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
size
SIZE(1) General Commands Manual SIZE(1)NAME
size - print the size of the sections in an object file
SYNOPSIS
size [ option ... ] [ object ... ]
DESCRIPTION
Size (without the -m option) prints the (decimal) number of bytes required by the __TEXT, __DATA and __OBJC segments. All other segments
are totaled and that size is listed in the `others' column. The final two columns is the sum in decimal and hexadecimal. If no file is
specified, a.out is used.
The options to size(1) are:
- Treat the remaining arguments as name of object files not options to size(1).
-m Print the sizes of the Mach-O segments and sections as well as the total sizes of the sections in each segment and the total size of
the segments in the file.
-l When used with the -m option, also print the addresses and offsets of the sections and segments.
-x When used with the -m option, print the values in hexadecimal (with leading 0x's) rather than decimal.
-arch arch_type
Specifies the architecture, arch_type, of the file for size(1) to operate on when the file is a fat file. (See arch(3) for the cur-
rently know arch_types.) The arch_type can be "all" to operate on all architectures in the file. The default is to display only
the host architecture, if the file contains it; otherwise, all architectures in the file are shown.
SEE ALSO otool(1)BUGS
The size of common symbols can't be reflected in any of the numbers for relocatable object files.
Apple Computer, Inc. May 23, 2002 SIZE(1)