python3编程实战_生信编程实战第3题（python）

image.png

wget ftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.chr.gtf.gz

grep -v "#" Homo_sapiens.GRCh38.87.chr.gtf.gz >hg38.gtf.gz

gunzip hg38.gtf.gz

做题之前我们先看看文件的内容是什么

image.png

gtf有9列

1.染色体名

2.注释信息的来源，比如”Genescan”、”Genbank”

等，可以为空，为空用”.”点号代替

3.注释信息的类型，比如Gene、cDNA、mRNA等，或者是SO对应的编号

4、5.开始和结束位置

6.得分，数字，是注释信息可能性的说明，可以是序列相似性比对时的E-values值或者基因预测是的P-values值。”.”表示为空。

7.序列的方向，

+表示正义链, -反义链 , ? 表示未知

8.阅读框：有数字0、1和2。0代表序列的第一个碱基为密码子的第一个碱基，1代表是密码子第二个，2代表第三个。

9.以多个键值对组成的注释信息描述，键与值之间用”=“；

以上图内容简单的理解一下

红线圈出来的范围一个gene信息，范围是11869-14409bp

在这个范围内有两个转录本（黄色部分）：

transcript1 来自基因的11869-14409

这个范围包括3个exon

transcript2来自基因的12010-13670

这个范围包括6个exon

那么本次要做的事情就主要包括一下几个方面吧

1.统计各个染色体基因数量的分布，包括总的基因和各中类型基因数量的分布

2.统计一下基因转录本数量的分布

就这2个吧，依然是分为python，R，shell三种编程方法

1.python

1.统计各个染色体基因数量的分布，包括总的基因和各中类型基因数量的分布

给出我写的脚本import sysimport collections

args=sys.argv

filename=args[1]

count_gene=collections.OrderedDict()with open (filename) as fh: for line in fh:

lineL=line.strip().split("\t")

chr_num="chr"+lineL[0]

type_info=lineL[2] if type_info=="gene":

All_gene="all"+"_"+type_info if chr_num not in count_gene:

count_gene[chr_num]={}

count_gene[chr_num][All_gene]=0

count_gene[chr_num][All_gene]+=1 #计算all gene个数

descrip_info=lineL[8]

descrip_info=descrip_info[:-1] #主要是有的biotype就是最后一部分了，这时候后面得到的b_type包含“;”,所以一开始就把最后的";"去掉

descrip_infoL=descrip_info.split("; ")

biotype=descrip_infoL[4]

biotypeL=biotype.split(" ")

b_type=biotypeL[1]

b_type=eval(b_type) if b_type not in count_gene[chr_num]:

count_gene[chr_num][b_type]=0

count_gene[chr_num][b_type]+=1for chr_num,countAll in count_gene.items(): for k,v in countAll.items():

print(chr_num,k,v)

