比较基因组从入门到放弃（4-1）

因为这些脚本是我自己写的，可以放出来供大家参考

# run1.py
import sys

f1 = open(sys.argv[1],'r')
f2 = open(sys.argv[2],'w')

for line in f1:
        line = line.strip()
        f2.write("cd align/"+line+" && echo "+line+" > id && cd ../../  \n" )

f1.close()
f2.close()

# run2.py
import sys

f1 = open(sys.argv[1],'r')
f2 = open(sys.argv[2],'w')

for line in f1:
        line = line.strip()
        f2.write("cd align/"+line+" && cp ../../p.sh ./ && sh p.sh && paste id z > Pout && cd ../../ \n" )

f1.close()
f2.close()

# p.py
import sys

f1 = open(sys.argv[1],'r')
f2 = open(sys.argv[2],'w')

for line in f1:
        line = line.strip().split()
        og = line[0]
        x1 = line[1]
        x2 = line[2]
        f2.write("pchisq("+x2+","+x1+", lower.tail = FALSE)\n")

f1.close()
f2.close()

# run.py
import sys

f1 = open(sys.argv[1],'r')
f2 = open(sys.argv[2],'w')

for line in f1:
        line = line.strip()
        f2.write("cd align/"+line+" && cp ../../codeml.ctl ./ && cp ../../tree ./ && cp ../../01.sh ./ && cp ../../02.sh ./ && sh 01.sh && sh 02.sh > "+"test.phy && singularity exec /home/wangyj20/SIF/paml_latest.sif codeml && cd ../.. \n" )

f1.close()
f2.close()