Hello,
I am searching large (~25gb) DNA sequence data in fasta short read format:
Code:
>ReadName
ACGTACGTACGT...[150charactersPerRead]
for short tandem repeats, meaning instances of any 2-6 character based run that are repeated in tandem a number of times given as an input variable. Seems like a reasonably simple job, but I'm having trouble developing a regex that will work. As a start, I have:
The substring constraints have to do with downstream requirements. But, I'm having trouble integrating in the regex that I want repeats of discrete motifs, not ANY 5 or more repeats (for example) of ANY 2-6 bases, which obviously returns every read.
Hello
on my cdrom, the length of the file names are 8 characters, not > 8. On a linux with the same cd, there are > 8 characters.
What's wrong.
Tanks
Urs (3 Replies)
I have a text file that I want to search for repeated lines and print those lines. These would be lines in the file that appear more than once. Is there a way to do this?
Thanks (4 Replies)
I need to search a very large file. 13g in size. i am looking for a record that has a value in the byte 4200 . how can i view the file or how can i search for value in the byte 4200? (1 Reply)
Hey All
Can any one please suggest the procedure to search a part of line in a very large file in which log entries are entered with very high speed.
i have trued with grep and egrep
grep 'text text text' <file-name>
egrep 'text text text' <file-name>
here 'text text text' is... (4 Replies)
I tried to make the title/subject detailed, but well.. have to keep it short as well.
I am wanting to take a large list of strings, and search through a large list of files to hopefully find numerous matches. I am not sure the quickest way to do this though.
// List of files
file1.txt... (2 Replies)
I've got a simple log file that looks something like this:
And I need to append it to look like this:
So I just want to add a timestamp and a static (non-variable) word to each line in the file. Is there an easy scripted way to cat the file and append that data to each line....?? (4 Replies)
without using conventional file searching commands like find etc, is it possible to locate a file if i just know that the file that i'm searching for contains a particular text like "Hello world" or something? (5 Replies)
if I wanted to know if the word DOG(followed by several random numbers) appears in col 1, how many times will that same word DOG* appeared in col 2? This is a very large file
Thanks! (7 Replies)
Hello,
I use UBUNTU 12.04.
I want to write a short program using awk to select some lines in a file based on a second file.
My first file has this format with about 400,000 lines and 47 fields:
SNP1 1 12.1
SNP2 1 13.2
SNP3 1 45.2
SNP4 1 23.4
My second file has this format:
SNP2
SNP3... (1 Reply)
Discussion started by: Homa
1 Replies
LEARN ABOUT DEBIAN
ppmtosixel
ppmtosixel(1) General Commands Manual ppmtosixel(1)NAME
ppmtosixel - convert a portable pixmap into DEC sixel format
SYNOPSIS
ppmtosixel [-raw] [-margin] [ppmfile]
DESCRIPTION
Reads a portable pixmap as input. Produces sixel commands (SIX) as output. The output is formatted for color printing, e.g. for a DEC
LJ250 color inkjet printer.
If RGB values from the PPM file do not have maxval=100, the RGB values are rescaled. A printer control header and a color assignment table
begin the SIX file. Image data is written in a compressed format by default. A printer control footer ends the image file.
OPTIONS -raw If specified, each pixel will be explicitly described in the image file. If -raw is not specified, output will default to com-
pressed format in which identical adjacent pixels are replaced by "repeat pixel" commands. A raw file is often an order of magni-
tude larger than a compressed file and prints much slower.
-margin
If -margin is not specified, the image will be start at the left margin (of the window, paper, or whatever). If -margin is speci-
fied, a 1.5 inch left margin will offset the image.
PRINTING
Generally, sixel files must reach the printer unfiltered. Use the lpr -x option or cat filename > /dev/tty0?.
BUGS
Upon rescaling, truncation of the least significant bits of RGB values may result in poor color conversion. If the original PPM maxval was
greater than 100, rescaling also reduces the image depth. While the actual RGB values from the ppm file are more or less retained, the
color palette of the LJ250 may not match the colors on your screen. This seems to be a printer limitation.
SEE ALSO ppm(5)AUTHOR
Copyright (C) 1991 by Rick Vinci.
26 April 1991 ppmtosixel(1)
09-03-2013
