Question

I have to read a text file which can begin with optional comments. In practice I have to skip any line at the beginning of the file that doesn’t begin with ‘@’ or ‘>’.
In my test case the file looks like:

# Sun Jul 12 22:04:52 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/solid0065/primary.20090712170542775 
# Cwd: /state/partition1/home/pipeline
# Title: solid0065_20090629_FC1_Tomate_Heinz_4_5_Kb_Tomate_Heinz_4_5_Kb_01
>125_963_316_F3
T1230330231223011323010013

So I have to skip the first 3 line (but in general I have to skip n lines). I have to repeat this with 2 or 4 files [which are inside FILE** inputFiles]. I’ve tried with this loop:

buffer = (char*) malloc (sizeof(char) * 5000);
if (buffer == NULL)
    notEnoughMemory();

for (i = 0; i < (cIn-1); i++){
    fgetpos(inputFiles[i], &position);
    fgets(buffer, 4999, inputFiles[i]);
    while ((buffer[0] != '@') && (buffer[0] != '>')){
        fgetpos(inputFiles[i], &position);
        fgets(buffer, 4999, inputFiles[i]);
    }
    fsetpos(inputFiles[i], &position);
}

Where cIn is number_of_input_files + 1.
Trying to debug it the loop correctly stops after it reads the fourth line. But when I use setpos it doesn’t go back to the beginning of the fourth line as I’d expect, but at the middle of the third.
In fact if, exactly after the fsetpos(), I print buffer after these operations:

fgets(buffer, 4999, inputFiles[i]);
fgets(buffer, 4999, inputFiles[i]);

I get:

FC1_Tomate_Heinz_4_5_Kb_Tomate_Heinz_4_5_Kb_01
>125_963_316_F3

Any idea?
Thanks in advance

Answer 1

You could just skip processing the lines you are not interrested in:

for (i = 0; i < (cIn-1); i++){

    while (fgets(buffer, 4999, inputFiles[i])){
       if(buffer[0] == '@' || buffer[0] == '>') {
          puts(buffer);
        }
        /* else do nothing*/
    }
}

Then you just replace the puts(buffer); with the code you need to handle the valid lines.
(allthough, from your example it sounds like you rather want to only ignore lines starting with a #, ?)