Python load_design_from_gff示例

示例#1

文件： input_bed.py 项目： VoigtLab/dnaplotlib

"""
	File input
"""

import dnaplotlib as dpl
import matplotlib.pyplot as plt
from matplotlib import gridspec
import numpy as np

__author__  = 'Thomas Gorochowski <*****@*****.**>, Voigt Lab, MIT'
__license__ = 'MIT'
__version__ = '1.0'

# Load the design from a GFF file
cur_region = [1700, 15880]
design = dpl.load_design_from_gff('plasmid.gff', 'chrom1', region=cur_region)
profile_fwd = dpl.load_profile_from_bed('plasmid_fwd_profile.txt', 'chrom1', [0, 22953])
profile_rev = dpl.load_profile_from_bed('plasmid_rev_profile.txt', 'chrom1', [0, 22953])

# Create the DNAplotlib renderer
dr = dpl.DNARenderer(scale=10.0)
part_renderers = dr.trace_part_renderers()

# Create the figure
fig = plt.figure(figsize=(3.5,2.0))
gs = gridspec.GridSpec(2, 1, height_ratios=[1, 0.2])
ax_dna = plt.subplot(gs[1])

# Redender the DNA to axis
start, end = dr.renderDNA(ax_dna, design, part_renderers)
ax_dna.set_xlim(cur_region)

示例#2

文件： input_gff.py 项目： VoigtLab/dnaplotlib

#!/usr/bin/env python
"""
	File input
"""

import dnaplotlib as dpl
import matplotlib.pyplot as plt
from matplotlib import gridspec

__author__  = 'Thomas Gorochowski <*****@*****.**>, Voigt Lab, MIT'
__license__ = 'MIT'
__version__ = '1.0'


# Load the design from a GFF file
design = dpl.load_design_from_gff('plasmid.gff', 'chrom1', region=[1700, 15880])

# Create the DNAplotlib renderer
dr = dpl.DNARenderer()
part_renderers = dr.SBOL_part_renderers()

# Create the figure
fig = plt.figure(figsize=(5.0,0.6))
gs = gridspec.GridSpec(1, 1)
ax_dna = plt.subplot(gs[0])

# Redender the DNA to axis
start, end = dr.renderDNA(ax_dna, design, part_renderers)
ax_dna.set_xlim([start, end])
ax_dna.set_ylim([-15,15])
ax_dna.set_aspect('equal')

示例#3

"""
	File input
"""

import dnaplotlib as dpl
import matplotlib.pyplot as plt
from matplotlib import gridspec
import numpy as np

__author__ = 'Thomas Gorochowski <*****@*****.**>, Voigt Lab, MIT'
__license__ = 'MIT'
__version__ = '1.0'

# Load the design from a GFF file
cur_region = [1700, 15880]
design = dpl.load_design_from_gff('plasmid.gff', 'chrom1', region=cur_region)
profile_fwd = dpl.load_profile_from_bed('plasmid_fwd_profile.txt', 'chrom1',
                                        [0, 22953])
profile_rev = dpl.load_profile_from_bed('plasmid_rev_profile.txt', 'chrom1',
                                        [0, 22953])

# Create the DNAplotlib renderer
dr = dpl.DNARenderer(scale=10.0)
part_renderers = dr.trace_part_renderers()

# Create the figure
fig = plt.figure(figsize=(3.5, 2.0))
gs = gridspec.GridSpec(2, 1, height_ratios=[1, 0.2])
ax_dna = plt.subplot(gs[1])

# Redender the DNA to axis

示例#4

#!/usr/bin/env python
"""
	File input
"""

import dnaplotlib as dpl
import matplotlib.pyplot as plt
from matplotlib import gridspec

__author__ = 'Thomas Gorochowski <*****@*****.**>, Voigt Lab, MIT'
__license__ = 'MIT'
__version__ = '1.0'

# Load the design from a GFF file
design = dpl.load_design_from_gff('plasmid.gff',
                                  'chrom1',
                                  region=[1700, 15880])

# Create the DNAplotlib renderer
dr = dpl.DNARenderer()
part_renderers = dr.SBOL_part_renderers()

# Create the figure
fig = plt.figure(figsize=(5.0, 0.6))
gs = gridspec.GridSpec(1, 1)
ax_dna = plt.subplot(gs[0])

# Redender the DNA to axis
start, end = dr.renderDNA(ax_dna, design, part_renderers)
ax_dna.set_xlim([start, end])
ax_dna.set_ylim([-15, 15])

示例#5

文件： input_bed.py 项目： hainm/dnaplotlib

"""
	File input
"""

import dnaplotlib as dpl
import matplotlib.pyplot as plt
from matplotlib import gridspec
import numpy as np

__author__ = "Thomas Gorochowski <*****@*****.**>, Voigt Lab, MIT"
__license__ = "OSI OSL 3.0"
__version__ = "1.0"

# Load the design from a GFF file
cur_region = [1700, 15880]
design = dpl.load_design_from_gff("plasmid.gff", "chrom1", region=cur_region)
profile_fwd = dpl.load_profile_from_bed("plasmid_fwd_profile.txt", "chrom1", [0, 22953])
profile_rev = dpl.load_profile_from_bed("plasmid_rev_profile.txt", "chrom1", [0, 22953])

# Create the DNAplotlib renderer
dr = dpl.DNARenderer(scale=10.0)
part_renderers = dr.trace_part_renderers()

# Create the figure
fig = plt.figure(figsize=(3.5, 2.0))
gs = gridspec.GridSpec(2, 1, height_ratios=[1, 0.2])
ax_dna = plt.subplot(gs[1])

# Redender the DNA to axis
start, end = dr.renderDNA(ax_dna, design, part_renderers)
ax_dna.set_xlim(cur_region)