Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Clipping -awk
Top Forums UNIX for Dummies Questions & Answers Clipping -awk Post 302948837 by Xterra on Thursday 2nd of July 2015 10:28:24 PM
Old 07-02-2015
Don
I apologize -in my defense, English is not my mother tongue, not an excuse just and explanation.
You see, the input file is a DNA alignment. The aligment tool (mafft), aligns each nucleotide (ATGC) in all sequences (multiple alignment). If one of the sequences is shorter, like the Reference in my example above, the alignment tool adds hyphens at the ends. I need to find the References sequence and scan it till I find the first nucleotide, in this case "a", and cut all sequences at that nucleotide position. Then, I must scan the Reference sequence till I find the last nucleotide, in this case another "a", and cut all sequences at that very same position. Thus, all sequences will have the same length. Sometimes, the DNA sequences have mismatches at the ends maki g nearly impossible to trim them based on a nucleotide pattern -mafft takes care of that since mutations do not disturbe the alignment.
I hope this explains better what I am trying to accomplish
Thanks!
PS. The reference does not contain gaps (hyphens) in between nucleotides. Thus, the string of hyphens in the flanks mark the beggining and end of the reference sequence
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Awk problem: How to express the single quote(') by using awk print function

Actually I got a list of file end with *.txt I want to use the same command apply to all the *.txt Thus I try to find out the fastest way to write those same command in a script and then want to let them run automatics. For example: I got the file below: file1.txt file2.txt file3.txt... (4 Replies)
Discussion started by: patrick87
4 Replies

2. Shell Programming and Scripting

scripting/awk help : awk sum output is not comming in regular format. Pls advise.

Hi Experts, I am adding a column of numbers with awk , however not getting correct output: # awk '{sum+=$1} END {print sum}' datafile 2.15291e+06 How can I getthe output like : 2152910 Thank you.. # awk '{sum+=$1} END {print sum}' datafile 2.15079e+06 (3 Replies)
Discussion started by: rveri
3 Replies

3. Shell Programming and Scripting

awk: assign variable with -v didn't work in awk filter

I want to filter 2nd column = 2 using awk $ cat t 1 2 2 4 $ VAR=2 #variable worked in print $ cat t | awk -v ID=$VAR ' { print ID}' 2 2 # but variable didn't work in awk filter $ cat t | awk -v ID=$VAR '$2~/ID/ { print $0}' (2 Replies)
Discussion started by: honglus
2 Replies

4. Shell Programming and Scripting

Read content between xml tags with awk, grep, awk or what ever...

Hello, I trying to extract text that is surrounded by xml-tags. I tried this cat tst.xml | egrep "<SERVER>.*</SERVER>" |sed -e "s/<SERVER>\(.*\)<\/SERVER>/\1/"|tr "|" " " which works perfect, if the start-tag and the end-tag are in the same line, e.g.: <tag1>Hello Linux-Users</tag1> ... (5 Replies)
Discussion started by: Sebi0815
5 Replies

5. Shell Programming and Scripting

Problem with awk awk: program limit exceeded: sprintf buffer size=1020

Hi I have many problems with a script. I have a script that formats a text file but always prints the same error when i try to execute it The code is that: { if (NF==17){ print $0 }else{ fields=NF; all=$0; while... (2 Replies)
Discussion started by: fate
2 Replies

6. Shell Programming and Scripting

Comparison and editing of files using awk.(And also a possible bug in awk for loop?)

I have two files which I would like to compare and then manipulate in a way. File1: pictures.txt 1.1 1.3 dance.txt 1.2 1.4 treehouse.txt 1.3 1.5 File2: pictures.txt 1.5 ref2313 1.4 ref2345 1.3 ref5432 1.2 ref4244 dance.txt 1.6 ref2342 1.5 ref2352 1.4 ref0695 1.3 ref5738 1.2... (1 Reply)
Discussion started by: linuxkid
1 Replies

7. Shell Programming and Scripting

awk command to compare a file with set of files in a directory using 'awk'

Hi, I have a situation to compare one file, say file1.txt with a set of files in directory.The directory contains more than 100 files. To be more precise, the requirement is to compare the first field of file1.txt with the first field in all the files in the directory.The files in the... (10 Replies)
Discussion started by: anandek
10 Replies

8. Shell Programming and Scripting

HELP with AWK one-liner. Need to employ an If condition inside AWK to check for array variable ?