结果如下chr1 protein_coding 2052

chr1 TEC 28

chr1 polymorphic_pseudogene 6

chr1 snRNA 219

chr1 antisense 505

chr1 pseudogene 5

chr1 sense_intronic 66

chr1 processed_transcript 31

chr1 all_gene 5194

chr1 sense_overlapping 17

chr1 processed_pseudogene 897

chr1 rRNA 69

chr1 snoRNA 68

chr1 miRNA 126

chr1 lincRNA 576

chr1 IG_V_pseudogene 1

chr1 unprocessed_pseudogene 206

chr1 transcribed_unitary_pseudogene 4

chr1 unitary_pseudogene 26

chr1 scaRNA 14

chr1 misc_RNA 192

chr1 3prime_overlapping_ncRNA 4

chr1 transcribed_processed_pseudogene 33

chr1 bidirectional_promoter_lncRNA 1

chr1 transcribed_unprocessed_pseudogene 48

chr2 protein_coding 1255

chr2 IG_C_gene 1

chr2 TEC 51

chr2 polymorphic_pseudogene 2

chr2 snRNA 157

chr2 antisense 364

chr2 IG_V_gene 46

chr2 pseudogene 1

chr2 transcribed_unitary_pseudogene 3

chr2 processed_transcript 42

chr2 miRNA 105

chr2 sense_overlapping 10

chr2 processed_pseudogene 751

chr2 rRNA 41

chr2 snoRNA 64

chr2 transcribed_unprocessed_pseudogene 39

chr2 all_gene 3971

chr2 lincRNA 577

chr2 IG_J_gene 5

chr2 IG_V_pseudogene 45

chr2 unprocessed_pseudogene 155

chr2 sense_intronic 37

chr2 unitary_pseudogene 7

chr2 scaRNA 7

chr2 misc_RNA 176

chr2 3prime_overlapping_ncRNA 7

chr2 scRNA 1

chr2 transcribed_processed_pseudogene 22

chr3 protein_coding 1076

chr3 TEC 26

chr3 polymorphic_pseudogene 2

chr3 snRNA 133

chr3 antisense 299

chr3 transcribed_unitary_pseudogene 9

chr3 processed_transcript 22

chr3 miRNA 77

chr3 sense_overlapping 7

chr3 processed_pseudogene 616

chr3 rRNA 29

chr3 snoRNA 56

chr3 sRNA 1

chr3 all_gene 3010

chr3 lincRNA 353

chr3 unprocessed_pseudogene 87

chr3 sense_intronic 29

chr3 unitary_pseudogene 9

chr3 scaRNA 2

chr3 misc_RNA 134

chr3 3prime_overlapping_ncRNA 1

chr3 transcribed_processed_pseudogene 19

chr3 transcribed_unprocessed_pseudogene 23

chr4 protein_coding 751

chr4 TEC 37

chr4 polymorphic_pseudogene 1

chr4 snRNA 116

chr4 antisense 207

chr4 pseudogene 1

chr4 sense_intronic 18

chr4 processed_transcript 16

chr4 miRNA 57

chr4 sense_overlapping 9

chr4 processed_pseudogene 561

chr4 ribozyme 1

chr4 rRNA 24

chr4 snoRNA 30

chr4 all_gene 2505

chr4 lincRNA 405

chr4 unprocessed_pseudogene 113

chr4 transcribed_unitary_pseudogene 2

chr4 unitary_pseudogene 2

chr4 scaRNA 1

chr4 misc_RNA 104

chr4 transcribed_processed_pseudogene 31

chr4 bidirectional_promoter_lncRNA 1

chr4 transcribed_unprocessed_pseudogene 17

chr5 protein_coding 876

chr5 all_gene 2868

chr5 lincRNA 490

chr5 rRNA 25

chr5 miRNA 66

chr5 unprocessed_pseudogene 57

chr5 transcribed_unitary_pseudogene 4

chr5 sense_intronic 24

chr5 unitary_pseudogene 4

chr5 snRNA 103

chr5 transcribed_unprocessed_pseudogene 22

chr5 processed_transcript 23

chr5 misc_RNA 119

chr5 TEC 73

chr5 sense_overlapping 10

chr5 transcribed_processed_pseudogene 9

chr5 processed_pseudogene 625

chr5 vaultRNA 1

chr5 antisense 297

chr5 snoRNA 40

chr6 protein_coding 1045

chr6 TEC 36

chr6 polymorphic_pseudogene 3

chr6 snRNA 107

chr6 antisense 238

chr6 non_coding 1

chr6 transcribed_unitary_pseudogene 2

