Thanks for your help. I've tried the code and extracts the sequences.
Some other things may be pending for me, but I'll investigate how to do it (like printing some bytes as decimal, etc).
I was trying to print all the sequences for each block in the same line, but I'm only able to print correctly the firsts sequences fine, but the sequences of sub-block still appears in different line.
I was trying modifying the print routine as below, but is no correct yet for my goal.
The desired output is:
Thanks again.
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)
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)
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)
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)
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)
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)
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)
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)
I have a text file, input.fasta contains some protein sequences. input.fasta is shown below.
>P02649
MKVLWAALLVTFLAGCQAKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQT
LSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQA
RLGADMEDVCGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVY... (8 Replies)
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
LEARN ABOUT BSD
calloc
MALLOC(3) Library Functions Manual MALLOC(3)NAME
malloc, free, realloc, calloc, alloca - memory allocator
SYNOPSIS
char *malloc(size)
unsigned size;
free(ptr)
char *ptr;
char *realloc(ptr, size)
char *ptr;
unsigned size;
char *calloc(nelem, elsize)
unsigned nelem, elsize;
char *alloca(size)
int size;
DESCRIPTION
Malloc and free provide a general-purpose memory allocation package. Malloc returns a pointer to a block of at least size bytes beginning
on a word boundary.
The argument to free is a pointer to a block previously allocated by malloc; this space is made available for further allocation, but its
contents are left undisturbed.
Needless to say, grave disorder will result if the space assigned by malloc is overrun or if some random number is handed to free.
Malloc maintains multiple lists of free blocks according to size, allocating space from the appropriate list. It calls sbrk (see brk(2))
to get more memory from the system when there is no suitable space already free.
Realloc changes the size of the block pointed to by ptr to size bytes and returns a pointer to the (possibly moved) block. The contents
will be unchanged up to the lesser of the new and old sizes.
In order to be compatible with older versions, realloc also works if ptr points to a block freed since the last call of malloc, realloc or
calloc; sequences of free, malloc and realloc were previously used to attempt storage compaction. This procedure is no longer recommended.
Calloc allocates space for an array of nelem elements of size elsize. The space is initialized to zeros.
Alloca allocates size bytes of space in the stack frame of the caller. This temporary space is automatically freed on return.
Each of the allocation routines returns a pointer to space suitably aligned (after possible pointer coercion) for storage of any type of
object. If the space is of pagesize or larger, the memory returned will be page-aligned.
SEE ALSO brk(2), pagesize(2)DIAGNOSTICS
Malloc, realloc and calloc return a null pointer (0) if there is no available memory or if the arena has been detectably corrupted by stor-
ing outside the bounds of a block. Malloc may be recompiled to check the arena very stringently on every transaction; those sites with a
source code license may check the source code to see how this can be done.
BUGS
When realloc returns 0, the block pointed to by ptr may be destroyed.
The current implementation of malloc does not always fail gracefully when system memory limits are approached. It may fail to allocate
memory when larger free blocks could be broken up, or when limits are exceeded because the size is rounded up. It is optimized for sizes
that are powers of two.
Alloca is machine dependent; its use is discouraged.
4th Berkeley Distribution May 14, 1986 MALLOC(3)