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)
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)
Hi,
I have a string say "whateverCluster".
I need everthing apart from the string "Cluster"
Input:
whateverCluster
Desired output:
whatever (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 with thousands of sequences of different lengths. infile1 contains the actual sequences and infile2 the scores for each A, T, G and C in infile1. Something like this:
infile1:
>HZVJKYI01ECH5R
TTGATGTGCCAGCTGCCGTTGGTGTGCCAA
>HZVJKYI01AQWJ8
GGATATGATGATGAACTGGTTTGGCACACC... (4 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)
I have a list of IDs in file1 and a list of sequences in file2. I can print sequences from file2, but I'm asking for help in printing the sequences in the same order as the IDs appear in file1.
file1:
EN_comp12952_c0_seq3:367-1668
ES_comp17168_c1_seq6:1-864
EN_comp13395_c3_seq14:231-1088... (5 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 OPENDARWIN
set_color
set_color(1) fish set_color(1)NAME
set_color - set_color - set the terminal color
set_color - set the terminal color
Synopsis
set_color [-v --version] [-h --help] [-b --background COLOR] [COLOR]
Description
Change the foreground and/or background color of the terminal. COLOR is one of black, red, green, brown, yellow, blue, magenta, purple,
cyan, white and normal.
o -b, --background Set the background color
o -c, --print-colors Prints a list of all valid color names
o -h, --help Display help message and exit
o -o, --bold Set bold or extra bright mode
o -u, --underline Set underlined mode
o -v, --version Display version and exit
Calling set_color normal will set the terminal color to whatever is the default color of the terminal.
Some terminals use the --bold escape sequence to switch to a brighter color set. On such terminals, set_color white will result in a grey
font color, while set_color --bold white will result in a white font color.
Not all terminal emulators support all these features. This is not a bug in set_color but a missing feature in the terminal emulator.
set_color uses the terminfo database to look up how to change terminal colors on whatever terminal is in use. Some systems have old and
incomplete terminfo databases, and may lack color information for terminals that support it. Download and install the latest version of
ncurses and recompile fish against it in order to fix this issue.
Version 1.23.1 Sun Jan 8 2012 set_color(1)