chr6 processed_transcript 8

chr6 miRNA 60

chr6 sense_overlapping 7

chr6 processed_pseudogene 639

chr6 rRNA 27

chr6 snoRNA 39

chr6 all_gene 2863

chr6 lincRNA 360

chr6 unprocessed_pseudogene 105

chr6 sense_intronic 23

chr6 unitary_pseudogene 10

chr6 scaRNA 1

chr6 misc_RNA 105

chr6 3prime_overlapping_ncRNA 2

chr6 transcribed_processed_pseudogene 23

chr6 transcribed_unprocessed_pseudogene 22

chr7 protein_coding 906

chr7 TEC 37

chr7 polymorphic_pseudogene 2

chr7 snRNA 84

chr7 antisense 252

chr7 pseudogene 3

chr7 transcribed_unprocessed_pseudogene 71

chr7 processed_transcript 40

chr7 miRNA 60

chr7 sense_overlapping 12

chr7 processed_pseudogene 577

chr7 TR_D_gene 1

chr7 rRNA 24

chr7 snoRNA 39

chr7 sRNA 1

chr7 all_gene 2867

chr7 lincRNA 286

chr7 unprocessed_pseudogene 189

chr7 sense_intronic 15

chr7 unitary_pseudogene 13

chr7 TR_J_gene 19

chr7 TR_V_pseudogene 17

chr7 TR_C_gene 4

chr7 transcribed_unitary_pseudogene 2

chr7 misc_RNA 143

chr7 TR_V_gene 57

chr7 transcribed_processed_pseudogene 13

chrX protein_coding 841

chrX pseudogene 3

chrX polymorphic_pseudogene 1

chrX snRNA 84

chrX misc_RNA 100

chrX transcribed_unitary_pseudogene 2

chrX processed_transcript 10

chrX TEC 14

chrX sense_overlapping 6

chrX processed_pseudogene 723

chrX rRNA 22

chrX snoRNA 46

chrX all_gene 2359

chrX lincRNA 136

chrX miRNA 105

chrX unprocessed_pseudogene 108

chrX sense_intronic 17

chrX unitary_pseudogene 3

chrX scaRNA 1

chrX antisense 101

chrX 3prime_overlapping_ncRNA 1

chrX transcribed_processed_pseudogene 12

chrX transcribed_unprocessed_pseudogene 23

chr8 protein_coding 676

chr8 TEC 32

chr8 IG_V_pseudogene 1

chr8 snRNA 84

chr8 antisense 253

chr8 transcribed_unitary_pseudogene 5

chr8 processed_transcript 16

chr8 miRNA 68

chr8 sense_overlapping 8

chr8 processed_pseudogene 468

chr8 rRNA 29

chr8 polymorphic_pseudogene 1

chr8 all_gene 2353

chr8 lincRNA 412

chr8 unprocessed_pseudogene 114

chr8 sense_intronic 45

chr8 unitary_pseudogene 4

chr8 misc_RNA 82

chr8 3prime_overlapping_ncRNA 1

chr8 transcribed_processed_pseudogene 14

chr8 snoRNA 33

chr8 transcribed_unprocessed_pseudogene 7

chr9 protein_coding 781

chr9 TEC 18

chr9 polymorphic_pseudogene 2

chr9 snRNA 65

chr9 misc_RNA 96

chr9 IG_C_pseudogene 1

chr9 pseudogene 1

chr9 transcribed_unprocessed_pseudogene 28

chr9 processed_transcript 17

chr9 miRNA 74

chr9 sense_overlapping 9

chr9 processed_pseudogene 461

chr9 ribozyme 2

chr9 rRNA 19

chr9 snoRNA 31

chr9 all_gene 2242

chr9 lincRNA 275

chr9 IG_V_pseudogene 4

chr9 unprocessed_pseudogene 132

chr9 sense_intronic 22

chr9 unitary_pseudogene 5

chr9 TR_V_pseudogene 4

chr9 scaRNA 1

chr9 transcribed_unitary_pseudogene 2

chr9 antisense 165

chr9 3prime_overlapping_ncRNA 1

chr9 transcribed_processed_pseudogene 23

chr9 TR_V_gene 3

chr11 protein_coding 1276

chr11 TEC 76

chr11 polymorphic_pseudogene 22

chr11 snRNA 71

chr11 antisense 326

chr11 transcribed_unprocessed_pseudogene 30

chr11 processed_transcript 20

chr11 pseudogene 2

chr11 sense_overlapping 17

chr11 all_gene 3235

