Login or Register to Ask a Question and Join Our Community


UNIX for Dummies Questions & Answers

Reporting characters after string

 
Thread Tools Search this Thread
Top Forums UNIX for Dummies Questions & Answers Reporting characters after string
Prev   Next
# 11  
Old 04-12-2016
No, that will not fly. This new sed code will match multiple lines per file, but whether you use global or not, this will still only one occurrence of a regular match or one reversed/complemented match per line, the latter only if there is no regular match on that line...

--
You could limit to 10 matches per file, like so, try:

Code:
awk -v len=4 -v string=AATTCCGG -v max=10 '
  BEGIN {
    FS=RS; RS=">"; OFS=""
    C["A"]="T"; C["T"]="A"; C["C"]="G"; C["G"]="C"  
  }
  function reverse_complement(s,        t,i,n,F) {
    n=split(s,F,"")
    for(i=1;i<=n;i++)
      t=C[F[i]] t
    return t
  }
  FNR==1{
    split(FILENAME, F, ".")
    c=1
    next
  } 
  { 
    label=$1
    $1=""
    rec=$0 FS reverse_complement($0)
    while(c<=max && match(rec,string)) { 
      print F[1] ":" label ":" substr(rec,RSTART+RLENGTH, len)
      rec=substr(rec, RSTART+RLENGTH+len)
      c++
    }
  }
' file*.txt

Last edited by Scrutinizer; 04-12-2016 at 11:00 PM.. Reason: Swapped Function for the faster option...
 
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Outputting characters after a given string and reporting the characters in the row below --sed

I have this fastq file: @M04961:22:000000000-B5VGJ:1:1101:9280:7106 1:N:0:86 GGGGGGGGGGGGCATGAAAACATACAAACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGAAAAATATCAACCACACCA +test-1 GGGGGGGGGGGGGGGGGCCGGGGGFF,EDFFGEDFG,@DGGCGGEGGG7DCGGGF68CGFFFGGGG@CGDGFFDFEFEFF:30CGAFFDFEFF8CAF;;8... (10 Replies)
Discussion started by: Xterra
10 Replies

2. UNIX for Beginners Questions & Answers

Extract characters from a string name

Hi All, I am trying to extract only characters from a string value eg: abcdedg1234.cnf How can I extract only characters abcdedg and assign to a variable. Please help. Thanks (2 Replies)
Discussion started by: abhi_123
2 Replies

3. Shell Programming and Scripting

remove characters from string based on occurrence of a string

Hello Folks.. I need your help .. here the example of my problem..i know its easy..i don't all the commands in unix to do this especiallly sed...here my string.. dwc2_dfg_ajja_dfhhj_vw_dec2_dfgh_dwq desired output is.. dwc2_dfg_ajja_dfhhj it's a simple task with tail... (5 Replies)
Discussion started by: victor369
5 Replies

4. Programming

C++ Special Characters in a String?

Hello. How can i put all of the special characters on my keyboard into a string in c++ ? I tried this but it doesn't work. string characters("~`!@#$%^&*()_-+=|\}]{ How can i accomplish this? Thanks in advance. (1 Reply)
Discussion started by: cbreiny
1 Replies

5. UNIX for Dummies Questions & Answers

Count the characters in a string

Hi all, I like to know how to get the count of each character in a given word. Using the commands i can easily get the output. How do it without using the commands ( in shell programming or any programming) if you give outline of the program ( pseudo code ) i used the following commands ... (3 Replies)
Discussion started by: itkamaraj
3 Replies

6. Shell Programming and Scripting

get certain characters in a string

Hi Everyone, I have a.txt 12341" <sip:191@vo.my>;asdf=q" 116aaaa<sip:00091@vo.my>;penguin would like to get the output 191 00091 Please advice. Thanks (4 Replies)
Discussion started by: jimmy_y
4 Replies

7. Programming

string with invalid characters

This is a pretty straight-forward question. Within a program of mine, I have a string that's going to be used as a filename, but it might have some invalid characters in it that wouldn't be valid in a filename. If there are any invalid characters, I want to get rid of them and essentially squeeze... (4 Replies)
Discussion started by: cleopard
4 Replies

8. Shell Programming and Scripting

Add string after another string with special characters

Hello everyone, I'm writing a script to add a string to an XML file, right after a specified string that only occurs once in the file. For testing purposes I created a file 'testfile' that looks like this: 1 2 3 4 5 6 6 7 8 9 And this is the script as far as I've managed: ... (2 Replies)
Discussion started by: heliode
2 Replies

9. Shell Programming and Scripting

Looking for a string in files and reporting matches

Can someone please help me figure out what the command syntax I need to use is? Here is what I am wanting to do. I have hundreds of thousands of files I need to look for a specific search string in. These files are spread across multiple subdirectories from one main directory. I would like... (4 Replies)
Discussion started by: btrotter
4 Replies

10. Shell Programming and Scripting

Removing characters from a string

I need help to strip out the first two characters of the variable $FileName. Please help. FileName=`find . -mtime +0 -name '*'` Contents of variable $FileName: ./SRIZVI4.MCR_IDEAS_REPORT.LAST.052705.075405.csv I want to strip out "./" and place the contents in another variable. How do I... (3 Replies)
Discussion started by: mh53j_fe
3 Replies
Login or Register to Ask a Question

LEARN ABOUT CENTOS

paps

PAPS(1) 						      General Commands Manual							   PAPS(1)

NAME

       paps - UTF-8 to PostScript converter using Pango

SYNOPSIS

       paps [options] files...

DESCRIPTION

       paps reads a UTF-8 encoded file and generates a PostScript language rendering of the file. The rendering is done by creating outline curves
       through the pango ft2 backend.

OPTIONS

       These programs follow the usual GNU command line syntax, with long options starting with  two  dashes  (`-').   A  summary  of  options	is
       included below.

       --landscape
	      Landscape output. Default is portrait.

       --columns=cl
	      Number of columns output. Default is 1.

       --font=desc
	      Set the font description. Default is Monospace 12.

       --rtl  Do rtl layout.

       --paper ps
	      Choose paper size. Known paper sizes are legal, letter, a4. Default is A4.

       --bottom-margin=bm
	      Set bottom margin in postscript points (1/72 inch). Default is 36.

       --top-margin=tm
	      Set top margin. Default is 36.

       --left-margin=lm
	      Set left margin. Default is 36.

       --right-margin=rm
	      Set right margin. Default is 36.

       --help Show summary of options.

       --header
	      Draw page header for each page.

       --markup
	      Interpret the text as pango markup.

       --encoding=ENCODING
	      Assume the documentation encoding is ENCODING.

       --lpi  Set the lines per inch. This determines the line spacing.

       --cpi  Set the characters per inch. This is an alternative method of specifying the font size.

       --stretch-chars
	      Indicates  that  characters  should be stretched in the y-direction to fill up their vertical space. This is similar to the texttops
	      behaviour.

AUTHOR

       paps was written by Dov Grobgeld <dov.grobgeld@gmail.com>.

       This manual page was written by Lior Kaplan <kaplan@debian.org>, for the Debian project (but may be used by others).

								  April  17, 2006							   PAPS(1)