Genomic Genetic Load Analysis   

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This depends on your outgroup, if your allele in outgroup is 1/1, then 0/0 is the derived allele, so you still have to keep it. If you don't have a suitable outgroup, you can only define the ancestral alleles in terms of relatively high frequency alleles.

Tian Xia

Kunming Institute of Botany

张同学，请问您找出了于黎老师提供的这个python脚本的输入文件的格式了吗？

tian Xia

Southwest University

同学您好，我想问问大家在划分LOF的时候，除了于老师提到的几种类型，还包括了哪些类型呢？或者是否应该包含splice_region_variant 和stop_lost呢？

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Leu Pro

Ser Pro

Leu Ile

His Tyr

Arg Gly

Pro Leu

Pro Ala

Gly Arg

Ser Asn

Ile Thr

Glu Lys

Glu Gly

黎 于

Leu Pro

Ser Pro

Leu Ile

His Tyr

Arg Gly

Pro Leu

Pro Ala

Gly Arg

Ser Asn

Ile Thr

Glu Lys

Glu Gly

黎 于

Leu Pro

Ser Pro

Leu Ile

His Tyr

Arg Gly

Pro Leu

Pro Ala

Gly Arg

Ser Asn

Ile Thr

Glu Lys

Glu Gly

黎 于

Leu Pro

Ser Pro

Leu Ile

His Tyr

Arg Gly

Pro Leu

Pro Ala

Gly Arg

Ser Asn

Ile Thr

Glu Lys

Glu Gly

黎 于

Leu Pro

Ser Pro

Leu Ile

His Tyr

Arg Gly

Pro Leu

Pro Ala

Gly Arg

Ser Asn

Ile Thr

Glu Lys

Glu Gly

黎 于

Leu Pro

Ser Pro

Leu Ile

His Tyr

Arg Gly

Pro Leu

Pro Ala

Gly Arg

Ser Asn

Ile Thr

Glu Lys

Glu Gly

跃飞 汪

西北农林科技大学

missense_variants.vcf | grep -v '#' | awk -F"\t|\\\\|" '{printf ("%s\t%s\t%s\t%s\t%s\n", $18,$1,$2,$4,$5)}' | awk -F"\t" '{OFS = FS} { gsub(/p\./,"", $1); print }' | awk '{sub(/[0-9]+/," ",$1); print}'

可以通过以上代码将文件转化为输入文件

mx wu

中南林业科技大学研究生院

同学你好，我目前也有同样的疑问，请问你解决了吗，能否指教一下

黎 于

# Python

# Authorship: Guoliang Lin/Hu jingyang

# Date: 2022-12-16 11:11:11

import sys

def print_hi(name):

  print(f'Hi, {name}') 

Score_matrix={'Ser': {'Arg':110, 'Leu':145, 'Pro':74, 'Thr':58, 'Ala':99, 'Val':124, 'Gly':56, 'Ile':142, 'Phe':155, 'Try':144, 'Cys':112, 'His':89, 'Gln':68, 'Asn':46, 'Lys':121, 'Asp':65, 'Glu':80, 'Met':135, 'Trp':177},

'Arg': {'Arg':0, 'Leu':102, 'Pro':103, 'Thr':71, 'Ala':112, 'Val':96, 'Gly':125, 'Ile':97, 'Phe':97, 'Try':77, 'Cys':180, 'His':29, 'Gln':43, 'Asn':86, 'Lys':26, 'Asp':96, 'Glu':54, 'Met':91, 'Trp':101, 'Ser':0},

'Leu': {'Arg':0, 'Leu':0, 'Pro':98, 'Thr':92, 'Ala':96, 'Val':32, 'Gly':138, 'Ile':5, 'Phe':22, 'Try':36, 'Cys':198, 'His':99, 'Gln':113, 'Asn':153, 'Lys':107, 'Asp':172, 'Glu':138, 'Met':15, 'Trp':61, 'Ser':0},

'Pro': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':38, 'Ala':27, 'Val':68, 'Gly':42, 'Ile':95, 'Phe':114, 'Try':110, 'Cys':169, 'His':77, 'Gln':76, 'Asn':91, 'Lys':103, 'Asp':108, 'Glu':93, 'Met':87, 'Trp':147, 'Ser':0},

'Thr': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':58, 'Val':69, 'Gly':59, 'Ile':89, 'Phe':103, 'Try':92, 'Cys':149, 'His':47, 'Gln':42, 'Asn':65, 'Lys':78, 'Asp':85, 'Glu':65, 'Met':81, 'Trp':128, 'Ser':0},

'Ala': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':64, 'Gly':60, 'Ile':94, 'Phe':113, 'Try':112, 'Cys':195, 'His':86, 'Gln':91, 'Asn':111, 'Lys':106, 'Asp':126, 'Glu':107, 'Met':84, 'Trp':148, 'Ser':0},

'Val': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':109, 'Ile':29, 'Phe':50, 'Try':55, 'Cys':192, 'His':84, 'Gln':96, 'Asn':133, 'Lys':97, 'Asp':152, 'Glu':121, 'Met':21, 'Trp':88, 'Ser':0},

'Gly': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':135, 'Phe':153, 'Try':147, 'Cys':159, 'His':98, 'Gln':87, 'Asn':80, 'Lys':127, 'Asp':94, 'Glu':98, 'Met':127, 'Trp':184, 'Ser':0},

'Ile': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':0, 'Phe':21, 'Try':33, 'Cys':198, 'His':94, 'Gln':109, 'Asn':149, 'Lys':102, 'Asp':168, 'Glu':134, 'Met':10, 'Trp':61, 'Ser':0},

'Phe': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':0, 'Phe':0, 'Try':22, 'Cys':205, 'His':100, 'Gln':116, 'Asn':158, 'Lys':102, 'Asp':177, 'Glu':140, 'Met':28, 'Trp':40, 'Ser':0},

'Try': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':0, 'Phe':0, 'Try':0, 'Cys':194, 'His':83, 'Gln':99, 'Asn':143, 'Lys':85, 'Asp':160, 'Glu':122, 'Met':36, 'Trp':37, 'Ser':0},

'Cys': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':0, 'Phe':0, 'Try':0, 'Cys':0, 'His':174, 'Gln':154, 'Asn':139, 'Lys':202, 'Asp':154, 'Glu':170, 'Met':196, 'Trp':215, 'Ser':0},

'His': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':0, 'Phe':0, 'Try':0, 'Cys':0, 'His':0, 'Gln':24, 'Asn':68, 'Lys':32, 'Asp':81, 'Glu':40, 'Met':87, 'Trp':115, 'Ser':0},

'Gln': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':0, 'Phe':0, 'Try':0, 'Cys':0, 'His':0, 'Gln':0, 'Asn':46, 'Lys':53, 'Asp':61, 'Glu':29, 'Met':101, 'Trp':130, 'Ser':0},

'Asn': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':0, 'Phe':0, 'Try':0, 'Cys':0, 'His':0, 'Gln':0, 'Asn':0, 'Lys':94, 'Asp':23, 'Glu':42, 'Met':142, 'Trp':174, 'Ser':0},

'Lys': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':0, 'Phe':0, 'Try':0, 'Cys':0, 'His':0, 'Gln':0, 'Asn':0, 'Lys':0, 'Asp':101, 'Glu':56, 'Met':95, 'Trp':110, 'Ser':0},

'Asp': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':0, 'Phe':0, 'Try':0, 'Cys':0, 'His':0, 'Gln':0, 'Asn':0, 'Lys':0, 'Asp':0, 'Glu':45, 'Met':160, 'Trp':181, 'Ser':0},

'Glu': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':0, 'Phe':0, 'Try':0, 'Cys':0, 'His':0, 'Gln':0, 'Asn':0, 'Lys':0, 'Asp':0, 'Glu':0, 'Met':126, 'Trp':152, 'Ser':0},

'Met': {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':0, 'Phe':0, 'Try':0, 'Cys':0, 'His':0, 'Gln':0, 'Asn':0, 'Lys':0, 'Asp':0, 'Glu':0, 'Met':0, 'Trp':67, 'Ser':0},