chr11 processed_pseudogene 473

chr11 ribozyme 1

chr11 rRNA 24

chr11 snoRNA 52

chr11 sRNA 2

chr11 miRNA 81

chr11 lincRNA 305

chr11 unprocessed_pseudogene 279

chr11 sense_intronic 40

chr11 unitary_pseudogene 20

chr11 scaRNA 3

chr11 transcribed_unitary_pseudogene 3

chr11 misc_RNA 97

chr11 3prime_overlapping_ncRNA 1

chr11 transcribed_processed_pseudogene 14

chr10 protein_coding 732

chr10 pseudogene 1

chr10 IG_V_pseudogene 1

chr10 snRNA 86

chr10 misc_RNA 89

chr10 transcribed_unprocessed_pseudogene 39

chr10 processed_transcript 29

chr10 TEC 31

chr10 sense_overlapping 9

chr10 processed_pseudogene 422

chr10 ribozyme 2

chr10 rRNA 29

chr10 snoRNA 28

chr10 polymorphic_pseudogene 1

chr10 all_gene 2204

chr10 lincRNA 280

chr10 miRNA 61

chr10 unprocessed_pseudogene 85

chr10 sense_intronic 33

chr10 unitary_pseudogene 5

chr10 transcribed_unitary_pseudogene 2

chr10 antisense 226

chr10 transcribed_processed_pseudogene 13

chr12 protein_coding 1034

chr12 TEC 99

chr12 snRNA 99

chr12 antisense 304

chr12 non_coding 1

chr12 transcribed_unprocessed_pseudogene 18

chr12 processed_transcript 22

chr12 miRNA 62

chr12 sense_overlapping 5

chr12 processed_pseudogene 490

chr12 rRNA 27

chr12 snoRNA 37

chr12 all_gene 2940

chr12 lincRNA 438

chr12 unprocessed_pseudogene 69

chr12 sense_intronic 75

chr12 unitary_pseudogene 6

chr12 scaRNA 2

chr12 transcribed_unitary_pseudogene 5

chr12 misc_RNA 115

chr12 3prime_overlapping_ncRNA 2

chr12 macro_lncRNA 1

chr12 transcribed_processed_pseudogene 29

chr13 protein_coding 327

chr13 unprocessed_pseudogene 52

chr13 all_gene 1304

chr13 lincRNA 241

chr13 snRNA 41

chr13 miRNA 31

chr13 antisense 105

chr13 sense_intronic 39

chr13 unitary_pseudogene 1

chr13 transcribed_unitary_pseudogene 1

chr13 transcribed_unprocessed_pseudogene 15

chr13 processed_transcript 12

chr13 misc_RNA 75

chr13 TEC 29

chr13 snoRNA 17

chr13 processed_pseudogene 295

chr13 rRNA 15

chr13 transcribed_processed_pseudogene 8

chr14 protein_coding 623

chr14 IG_C_gene 9

chr14 TEC 20

chr14 polymorphic_pseudogene 3

chr14 TR_J_pseudogene 4

chr14 snRNA 64

chr14 IG_pseudogene 1

chr14 antisense 179

chr14 IG_V_gene 49

chr14 IG_C_pseudogene 2

chr14 non_coding 1

chr14 pseudogene 1

chr14 transcribed_unprocessed_pseudogene 14

chr14 processed_transcript 21

chr14 miRNA 91

chr14 ribozyme 2

chr14 IG_J_pseudogene 3

chr14 processed_pseudogene 324

chr14 TR_D_gene 3

chr14 rRNA 10

chr14 snoRNA 72

chr14 bidirectional_promoter_lncRNA 1

chr14 all_gene 2224

chr14 lincRNA 297

chr14 IG_J_gene 6

chr14 IG_V_pseudogene 84

chr14 unprocessed_pseudogene 47

chr14 sense_intronic 21

chr14 unitary_pseudogene 2

chr14 TR_J_gene 60

chr14 TR_V_pseudogene 9

chr14 TR_C_gene 2

chr14 scaRNA 2

chr14 transcribed_unitary_pseudogene 2

chr14 misc_RNA 79

chr14 IG_D_gene 27

chr14 transcribed_processed_pseudogene 30

chr14 sense_overlapping 11

chr14 TR_V_gene 48

chr15 protein_coding 597

chr15 TEC 47

chr15 IG_V_pseudogene 6

chr15 snRNA 64

chr15 misc_RNA 93

chr15 IG_V_gene 6

chr15 pseudogene 1

chr15 sense_intronic 79

