Hi,
I'm trying to assign a score to each row which will allow me to identify which rows differ. In the example file below, I've used "," to indicate column separators (my actual file has tab separators). In this example, I'd like to identify that row 1 and row 5 are the same, and row 2 and row... (4 Replies)
My files look like this
And I need to cut the sequences at the last "A" found in the following 'pattern' -highlighted for easier identification, the pattern is the actual file is not highlighted.
The expected result should look like this
Thus, all the sequences would end with AGCCCTA... (2 Replies)
This is what I would like to accomplish, I have an input file (file A) that consist of thousands of sequence elements with the same number of characters (length), each headed by a free text header starting with the chevron ‘>' character followed by the ID (all different IDs with different lenghts)... (9 Replies)
My file looks something like this
Wnat I need is to look for the Reference sequence (">Reference1") and based on the length of that sequence trim all the entries in that file. So, the rersulting file will contain all sequences with the same length, like this
Thus, all sequences will keep... (5 Replies)
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 two files containing hundreds of different sequences with the same Identifiers (ID-001, ID-002, etc.,), something like this:
Infile1:
ID-001 ATGGGAGCGGGGGCGTCTGCCTTGAGGGGAGAGAAGCTAGATACA
ID-002 ATGGGAGCGGGGGCGTCTGTTTTGAGGGGAGAGAAGCTAGATACA
ID-003... (18 Replies)
I have to remove sequences from a file based on the distance value. I am attaching the file containing the distances (Distance.xls)
The second file looks something like this:
Sequences.txt
>Sample1 Freq 59
ggatatgatgatgaactggt
>Sample1 Freq 54
ggatatgatgttgaactggt
>Sample1 Freq 44... (2 Replies)
Hi experts,
I have a score matrix like below, where the 3rd column ( 1 max, 0 min) says how close the 2nd column variable is to the 1st column variable
a b 0.3
a c 0.87
a d 0.75
b x 0.67
b y 0.98
b z 0.24
c ... (4 Replies)
I have this file:
>ID1
AA
>ID2
TTTTTT
>ID-3
AAAAAAAAA
>ID4
TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC
Add I am trying to use this script to output sequences longer than 15 characters:
sed -r '/^>/N;{/^.{,15}$/d}'
The desire output would be this:
>ID4... (8 Replies)
Discussion started by: Xterra
8 Replies
LEARN ABOUT MOJAVE
getdelim
GETLINE(3) BSD Library Functions Manual GETLINE(3)NAME
getdelim, getline -- get a line from a stream
LIBRARY
Standard C Library (libc, -lc)
SYNOPSIS
#include <stdio.h>
ssize_t
getdelim(char ** restrict linep, size_t * restrict linecapp, int delimiter, FILE * restrict stream);
ssize_t
getline(char ** restrict linep, size_t * restrict linecapp, FILE * restrict stream);
DESCRIPTION
The getdelim() function reads a line from stream, delimited by the character delimiter. The getline() function is equivalent to getdelim()
with the newline character as the delimiter. The delimiter character is included as part of the line, unless the end of the file is reached.
The caller may provide a pointer to a malloced buffer for the line in *linep, and the capacity of that buffer in *linecapp. These functions
expand the buffer as needed, as if via realloc(). If linep points to a NULL pointer, a new buffer will be allocated. In either case, *linep
and *linecapp will be updated accordingly.
RETURN VALUES
The getdelim() and getline() functions return the number of characters written, excluding the terminating NUL character. The value -1 is
returned if an error occurs, or if end-of-file is reached.
EXAMPLES
The following code fragment reads lines from a file and writes them to standard output. The fwrite() function is used in case the line con-
tains embedded NUL characters.
char *line = NULL;
size_t linecap = 0;
ssize_t linelen;
while ((linelen = getline(&line, &linecap, fp)) > 0)
fwrite(line, linelen, 1, stdout);
ERRORS
These functions may fail if:
[EINVAL] Either linep or linecapp is NULL.
[EOVERFLOW] No delimiter was found in the first SSIZE_MAX characters.
These functions may also fail due to any of the errors specified for fgets() and malloc().
SEE ALSO fgetln(3), fgets(3), malloc(3)STANDARDS
The getdelim() and getline() functions conform to IEEE Std 1003.1-2008 (``POSIX.1'').
HISTORY
These routines first appeared in FreeBSD 8.0.
BUGS
There are no wide character versions of getdelim() or getline().
BSD November 30, 2010 BSD