'Trp':  {'Arg':0, 'Leu':0, 'Pro':0, 'Thr':0, 'Ala':0, 'Val':0, 'Gly':0, 'Ile':0, 'Phe':0, 'Try':0, 'Cys':0, 'His':0, 'Gln':0, 'Asn':0, 'Lys':0, 'Asp':0, 'Glu':0, 'Met':0, 'Trp':0 , 'Ser':0}}

if __name__ == '__main__':

  if len(sys.argv)<3:

    print("Error!")

    print("Usage:python get_score.py inputfile outputfile")

    sys.exit(-1)

  # print_hi('PyCharm')

  with open(sys.argv[1]) as infile:

    with open(sys.argv[2],'w') as outfile:

      for item in infile:

        item=item.strip()

        itemlist=item.split()

        if (itemlist[0] in Score_matrix) and (itemlist[1] in Score_matrix[itemlist[0]]):

          score=Score_matrix[itemlist[0]][itemlist[1]]

        else:

          score=0

        outfile.write(f"{itemlist[0]} {itemlist[1]} {score} ")

跃飞 汪

西北农林科技大学

老师，这个矩阵可能有问题，这个脚本写的0填充，但是我看原文章可能的意思是对称，类似下图
1 S R L P T A V G I F Y C H Q N K D E M W
S 0 110 145 74 58 99 124 56 142 155 144 112 89 68 46 121 65 80 135 177
R 110 0 102 103 71 112 96 125 97 97 77 180 29 43 86 26 96 54 91 101
L 145 102 0 98 92 96 32 138 5 22 36 198 99 113 153 107 172 138 15 61
P 74 103 98 0 38 27 68 42 95 114 110 169 77 76 91 103 108 93 87 147
T 58 71 92 38 0 58 69 59 89 103 92 149 47 42 65 78 85 65 81 128
A 99 112 96 27 58 0 64 60 94 113 112 195 86 91 111 106 126 107 84 148
V 124 96 32 68 69 64 0 109 29 50 55 192 84 96 133 97 152 121 21 88
G 56 125 138 42 59 60 109 0 135 153 147 159 98 87 80 127 94 98 127 184
I 142 97 5 95 89 94 29 135 0 21 33 198 94 109 149 102 168 134 10 61
F 155 97 22 114 103 113 50 153 21 0 22 205 100 116 158 102 177 140 28 40
Y 144 77 36 110 92 112 55 147 33 22 0 194 83 99 143 85 160 122 36 37
C 112 180 198 169 149 195 192 159 198 205 194 0 174 154 139 202 154 170 196 215
H 89 29 99 77 47 86 84 98 94 100 83 174 0 24 68 32 81 40 87 115
Q 68 43 113 76 42 91 96 87 109 116 99 154 24 0 46 53 61 29 101 130
N 46 86 153 91 65 111 133 80 149 158 143 139 68 46 0 94 23 42 142 174
K 121 26 107 103 78 106 97 127 102 102 85 202 32 53 94 0 101 56 95 110
D 65 96 172 108 85 126 152 94 168 177 160 154 81 61 23 101 0 45 160 181
E 80 54 138 93 65 107 121 98 134 140 122 170 40 29 42 56 45 0 126 152
M 135 91 15 87 81 84 21 127 10 28 36 196 87 101 142 95 160 126 0 67
W 177 101 61 147 128 148 88 184 61 40 37 215 115 130 174 110 181 152 67 0

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输入文件是SnpEff 注释的 vcf 文件中的missense variants位点，然后计算的方法是python脚本Grantham_score_calculator.py（https://github.com/ashutoshkpandey/Annotation/blob/master/Grantham_score_calculator.py）

Jie xiao

Huazhong agriculture university

请问这个Grantham_score_calculator.py具体如何使用呢？python Grantham_score_calculator.py missense.vcf 这个命令吗？谢谢

黎 于

这是一个python脚本。源代码是针对单个位点的计算。所以建议找熟悉python的人修改成批量执行，或者就是把vcf拆分成单个位点再去执行。