chr15 processed_transcript 25

chr15 all_gene 2152

chr15 sense_overlapping 8

chr15 processed_pseudogene 287

chr15 rRNA 12

chr15 snoRNA 114

chr15 miRNA 57

chr15 lincRNA 300

chr15 unprocessed_pseudogene 118

chr15 IG_D_gene 10

chr15 unitary_pseudogene 1

chr15 scaRNA 3

chr15 transcribed_unitary_pseudogene 3

chr15 antisense 225

chr15 3prime_overlapping_ncRNA 2

chr15 transcribed_processed_pseudogene 29

chr15 transcribed_unprocessed_pseudogene 65

chr16 protein_coding 866

chr16 TEC 136

chr16 IG_V_pseudogene 8

chr16 snRNA 52

chr16 antisense 307

chr16 IG_V_gene 6

chr16 pseudogene 1

chr16 transcribed_unprocessed_pseudogene 53

chr16 processed_transcript 31

chr16 all_gene 2511

chr16 sense_overlapping 12

chr16 processed_pseudogene 252

chr16 rRNA 32

chr16 snoRNA 33

chr16 polymorphic_pseudogene 1

chr16 miRNA 69

chr16 lincRNA 360

chr16 unprocessed_pseudogene 112

chr16 sense_intronic 83

chr16 unitary_pseudogene 12

chr16 scaRNA 1

chr16 transcribed_unitary_pseudogene 2

chr16 misc_RNA 51

chr16 3prime_overlapping_ncRNA 5

chr16 bidirectional_promoter_lncRNA 1

chr16 transcribed_processed_pseudogene 25

chr17 transcribed_unprocessed_pseudogene 64

chr17 protein_coding 1197

chr17 unprocessed_pseudogene 105

chr17 TEC 99

chr17 lincRNA 338

chr17 snRNA 86

chr17 miRNA 75

chr17 misc_RNA 99

chr17 transcribed_unitary_pseudogene 3

chr17 unitary_pseudogene 6

chr17 scaRNA 5

chr17 sense_intronic 69

chr17 processed_transcript 48

chr17 antisense 376

chr17 all_gene 2995

chr17 sense_overlapping 3

chr17 transcribed_processed_pseudogene 43

chr17 processed_pseudogene 310

chr17 rRNA 17

chr17 snoRNA 52

chr18 protein_coding 270

chr18 TEC 50

chr18 snRNA 46

chr18 misc_RNA 41

chr18 IG_C_pseudogene 1

chr18 transcribed_unitary_pseudogene 1

chr18 processed_transcript 11

chr18 miRNA 30

chr18 sense_overlapping 1

chr18 processed_pseudogene 207

chr18 rRNA 13

chr18 snoRNA 17

chr18 sRNA 1

chr18 all_gene 1170

chr18 lincRNA 246

chr18 unprocessed_pseudogene 14

chr18 sense_intronic 49

chr18 unitary_pseudogene 3

chr18 scaRNA 2

chr18 antisense 146

chr18 transcribed_processed_pseudogene 14

chr18 transcribed_unprocessed_pseudogene 7

chr20 protein_coding 544

chr20 all_gene 1386

chr20 lincRNA 214

chr20 snRNA 46

chr20 miRNA 39

chr20 unprocessed_pseudogene 32

chr20 sense_intronic 20

chr20 unitary_pseudogene 5

chr20 transcribed_unitary_pseudogene 3

chr20 scaRNA 1

chr20 transcribed_unprocessed_pseudogene 8

chr20 processed_transcript 9

chr20 misc_RNA 68

chr20 TEC 10

chr20 antisense 138

chr20 transcribed_processed_pseudogene 3

chr20 processed_pseudogene 198

chr20 sense_overlapping 3

chr20 rRNA 20

chr20 snoRNA 25

chr19 protein_coding 1470

chr19 TEC 74

chr19 lincRNA 236

chr19 snRNA 29

chr19 miRNA 115

chr19 unprocessed_pseudogene 159

chr19 polymorphic_pseudogene 2

chr19 sense_intronic 55

chr19 misc_RNA 61

chr19 unitary_pseudogene 7

chr19 transcribed_unprocessed_pseudogene 53

chr19 processed_transcript 36

chr19 antisense 293

chr19 3prime_overlapping_ncRNA 2

chr19 all_gene 2926

chr19 sense_overlapping 6

chr19 snoRNA 22