Hello experts, I'm stuck with this script for three days now. Here's what i need. I need to split a large delimited (,) file into 2 files based on the value present in the last field. Samp: Something.csv bca,adc,asdf,123,12C bca,adc,asdf,123,13C def,adc,asdf,123,12A I need this split... (6 Replies)
Discussion started by: shell_boy23
6 Replies

9. Shell Programming and Scripting

Passing awk variable argument to a script which is being called inside awk

consider the script below sh /opt/hqe/hqapi1-client-5.0.0/bin/hqapi.sh alert list --host=localhost --port=7443 --user=hqadmin --password=hqadmin --secure=true >/tmp/alerts.xml awk -F'' '{for(i=1;i<=NF;i++){ if($i=="Alert id") { if(id!="") if(dt!=""){ cmd="sh someScript.sh... (2 Replies)
Discussion started by: vivek d r
2 Replies

10. Shell Programming and Scripting

awk output yields error: awk:can't open job_name (Autosys)

Good evening, Im newbie at unix specially with awk From an scheduler program called Autosys i want to extract some data reading an inputfile that comprises jobs names, then formating the output to columns for example 1. This is the inputfile: $ more MapaRep.txt ds_extra_nikira_usuarios... (18 Replies)
Discussion started by: alexcol
18 Replies

LEARN ABOUT DEBIAN

bup-margin

bup-margin(1)						      General Commands Manual						     bup-margin(1)

NAME

       bup-margin - figure out your deduplication safety margin

SYNOPSIS

       bup margin [options...]

DESCRIPTION

       bup margin  iterates  through  all  objects  in	your  bup repository, calculating the largest number of prefix bits shared between any two
       entries.  This number, n, identifies the longest subset of SHA-1 you could use and still encounter a collision between your object ids.

       For example, one system that was tested had a collection of 11 million objects (70 GB), and bup margin returned 45.  That  means  a  46-bit
       hash  would be sufficient to avoid all collisions among that set of objects; each object in that repository could be uniquely identified by
       its first 46 bits.

       The number of bits needed seems to increase by about 1 or 2 for every doubling of the number of objects.  Since SHA-1 hashes have 160 bits,
       that  leaves 115 bits of margin.  Of course, because SHA-1 hashes are essentially random, it's theoretically possible to use many more bits
       with far fewer objects.

       If you're paranoid about the possibility of SHA-1 collisions, you can monitor your repository by running bup margin occasionally to see	if
       you're getting dangerously close to 160 bits.

OPTIONS

       --predict
	      Guess  the offset into each index file where a particular object will appear, and report the maximum deviation of the correct answer
	      from the guess.  This is potentially useful for tuning an interpolation search algorithm.

       --ignore-midx
	      don't use .midx files, use only .idx files.  This is only really useful when used with --predict.

EXAMPLE

	      $ bup margin
	      Reading indexes: 100.00% (1612581/1612581), done.
	      40
	      40 matching prefix bits
	      1.94 bits per doubling
	      120 bits (61.86 doublings) remaining
	      4.19338e+18 times larger is possible

	      Everyone on earth could have 625878182 data sets
	      like yours, all in one repository, and we would
	      expect 1 object collision.

	      $ bup margin --predict
	      PackIdxList: using 1 index.
	      Reading indexes: 100.00% (1612581/1612581), done.
	      915 of 1612581 (0.057%)

SEE ALSO

       bup-midx(1), bup-save(1)

BUP

       Part of the bup(1) suite.

AUTHORS

       Avery Pennarun <apenwarr@gmail.com>.

Bup unknown-															     bup-margin(1)
All times are GMT -4. The time now is 06:28 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy