Sponsored Content
Top Forums Shell Programming and Scripting Differential substring removal using coordinates Post 302584291 by vectorborne5 on Thursday 22nd of December 2011 04:20:27 PM
Old 12-22-2011
Works brilliantly!!! Thank you ahamed!

I made one slight adjustment so as to retain the unique id along with the core string:
Code:
awk 'NR==FNR{split($2,c,",");split($3,b,",");a[$1]=c[2]" "b[1]; next}{if($1 in a){split(a[$1],d," "); print $1 "\t" substr($2,d[1]+1,d[2]-d[1]-1)}}' coordinates.file tabular-fasta.file > ouput.file

 

9 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

Tar differential backup

I am backing up some data to an NTFS formatted backup drive. I have to preserve the Unix permissions of the data being backed up and therfore use backup into a tar file. I would like to backup the differnential data in the tar file similiar to how Rsync works so as to save on backup time as it... (1 Reply)
Discussion started by: jelloir
1 Replies

2. High Performance Computing

Differential Equations

I`m having a cluster with Rocks 5.2 distribution and I want to solve differential equations and I`m interested to know if are some programs already developed to do this. (3 Replies)
Discussion started by: rapo
3 Replies

3. UNIX for Advanced & Expert Users

Differential or Incremental backups in Unix

Hi, Just wanted to know is there any way that we can take differential or incremental backups in Unix(Solaris/AIX/Linux or Hpunix).What is the procedure. Is any doc avaialble on this? Its urgent and any help/suggestions would be highly appreciable. Regards, Ravi Dwivedi (3 Replies)
Discussion started by: dwiravi
3 Replies

4. Shell Programming and Scripting

Search for particular tag and arrange as coordinates

Hi I have a file whose sample contents are shown here, 1.2.3.4->2.4.2.4 a(10) b(20) c(30) 1.2.3.4->2.9.2.4 a(10) c(20) 2.3.4.3->3.6.3.2 b(40) d(50) c(20) 2.3.4.3->3.9.0.2 a(40) e(50) c(20) 1.2.3.4->3.4.2.4 a(10) c(30) 6.2.3.4->2.4.2.5 c(10) . . . . Here I need to search... (5 Replies)
Discussion started by: AKD
5 Replies

5. Shell Programming and Scripting

Determination n points between two coordinates

Hi guys. Can anyone tell me how to determine points between two coardinates. For example: Which type of command line gives me 50 points between (8, -5, 7) and (2, 6, 9) points Thanks (5 Replies)
Discussion started by: rpf
5 Replies

6. UNIX for Dummies Questions & Answers

removal by substring

Hi guys, I am trying to remove lines that have a duplicate substring from any part in the file. So, for ex: 433043950359.3 5033 305935 2 2dd 5ffgs DOG43453552.A 3443565634 95460 3435 45 23d 56ggh DOG343211 3423895702359 34 66699 9455 2324 DOG43453552.B This is a very large file, and... (1 Reply)
Discussion started by: verse123
1 Replies

7. UNIX for Dummies Questions & Answers

[SOLVED] Restoring differential backup files

I'm using a script (automysqlbackup) to dump mysql db's to .sql file followed by taking one full backup of the .sql file and the differential backups of the newer sql file every day using the tool diff. Now the backup destination folder contains files like, I would like to how do i restore... (3 Replies)
Discussion started by: csengineer
3 Replies

8. UNIX for Dummies Questions & Answers

overlapped genomic coordinates

Hi, I would like to know how can I get the ID of a feature if its genomic coordinates overlap the coordinates of another file. Example: Get the 4th column (ID) of this file1: chr1 10 100 gene1 chr2 3000 5000 gene2 chr3 200 1500 gene3 if it overlaps with a feature in this file2: chr2... (1 Reply)
Discussion started by: fadista
1 Replies

9. UNIX for Beginners Questions & Answers

Help with processing coordinates in a file.

I have a variation table (variation.txt) which is a very big file. The first column in the chromosome number and the second column is the position of the variation. I have a second file annotation.txt which has a list of 37,000 genes (1st column), their chromosome number(2nd column), their start... (1 Reply)
Discussion started by: Sanchari
1 Replies
split(3tcl)						       Tcl Built-In Commands						       split(3tcl)

__________________________________________________________________________________________________________________________________________________

NAME
split - Split a string into a proper Tcl list SYNOPSIS
split string ?splitChars? _________________________________________________________________ DESCRIPTION
Returns a list created by splitting string at each character that is in the splitChars argument. Each element of the result list will con- sist of the characters from string that lie between instances of the characters in splitChars. Empty list elements will be generated if string contains adjacent characters in splitChars, or if the first or last character of string is in splitChars. If splitChars is an empty string then each character of string becomes a separate element of the result list. SplitChars defaults to the standard white-space char- acters. EXAMPLES
Divide up a USENET group name into its hierarchical components: split "comp.lang.tcl.announce" . -> comp lang tcl announce See how the split command splits on every character in splitChars, which can result in information loss if you are not careful: split "alpha beta gamma" "temp" -> al {ha b} {} {a ga} {} a Extract the list words from a string that is not a well-formed list: split "Example with {unbalanced brace character" -> Example with {unbalanced brace character Split a string into its constituent characters split "Hello world" {} -> H e l l o { } w o r l d PARSING RECORD-ORIENTED FILES Parse a Unix /etc/passwd file, which consists of one entry per line, with each line consisting of a colon-separated list of fields: ## Read the file set fid [open /etc/passwd] set content [read $fid] close $fid ## Split into records on newlines set records [split $content " "] ## Iterate over the records foreach rec $records { ## Split into fields on colons set fields [split $rec ":"] ## Assign fields to variables and print some out... lassign $fields userName password uid grp longName homeDir shell puts "$longName uses [file tail $shell] for a login shell" } SEE ALSO
join(3tcl), list(3tcl), string(3tcl) KEYWORDS
list, split, string Tcl split(3tcl)
All times are GMT -4. The time now is 02:51 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy