Hello,
Using Linux (or may be R), what is the most efficient way to transform long genotype format into short format?
Input file:
11130012
33221200
Transformation: 11 into 0; 12 or 13 into 1; 22 or 33 into 2 and 00 into 5.
The output file would be:
0151
2215
•
written
by
admamajdi •
efficient ?
using Flex + gcc:
file: biostar.l
%option noyywrap
%%
11 putchar('0');
(12|13) putchar('1');
(22|33) putchar('2');
00 putchar('5');
\n ECHO;
. fprintf(stderr,"ERROR!");exit(-1);
%%
int main(int argc,char argv) { yylex();return 0;}
usage:
flex biostar.l && gcc -O3 lex.yy.c && echo -e '11130012\n33221200' | ./a.out
0151
2215
Thanks Pierre. Efficient because the file is too big. I got this error -bash: fg: %option: no such job
??? there is something wrong in you command. what is fg ?
what is the output of flex --version. should be something like:
$ flex --version
flex 2.6.0
fg is is for background jobs. it's unrelated to the present question.
$ flex --version
flex 2.5.37
Python
d = {"11": "0", "12" : "1", "13" : "1", "22" : "2", "33" : "2", "00" : "5"}
def long_to_short(input):
string = ""
output = ""
for i in input:
string += i
if len(string) == 2:
output += d[string]
string = ""
print(output)
It works well! Could you please modefy the code so it reads inputs from a file and sends outputs to a file?
This should work if you just replace the "input.txt" with the filename to your input file
import os
cwd = os.getcwd()
d = {"11": "0", "12" : "1", "13" : "1", "22" : "2", "33" : "2", "00" : "5"}
def long_to_short(input):
string = ""
output = ""
for i in input:
string += i
if len(string) == 2:
output += d[string]
string = ""
return(output)
f = open(input.txt, "r")
o = open(cwd + "/output.txt", "w")
for i in f.readlines():
o.write(long_to_short(i.replace("\n", "")) + "\n")
Thanks shussainather! Yup! It works just fine and does exactly what I want.
One thing: name of input file should be between " " i.e. "input.txt"
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