【三维基因组】PyGenomeTrack之CHIP峰图可视化
2020-07-12 本文已影响0人
XuningFan
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很多时候我们都需要画chip的峰图，而pyGenomeTrack（https://pygenometracks.readthedocs.io/en/latest/index.html）能够方便的帮我们完成这项工作。
在用pyGenomeTrack画峰图之前，我们需要几项准备工作：
注释基因（UCSC）
1.将gtf文件转化GenePred 文件
gtfToGenePred -genePredExt -geneNameAsName2 genes.gtf genePredName.txt
2.将GenePred 文件转换为UCSC Bed12
Bed12****格式:
chr1 3073252 3074322 4933401J01Rik 0 + 3074322 3074322 0 1 1070, 0,
chr1 3102015 3102125 Gm26206 0 + 3102125 3102125 0 1 110, 0,
chr1 3205900 3216344 Xkr4 0 - 3216344 3216344 0 2 1417,2736, 0,6291,
chr1 3206522 3215632 Xkr4 0 - 3215632 3215632 0 2 795,2194, 0,6121,
chr1 3214481 3671498 Xkr4 0 - 3216021 3671348 0 3 2487,200,947, 0,204733,248650,
chr1 3252756 3253236 Gm18956 0 + 3253236 3253236 0 1 480, 0,
chr1 3365730 3368549 Gm37180 0 - 3368549 3368549 0 1 2819, 0,
chr1 3375555 3377788 Gm37363 0 - 3377788 3377788 0 1 2233, 0,
chr1 3464976 3467285 Gm37686 0 - 3467285 3467285 0 1 2309, 0,
chr1 3466586 3513553 Gm1992 0 + 3513553 3513553 0 2 101,149, 0,46717,
可以参考以下代码进行转换：
def genePredName2bed12(file,bedpos):
fo = open(file[:-4] + "_bed12.bed","w")
with open(file) as f:
for line in f:
items = line.strip().split()
if items[-4]=="0":
name = "None"
else:
name =items[-4]
con = [items[1],items[3],items[4],name,"0",items[2],items[5],items[6],"0",items[7]]
#$2"\t"$4"\t"$5"\t"$1"\t0\t"$3"\t"$6"\t"$7"\t0\t"$8"\t"$9"\t"$10}
start_list = [int(ite) for ite in items[8].split(",")[:-1]]
end_list = [int(ite) for ite in items[9].split(",")[:-1]]
n = int(items[7])
length = []
distance = ["0"]
for i in range(n):
length.append(str(end_list[i]-start_list[I]))
for j in range(n-1):
distance.append(str(start_list[j+1]-end_list[j]))
con.extend([",".join(length)+",",",".join(distance)+","])
fo.write("\t".join(con) + "\n")
pos=items[1]+":" + items[3]+"-" + items[4] + "," + items[2]
if pos == bedpos[name]:
fo1.write("\t".join(con) + "\n")
fo.close()
注意bed****格式必须要sort,****因是0-based****的，start>end, ****不能start=end,****不然会报错[0,)
sort -k 1,1 -k 2,2n file.bed > out.bed
转换完gene注释文件之后，就可以进行配置了
来看一下config的设置：
[x-axis]
#optional
fontsize=6
# default is bottom meaning below the axis line
where=top
[spacer]
# height of space in cm (optional)
height = 0.5
#c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
##999999, #E69F00, #56B4E9, #009E73
#G0: MEF
#G1： PGFH3d, PGFH6d, PGFH9d, PGFHiHep
#G2: PGF3d,PGF6d,PGF9d
#G3: CRGF3d,CRGF6d,CRGF9d, CRGFiHep
[bigwig]
file=sam1.bw
title = sam1
height = 2
color = #7427A5
number of bins = 500
summary method = mean
show data range = yes
file_type = bigwig
[bigwig]
file=sam2.bw
title = sam2
height = 2
color = #955122
number of bins = 500
summary method = mean
show data range = yes
file_type = bigwig
[bigwig]
file=sam3.bw
title = sam3
height = 2
color = #4ECEC5
number of bins = 500
summary method = mean
show data range = yes
file_type = bigwig
[bigwig]
file=sam4.bw
title = sam4
height = 2
color = #178D7C
number of bins = 500
summary method = mean
show data range = yes
file_type = bigwig
[bigwig]
file=sam5.bw
title = sam5
height = 2
color = #4ECEC5
number of bins = 500
summary method = mean
show data range = yes
file_type = bigwig
[bigwig]
file=sam6.bw
title = sam6
height = 2
color = #178D7C
number of bins = 500
summary method = mean
show data range = yes
file_type = bigwig
[spacer]
[mm10_genePredName_bed12_filter]
file=Mus_musculus.GRCm38.90_genePredName_bed12.bed
height = 4
title = refGenes
fontsize = 6
style = UCSC
gene_rows = 2
color=black
border color = black
配置完成之后，通过以下命令就大功告成了.....
pyGenomeTracks --tracks config.ini --region chr11:4181821-4220502 --outFileName test.pdf --width 20 --height 20
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