Extract sequences of bytes from binary for differents blocks

Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Extract sequences of bytes from binary for differents blocks
# 57  
Old 09-04-2013
Hello Chubler_XL,

I've added the fflush(stdout) after several printf lines within the code and now the program processes 373 more blocks.
Before the addition of flush it stopped in the block 581,524 and now, with the flush, stops in block 581,897.

It seems that is not related with the size of the blocks, more it seems that is accumulating memory or something and when
reaches the limit, stops.

Maybe you can see if something could be fixed to avoid this issue.

Thanks for all help so far.
# 58  
Old 09-04-2013
Hello Chubler_XL,

I've generated a debug file of 1KB from last 3rd block before program crashes and if a run the C program over that debug file, doesn't print anything.

Maybe you or somebody could know why could stops the program.

Thanks in advance.
# 59  
Old 09-04-2013
In function remover_fs you don't malloc enough memory for the string (You need 1 extra char for the null terminator).

My advice is to not allocate any memory and just print the output as required.

Try this replacement function:

void remover_fs (const unsigned char * ptr, unsigned int len)
    unsigned int i;

    for (i = 0; i < len; i++)
        if ((ptr[i] >> 4) != 0xf)
            printf ("%01x", ptr[i] >> 4);
        if ((ptr[i] & 0xf) != 0xf)
            printf ("%01x", ptr[i] & 0xf);

# 60  
Old 09-05-2013
Hello Chubler_XL,

It works this time!!!Smilie Many thanks for your help!!!Smilie

After change the function with the code you posted, the script didn't stop, and I'm not sure, but it seems processed all blocks within binary.

Some minor issue only because when one pattern begins with 0x83 is printing one byte less.

Really thanks ahamed and Chubler_XL for the great help and time!

Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Blocks of text in a file - extract when matches...

I sat down yesterday to write this script and have just realised that my methodology is broken........ In essense I have..... ----------------------------------------------------------------- (This line really is in the file) Service ID: 12345 ... (7 Replies)
Discussion started by: Bashingaway
7 Replies

2. Shell Programming and Scripting

Extract the part of sequences from a file

Discussion started by: rahim42
8 Replies

3. Shell Programming and Scripting

Extract length wise sequences from fastq file

I have a fastq file from small RNA sequencing with sequence lengths between 15 - 30. I wanted to filter sequence lengths between 21-25 and write to another fastq file. how can i do that? (4 Replies)
Discussion started by: empyrean
4 Replies

4. Shell Programming and Scripting

Extract sequences based on the list

Hi, I have a file with more than 28000 records and it looks like below.. >mm10_refflat_ABCD range=chr1:1234567-2345678 tgtgcacactacacatgactagtacatgactagac....so on >mm10_refflat_BCD range=chr1:3234567-4545678... tgtgcacactacacatgactagtatgtgcacactacacatgactagta . . . . . so on ... (2 Replies)
Discussion started by: Diya123
2 Replies

5. UNIX for Dummies Questions & Answers

X bytes of 0, Y bytes of random data, Z bytes of 5, T bytes of 1. ??

Hello guys. I really hope someone will help me with this one.. So, I have to write this script who: - creates a file home/student/vmdisk of 10 mb - formats that file to ext3 - mounts that partition to /mnt/partition - creates a file /mnt/partition/data. In this file, there will... (1 Reply)
Discussion started by: razolo13
1 Replies

6. Linux

Why does ext3 allocate 8 blocks for files that are few bytes long

The title is clear: why does ext3 allocate 8 blocks for files that are few bytes long? If I create a file named "test", put a few chars in it, and then I run: stat test I get that "Blocks: 8" I searched in the web and found that ext does that, it allocates 8 blocks even if It doesn't need... (4 Replies)
Discussion started by: Tavo
4 Replies

7. Shell Programming and Scripting

extract blocks of text from a file

Hi, This is part of a large text file I need to separate out. I'd like some help to build a shell script that will extract the text between sets of dashed lines, write that to a new file using the whole or part of the first text string as the new file name, then move on to the next one and... (7 Replies)
Discussion started by: cajunfries
7 Replies

8. Shell Programming and Scripting

Extract sequence blocks

Hi, I have an one-line file consisting of a sequence of 660 letters. I would like to extract 9-letter blocks iteratively: ASDFGHJKLQWERTYUIOPZXCVBNM first block: ASDFGHJKL 1nd block: SDFGHJKLQ What I have so far only gives me the first block, can anyone please explain why? cat... (7 Replies)
Discussion started by: solli
7 Replies

9. UNIX for Advanced & Expert Users

Deal with binary sequences

Hello, I have come across the necessity for me to deal with binary sequences and I had a few questions. 1- Does any UNIX scripting language provide any tool or command for converting text data to binary sequences? Example of binary sequence: "0x97 0x93 0x85 0x40 0xd5 0xd6 0xd7" 2- If I want... (2 Replies)
Discussion started by: Indalecio
2 Replies

10. Shell Programming and Scripting

Remove first N bytes and last N bytes from a binary file on AIX.

Hi all, Does anybody know or guide me on how to remove the first N bytes and the last N bytes from a binary file? Is there any AWK or SED or any command that I can use to achieve this? Your help is greatly appreciated!! Best Regards, Naveen. (1 Reply)
Discussion started by: naveendronavall
1 Replies
Login or Register to Ask a Question