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Print specific pattern line in c++

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# 1  
Old 07-05-2011
Print specific pattern line in c++
Input file:
Code:
@HWI-BRUNOP1_header_1
GACCAATAAGTGATGATTGAATCGCGAGTGCTCGGCAGATTGCGATAAAC
+HWI-BRUNOP1_header_1
TNTTJTTTETceJSP__VRJea`_NfcefbWe[eagggggfgdggBBBBB
@HWI-BRUNOP1_header_2
CAGCAGACGCTTTGATTGCTCGATCTCTTGGTAAATACGGCATCATCTGC
+HWI-BRUNOP1_header_2
TJTTTJFFFFa`TWNMPJGTbZSTPZJHHGT^I^H^SKZeeeeeeb``RT

Desired output file:
Code:
>HWI-BRUNOP1_header_1
GACCAATAAGTGATGATTGAATCGCGAGTGCTCGGCAGATTGCGATAAAC
>HWI-BRUNOP1_header_2
CAGCAGACGCTTTGATTGCTCGATCTCTTGGTAAATACGGCATCATCTGC

Rules to follow when writing c++ program:
1. Print out the line start with "@HWI" and the content below "@HWI";
2. Change the "@HWI" into "#HWI" and save the output result into another file;
Command that I try to deal with 14Gb input file data:
Code:
[home@cpp]time grep -A1 '@HWI' input_file.txt | sed -e 's/--//g' -e 's/@HWI/#HWI/g' | sed '/^$/d' > output_file.txt
real    7m13.413s
user    5m25.382s
sys     1m37.668s
[1]+  Done       time grep -A1 '@HWI' input_file.txt | sed -e 's/--//g' -e 's/@HWI/#HWI/g' | sed '/^$/d' > output_file.txt           
[home@cpp]cat output_file.txt
>HWI-BRUNOP1_header_1
GACCAATAAGTGATGATTGAATCGCGAGTGCTCGGCAGATTGCGATAAAC
>HWI-BRUNOP1_header_2
CAGCAGACGCTTTGATTGCTCGATCTCTTGGTAAATACGGCATCATCTGC

Desired format to run the c++ program:
Code:
cplusplus_program_name input_file_name output_file_name

Thanks for any advice.
# 2  
Old 07-05-2011
You're already getting 30 megabytes per second translation rate, which comes to 60 megs/second transfer rate considering you're reading AND writing. Just how fast is your disk? Will a hardcoded solution actually be faster?

But if you really want a hardwired solution:

Code:
#include <stdio.h>
#include <string.h>

int main(void)
{
        char buf[4096];

       while(fgets(buf, 4096, stdin))
       {
               if(strncmp(buf, "@HWI", 4) == 0)
               {
                       buf[0]='#';
                       fputs(buf, stdout);
                       if(fgets(buf, 4096, stdin) == NULL) continue;
                       fputs(buf, stdout);
               }
       }
}

works pretty close to how you want:

Code:
./cname < infile > outfile

You can also do it in awk with
Code:
awk '/^@HWI/ { sub("@", "#", $1); print; getline ; print }' < infile > outfile

The C version seems faster than the awk one admittedly!
Last edited by Corona688; 07-05-2011 at 02:24 AM..
This User Gave Thanks to Corona688 For This Post:
cpp_beginner
# 3  
Old 07-05-2011
Hi Corona688,

Many thanks for your c++ program.
I'm very appreciate it.
Based on your experience, is it I should edit your program by using "argv", "f_read", "f_write" in order to get the desired program running format:
Code:
cplusplus_program_name input_file_name output_file_name

# 4  
Old 07-05-2011
It really doesn't matter whether the shell or the program does the file-opening for a simple program that always has one input file and one output file, but since you insist:
Code:
#include <stdio.h>
#include <string.h>

int main(int argc, char *argv[])
{
       char buf[4096];
       FILE *fin, *fout;

       if(argc != 3)
       {
               fprintf(stderr, "Usage:  %s filein fileout\n", argv[0]);
               return(1);
       }

       fin=fopen(argv[1], "r");
       if(fin == NULL)
       {
              fprintf(stderr, "Couldn't open %s\n", argv[1]);
              return(1);
       }


       fout=fopen(argv[2], "w");
       if(fout == NULL)
       {
              fprintf(stderr, "Couldn't open %s\n", argv[2]);
              return(1);
       }

       while(fgets(buf, 4096, fin))
       {
               if(strncmp(buf, "@HWI", 4) == 0)
               {
                       buf[0]='#';
                       fputs(buf, fout);
                       if(fgets(buf, 4096, fin) == NULL) continue;
                       fputs(buf, fout);
               }
       }

       fclose(fin);
       fclose(fout);
       return(0);
}

This User Gave Thanks to Corona688 For This Post:
cpp_beginner
# 5  
Old 07-05-2011
Many thanks, Corona688.
I just curious what does it really mean in "strncmp(buf, "@HWI", 4) == 0" and "fputs(buf, fout);" that you use in your source code?
I can't really get how to use string compare function in this case.
Many thanks for advice
# 6  
Old 07-05-2011
Quote:
Originally Posted by cpp_beginner
Many thanks, Corona688.
I just curious what does it really mean in "strncmp(buf, "@HWI", 4) == 0" and "fputs(buf, fout);" that you use in your source code?
compare the first 4 characters of two strings for strncmp, and print a string for fputs. 'man strcmp' and 'man fputs' may help.
# 7  
Old 07-06-2011
Many thanks, Corona688.
After I reading the 'man strcmp' and 'man fputs'. I understanding the reason why you using 'strcmp' and 'fputs' while coding Smilie
I just wondering why that "if(fgets(buf, 4096, fin)== NULL ) continue;" will print out only the line next to "@HWI instead of other line?
"fgets" will "Get string from stream" and read through it from the input file.
Code:
eg.
[home@cpp]cat input_file.txt
@HWI-BRUNOP1_header_1
GACCAATAAGTGATGATTGAATCGCGAGTGCTCGGCAGATTGCGATAAAC
+HWI-BRUNOP1_header_1
TNTTJTTTETceJSP__VRJea`_NfcefbWe[eagggggfgdggBBBBB

Many thanks to explain the reason that "if(fgets(buf, 4096, fin)== NULL ) continue;" will only print the second line shown in above example instead of other line.
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