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Merge branch 'master' of https://github.com/HuffordLab/NAM-genomes
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@aihudson
aihudson committed May 12, 2021
2 parents 713f3d7 + 2913fd4 commit c9d9e45
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104 changes: 104 additions & 0 deletions NLR-genes/Itol-Maize-Format2.py
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#!/usr/bin/env python
# coding=utf-8

#Usage: python Itol-Maize-Format2.py <list-of-tree-Maize-IDs> > <output_file>

import sys
import csv
import re
b73='(.*)1eb(.*)'
b97='(.*)18ab(.*)'
cml103='(.*)21ab(.*)'
cml228='(.*)22ab(.*)'
cml247='(.*)23ab(.*)'
cml277='(.*)24ab(.*)'
cml322='(.*)25ab(.*)'
cml333='(.*)26ab(.*)'
cml52='(.*)19ab(.*)'
cml69='(.*)20ab(.*)'

hp3='(.*)27ab(.*)'
il14h='(.*)28ab(.*)'
ki11='(.*)30ab(.*)'
ki3='(.*)29ab(.*)'
ky21='(.*)31ab(.*)'
m162w='(.*)33ab(.*)'
m37w='(.*)32ab(.*)'
mo18w='(.*)34ab(.*)'
ms71='(.*)35ab(.*)'
nc350='(.*)36ab(.*)'
nc358='(.*)37ab(.*)'
oh43='(.*)39ab(.*)'
oh7b='(.*)38ab(.*)'
p39='(.*)40ab(.*)'
tx303='(.*)41ab(.*)'
tzi8='(.*)42ab(.*)'
Sobic='(.*)Sobic(.*)'

with open(sys.argv[1]) as fi:

for line in fi:
if re.match(b73, line):
print(line.rstrip()+',range,#FFC125,b73')
if re.match(b97, line):
print(line.rstrip()+',range,#4169E1,b97')
if re.match(ky21, line):
print(line.rstrip()+',range,#4169E1,ky21')
if re.match(m162w, line):
print(line.rstrip()+',range,#4169E1,m162w')
if re.match(oh43, line):
print(line.rstrip()+',range,#4169E1,oh43')
if re.match(oh7b, line):
print(line.rstrip()+',range,#4169E1,oh7b')
if re.match(ms71, line):
print(line.rstrip()+',range,#4169E1,ms71')

if re.match(cml103, line):
print(line.rstrip()+',range,#32CD32,cml103')
if re.match(cml228, line):
print(line.rstrip()+',range,#32CD32,cml228')
if re.match(cml247, line):
print(line.rstrip()+',range,#32CD32,cml247')
if re.match(cml277, line):
print(line.rstrip()+',range,#32CD32,cml277')
if re.match(cml322, line):
print(line.rstrip()+',range,#32CD32,cml322')
if re.match(cml333, line):
print(line.rstrip()+',range,#32CD32,cml333')
if re.match(cml52, line):
print(line.rstrip()+',range,#32CD32,cml52')
if re.match(cml69, line):
print(line.rstrip()+',range,#32CD32,cml69')
if re.match(ki11, line):
print(line.rstrip()+',range,#32CD32,ki11')
if re.match(ki3, line):
print(line.rstrip()+',range,#32CD32,ki3')
if re.match(nc350, line):
print(line.rstrip()+',range,#32CD32,nc350')
if re.match(nc358, line):
print(line.rstrip()+',range,#32CD32,nc358')
if re.match(tzi8, line):
print(line.rstrip()+',range,#32CD32,tzi8')


if re.match(hp3, line):
print(line.rstrip()+',range,#DA70D6,hp301')

if re.match(il14h, line):
print(line.rstrip()+',range,#FF4500,il14h')
if re.match(p39, line):
print(line.rstrip()+',range,#FF4500,p39')

if re.match(m37w, line):
print(line.rstrip()+',range,#787878,m37w')
if re.match(mo18w, line):
print(line.rstrip()+',range,#787878,mo18w')
if re.match(tx303, line):
print(line.rstrip()+',range,#787878,tx303')


if re.match(Sobic, line):
print(line.rstrip()+',range,#94714f,Sobic')

#if re.match(, line):
#print(line)
147 changes: 147 additions & 0 deletions NLR-genes/Itol-Maize-domain-annotation.py
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#!/usr/bin/env python
# coding=utf-8
#Usage: python Itol-Maize-Domain-Annotation.py <NLR-ID.txt file from Plant_R_Genes > > <output_file>
#NB. Any domains not in list below will not be annotated
import sys
import csv
import re

A='(.*)ABC_trans_N(.*)'
B='(.*)BUD22(.*)'
D='(.*)DUF212(.*)'
F='(.*)F-box(.*)'
NAM='(.*)NAM-associated(.*)'
Nop='(.*)Nop14(.*)'
PA='(.*)PAH(.*)'
P2='(.*)PP2\((.*)'
P2C='(.*)PP2C(.*)'
PK='(.*)Pkinase(.*)'
PKT='(.*)Pkinase_Tyr(.*)'
S='(.*)SDA1(.*)'
TF='(.*)ThiF(.*)'
TX='(.*)Thioredoxin(.*)'
TA='(.*)Transpos_assoc(.*)'
U='(.*)UBA_e1_thiolCys(.*)'
UP='(.*)UPRTase(.*)'
WR='(.*)WRKY(.*)'
Z='(.*)zf-RVT(.*)'

"""
1.ABC_trans_N
2.BUD22
3.NAM
4.PAH
5.PKinase
6.PP2
7.Pkinase_Tyr
8.SDA1
9.Thioredoxin
10.WRKY
11.zf-RVT
"""


with open(sys.argv[1]) as fi:
for row in csv.reader(fi, delimiter=','):
if re.match(A, row[2]):
print(row[0]+',#829191,ABC_trans_N')
if re.match(B, row[2]):
print(row[0]+',#F2B7C6,BUD22')
if re.match(D, row[2]):
print(row[0]+',#694F5D,DUF212')
if re.match(F, row[2]):
print(row[0]+',#69656A,F-BOX')
if re.match(NAM, row[2]):
print(row[0]+',#744253,NAM')
if re.match(Nop, row[2]):
print(row[0]+',#000000,Nop')
if re.match(PA, row[2]):
print(row[0]+',#D2BF55,PAH')
if re.match(P2, row[2]):
print(row[0]+',#E8DB7D,PP2')
if re.match(P2C, row[2]):
print(row[0]+',#000000,PP2C')
if re.match(PK, row[2]):
print(row[0]+',#EDB458,PKinase')
if re.match(PKT, row[2]):
print(row[0]+',#F4F1BB,Pkinase_Tyr')
if re.match(S, row[2]):
print(row[0]+',#B3EFB2,SDA1')
if re.match(TF, row[2]):
print(row[0]+',#020402,ThiF')
if re.match(TX, row[2]):
print(row[0]+',#D9F8C1,Thioredoxin')
if re.match(U, row[2]):
print(row[0]+',#000000,UBA')
if re.match(TA, row[2]):
print(row[0]+',#000000,Transp')
if re.match(UP, row[2]):
print(row[0]+',#020402,UPRTase')
if re.match(WR, row[2]):
print(row[0]+',#C5D86D,WRKY')
if re.match(Z, row[2]):
print(row[0]+',#657153,zf-RVT')
"""
if re.match(b97, line):
print(line.rstrip()+',range,#4169E1,b97')
if re.match(ky21, line):
print(line.rstrip()+',range,#4169E1,ky21')
if re.match(m162w, line):
print(line.rstrip()+',range,#4169E1,m162w')
if re.match(oh43, line):
print(line.rstrip()+',range,#4169E1,oh43')
if re.match(oh7b, line):
print(line.rstrip()+',range,#4169E1,oh7b')
if re.match(ms71, line):
print(line.rstrip()+',range,#4169E1,ms71')
if re.match(cml103, line):
print(line.rstrip()+',range,#32CD32,cml103')
if re.match(cml228, line):
print(line.rstrip()+',range,#32CD32,cml228')
if re.match(cml247, line):
print(line.rstrip()+',range,#32CD32,cml247')
if re.match(cml277, line):
print(line.rstrip()+',range,#32CD32,cml277')
if re.match(cml322, line):
print(line.rstrip()+',range,#32CD32,cml322')
if re.match(cml333, line):
print(line.rstrip()+',range,#32CD32,cml333')
if re.match(cml52, line):
print(line.rstrip()+',range,#32CD32,cml52')
if re.match(cml69, line):
print(line.rstrip()+',range,#32CD32,cml69')
if re.match(ki11, line):
print(line.rstrip()+',range,#32CD32,ki11')
if re.match(ki3, line):
print(line.rstrip()+',range,#32CD32,ki3')
if re.match(nc350, line):
print(line.rstrip()+',range,#32CD32,nc350')
if re.match(nc358, line):
print(line.rstrip()+',range,#32CD32,nc358')
if re.match(tzi8, line):
print(line.rstrip()+',range,#32CD32,tzi8')
if re.match(hp3, line):
print(line.rstrip()+',range,#DA70D6,hp301')
if re.match(il14h, line):
print(line.rstrip()+',range,#FF4500,il14h')
if re.match(p39, line):
print(line.rstrip()+',range,#FF4500,p39')
if re.match(m37w, line):
print(line.rstrip()+',range,#787878,m37w')
if re.match(mo18w, line):
print(line.rstrip()+',range,#787878,mo18w')
if re.match(tx303, line):
print(line.rstrip()+',range,#787878,tx303')
if re.match(Sobic, line):
print(line.rstrip()+',range,#787878,Sobic')
#if re.match(, line):
#print(line)
"""
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