06-23-2010
Trimming sequences based on specific pattern
My files look like this
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCTTGGTGTGTATCATTTCTGGGAAGCCCTACGCCCCGGGGC
>GHXCZCC01APUO5
T-ATGTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCAGCCCTACCCGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTA---AGCTGGATTTTCTGGGACGCCCCGGGGAGCCCTA
>GHXCZCC01AQSRP
TTGTTGCCAGCTAGCTGAGCCCTAGATTTTCTGGGGCCCCGGGG
>GHXCZCC01AQSRP
TTGATGTTGCCCAGCCCTATAGCTGGATTTTCTGGGACGCCCCGGGGTGC
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
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCTTGGTGTGTATCATTTCTGGGAAGCCCTA
>GHXCZCC01APUO5
T-ATGTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCAGCCCTA
>GHXCZCC01AQSRP
TTGATGTTA---AGCTGGATTTTCTGGGACGCCCCGGGGAGCCCTA
>GHXCZCC01AQSRP
TTGTTGCCAGCTAGCTGAGCCCTA
>GHXCZCC01AQSRP
TTGATGTTGCCCAGCCCTA
Thus, all the sequences would end with
AGCCCTA but whatever is to the left of that particular pattern and the identifiers (>GHXCZCC01AJ8CJ) should be kept intact.
Thanks in advance
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
My input:
File_1:
2000_t
g1110.b1
abb.1
2001_t
g1111.b1
abb.2
abb.2
g1112.b1
abb.3
2002_t
.
.
File_2:
2000_t Ali england 135
abb.1 Zoe british 150
2001_t Ali england 305
g1111.b1 Lucy russia 126 (6 Replies)
Discussion started by: patrick87
6 Replies
2. Shell Programming and Scripting
Input
#GEO-1-type-1-fwd-Initial 890 1519
OPKHIJEFVTEFVHIJEFVOPKHIJTOPKEFVHIJTEFVOPKOPKHIJHIJHIJTTOPKHIJHIJEFVEFVOPKHIJOPKHIJOPKEFVEFVOPKHIJHIJEFVHIJHIJEFVTHIJOPKOPKTEFVEFVEFVOPKHIJOPKOPKHIJTTEFVEFVTEFV
#GEO-1-type-2-fwd-Terminal 1572 2030... (7 Replies)
Discussion started by: patrick87
7 Replies
3. Shell Programming and Scripting
My file looks like this:
But I would like to 'trim' all sequences to the same lenght 32 characters, keeping intact all the identifier (>GHXCZCC01AJ8CJ)
Would it be possible to use awk to perform this task? (2 Replies)
Discussion started by: Xterra
2 Replies
4. Shell Programming and Scripting
My file looks like this
But I need to remove the entry with the identifier >Reference1 along with the entire sequence. Thus, I will end up having the following file
Thanks in advance! (2 Replies)
Discussion started by: Xterra
2 Replies
5. Shell Programming and Scripting
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)
Discussion started by: Xterra
5 Replies
6. Shell Programming and Scripting
Hi Unix gurus,
I am trying to remove the filenames based on MMDDYYYY in the physical name as such so that the directory always has the recent 3 files based on MMDDYYYY. "HHMM" is just dummy in this case. You wont have two files with different HHMM on the same day.
For example in a... (4 Replies)
Discussion started by: shankar1dada
4 Replies
7. Shell Programming and Scripting
Input file
data20714 7327 7366 detail
data20714 7327 7366 main
data250821 56532 57634 detail
data250821 57527 57634 main
data250821 57359 57474 main
data250821 57212 57301 main
data250821 57140 57159 detail
data250821 56834 57082 main
data250821 56708 56779 main ... (3 Replies)
Discussion started by: perl_beginner
3 Replies
8. UNIX for Dummies Questions & Answers
Hi,
I have a string say "whateverCluster".
I need everthing apart from the string "Cluster"
Input:
whateverCluster
Desired output:
whatever (5 Replies)
Discussion started by: mohtashims
5 Replies
9. Shell Programming and Scripting
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
10. Shell Programming and Scripting
Hi all,
I have been trying to delete duplicates based on a certain pattern but failed to make it works. There are more than 1 pattern which are duplicated but i just want to remove 1 pattern only and remain the rest. I cannot use awk '!x++' inputfile.txt or sed '/pattern/d' or use uniq and sort... (7 Replies)
Discussion started by: redse171
7 Replies
FNMATCH(3) 1 FNMATCH(3)
fnmatch - Match filename against a pattern
SYNOPSIS
bool fnmatch (string $pattern, string $string, [int $flags])
DESCRIPTION
fnmatch(3) checks if the passed $string would match the given shell wildcard $pattern.
PARAMETERS
o $pattern
- The shell wildcard pattern.
o $string
- The tested string. This function is especially useful for filenames, but may also be used on regular strings. The average user
may be used to shell patterns or at least in their simplest form to '?' and '*' wildcards so using fnmatch(3) instead of
preg_match(3) for frontend search expression input may be way more convenient for non-programming users.
o $flags
- The value of $flags can be any combination of the following flags, joined with the binary OR (|) operator.
A list of possible flags for fnmatch(3)
+-------------+---------------------------------------------------+
| $Flag | |
| | |
| | Description |
| | |
+-------------+---------------------------------------------------+
| | |
|FNM_NOESCAPE | |
| | |
| | Disable backslash escaping. |
| | |
| | |
|FNM_PATHNAME | |
| | |
| | Slash in string only matches slash in the given |
| | pattern. |
| | |
| | |
| FNM_PERIOD | |
| | |
| | Leading period in string must be exactly matched |
| | by period in the given pattern. |
| | |
| | |
|FNM_CASEFOLD | |
| | |
| | Caseless match. Part of the GNU extension. |
| | |
+-------------+---------------------------------------------------+
RETURN VALUES
Returns TRUE if there is a match, FALSE otherwise.
CHANGELOG
+--------+---------------------------------------------------+
|Version | |
| | |
| | Description |
| | |
+--------+---------------------------------------------------+
| 5.3.0 | |
| | |
| | This function is now available on Windows plat- |
| | forms. |
| | |
+--------+---------------------------------------------------+
EXAMPLES
Example #1
Checking a color name against a shell wildcard pattern
<?php
if (fnmatch("*gr[ae]y", $color)) {
echo "some form of gray ...";
}
?>
NOTES
Warning
For now, this function is not available on non-POSIX compliant systems except Windows.
SEE ALSO
glob(3), preg_match(3), sscanf(3), printf(3), sprintf(3).
PHP Documentation Group FNMATCH(3)