chr19 processed_pseudogene 263

chr19 rRNA 13

chr19 transcribed_processed_pseudogene 30

chrY protein_coding 53

chrY unprocessed_pseudogene 216

chrY all_gene 523

chrY lincRNA 52

chrY snRNA 17

chrY antisense 5

chrY sense_intronic 1

chrY transcribed_unprocessed_pseudogene 27

chrY processed_transcript 1

chrY misc_RNA 7

chrY snoRNA 3

chrY processed_pseudogene 130

chrY rRNA 7

chrY transcribed_processed_pseudogene 4

chr22 protein_coding 438

chr22 IG_C_gene 4

chr22 TEC 9

chr22 IG_V_pseudogene 43

chr22 snRNA 26

chr22 antisense 134

chr22 IG_V_gene 37

chr22 IG_C_pseudogene 5

chr22 transcribed_unprocessed_pseudogene 36

chr22 processed_transcript 18

chr22 miRNA 32

chr22 sense_overlapping 9

chr22 processed_pseudogene 156

chr22 rRNA 6

chr22 snoRNA 11

chr22 polymorphic_pseudogene 2

chr22 all_gene 1318

chr22 lincRNA 165

chr22 IG_J_gene 7

chr22 unprocessed_pseudogene 75

chr22 sense_intronic 31

chr22 unitary_pseudogene 3

chr22 scaRNA 3

chr22 misc_RNA 62

chr22 transcribed_processed_pseudogene 6

chr21 protein_coding 233

chr21 all_gene 835

chr21 lincRNA 191

chr21 snRNA 21

chr21 miRNA 26

chr21 unprocessed_pseudogene 32

chr21 IG_V_gene 1

chr21 sense_intronic 17

chr21 pseudogene 1

chr21 transcribed_unprocessed_pseudogene 6

chr21 processed_transcript 7

chr21 misc_RNA 24

chr21 3prime_overlapping_ncRNA 1

chr21 TEC 16

chr21 antisense 81

chr21 transcribed_processed_pseudogene 3

chr21 processed_pseudogene 143

chr21 sense_overlapping 8

chr21 rRNA 9

chr21 snoRNA 15

chrMT Mt_rRNA 2

chrMT protein_coding 13

chrMT Mt_tRNA 22

chrMT all_gene 37

可视化一下吧

因为all_gene值太高，所以把它单独拿出来grep "all_gene" count_all.txt >count_gene.txtlibrary(ggplot2)

data <- read.table("C:/Users/pc/Desktop/count_gene.txt")

chr_name <- data$V1type <- data$V2 number <- data$V3p <- ggplot(data,aes(x=chr_name,y=number))+theme_bw()+theme(axis.text.x=element_text(angle=90,size =8,vjust = 0.5,hjust = 0.5),panel.grid = element_blank())+geom_bar(aes(fill=chr_name),stat = "identity",position="dodge",width=0.8)

image.png

所有类型基因的可视化如下

看一下一号染色体：grep "chr1 " count_else.txt >count_else.chr1.txt

image.png

编码蛋白的基因数量还是最多的

最后show一下怎么把多个染色体的图堆在一起，用到ggplot2中的facetgrep "chr2" count_else.txt >count_else.chr2_all.txt#取出2，20，22号染色体

image.png

这里只是想展示一下这种画图方法，但是如果把所有染色体都放上就压缩了，图看不清楚。

2.统计一下基因转录本数量的分布

脚本如下：import sysimport collections

args=sys.argv

filename=args[1]

count_transcript=collections.OrderedDict()with open (filename) as fh: for line in fh:

lineL=line.strip().split("\t")

chr_num="chr"+lineL[0]

type_info=lineL[2] if type_info=="transcript": if chr_num not in count_transcript:

count_transcript[chr_num]={}

descrip_info=lineL[8]

descrip_infoL=descrip_info.split("; ")

gene_ID=descrip_infoL[0]

gene_IDL=gene_ID.split(" ")

gene_ID=gene_IDL[1]

gene_ID=eval(gene_ID) if gene_ID not in count_transcript[chr_num]:

count_transcript[chr_num][gene_ID]=0

count_transcript[chr_num][gene_ID]+=1for chr_num,countAll in count_transcript.items(): for k,v in countAll.items():

作者：天秤座的机器狗

链接：https://www.jianshu.com/p/5ffc2b487109

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