos
self.arrows_parameters.append(parameter_dict)
self.box_num = len(box)
if sum(box[0]) == 0:
return 0
return len(box)
def view_feature(self, ax):
self.ax = ax
url_list = []
for n, parameters in enumerate(self.arrows_parameters):
arrow = self.ax.arrow(parameters["xpos"], parameters["ypos"], parameters["dx"], 0, width=self.width, head_length=self.hl, head_width=self.width, facecolor="#FFFFEF", edgecolor=parameters["edgecolor"], lw=1.5)
arrow.set_url("Annotation_" + str(n))
url_list.append("https://www.ncbi.nlm.nih.gov/nuccore/%s?from=%d&to=%d" % (self.gb.id,parameters["start"],parameters["end"]))
if 4.5 * len(parameters["annotation"]) < 346 * (1.0 * abs(parameters["dx"]) / self.length):
pass
self.ax.text(parameters["xpos"] + 0.5 * parameters["dx"], parameters["ypos"], "%s" % (parameters["annotation"]), horizontalalignment='center', verticalalignment='center', fontsize=6, family="Courier New", weight="bold")
self.ax.set_xlim(0,self.length)
self.ax.set_ylim(1.01-0.03 * self.box_num,1.02)
self.ax.spines["top"].set_color("none")
self.ax.spines["bottom"].set_color("none")
self.ax.spines["right"].set_color("none")
self.ax.spines["left"].set_color("none")
self.ax.yaxis.set_ticks([])
self.ax.yaxis.set_ticklabels([])
self.ax.xaxis.set_ticks([])
self.ax.xaxis.set_ticklabels([])
url_output = open("annotaiton_url_list.txt","w")
for url in url_list:
url_output.write(url + "\n")
def extract(self, start_pos, end_pos, make_file=False):
range_set = set(range(start_pos, end_pos))
partial_gb = SeqRecord(Seq(str(self.gb.seq[start_pos:end_pos]),Alphabet.DNAAlphabet()))
for afeat in self.gb.features:
afeat_range = set(range(afeat.location.start, afeat.location.end))
if len(afeat_range & range_set) > 0:
partial_gb.features.append(afeat)
if make_file == True:
record_handle = open(partial_gb.id + "_" + str(start_pos) + "_" + str(end_pos),"w")
SeqIO.write(partial_gb, record_handle, "genbank")
return partial_gb
if __name__ == "__main__":
fig,ax = plt.subplots(figsize=(18,2))
gb = SeqIO.read(sys.argv[1],"genbank")
if set(str(gb.seq)) == set(["N"]):
fasta = SeqIO.read(sys.argv[2],"fasta")
gb.seq = fasta.seq
else:
pass
SeqIO.read(sys.argv[1],"genbank")
GV = GenbView(gb,ax,fig)
GV.view_feature(133000,136000,feature_name="all")
fig.savefig("test_gv.pdf")