Sponsored Content
Top Forums Shell Programming and Scripting Challenging Awk array problem Post 302423694 by alister on Friday 21st of May 2010 05:52:41 PM
Old 05-21-2010
Quote:
Originally Posted by polsum
File 2:
Code:
4|17999 - gi|149361523|ref|NC_000074.5|NC_000074 chr1  3000072  TTTATCGTCATCGTC
28|3721 + gi|149352351|ref|NC_000069.5|NC_000069  chr3  154935392 GAGTTTTACAGTCCA
28|3721 +  gi|149288852|ref|NC_000067.5|NC_000067 chr1  152633707 GAGTTTTACAGTCCA
28|3721  + gi|149361432|ref|NC_000073.5|NC_000073 chr7  86595415 GAGTTTTACAGTCCA
34|3145  - gi|149321426|ref|NC_000084.5|NC_000084 chr18  43464724 ACGGCTTACGA
34|3145  - gi|149354224|ref|NC_000071.5|NC_000071 chr5  37676290 ACGGCTTACGA

...<snip>...

Ok for example - field 4 of file 2 i.e. chr1 is same as field 6 of file 1. Then see if field 5 of file 2 i.e.3000072 (which is always a number) lies in the range of fields 7 and 8 (3000001 3000156) of file 1. So, I need the output (the line from file 2 plus fields 11,12 and 13 of file 1) in a separate file as
What's the delimiter in file 2? The pipe, "|" ? If so, taking the first line in file 2, isn't field 4 "ref"? And field 5 is "NC_000074.5"?

Regards and welcome to the forum,
Alister

---------- Post updated at 05:52 PM ---------- Previous update was at 05:50 PM ----------

Nevermind. The pipes threw me. I see that it's whitespace delimited. Duh! Great first impression, huh? Smilie
This User Gave Thanks to alister For This Post:
 

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

A Challenging Situation : i hope the moderators will respond to this problem..

I have the following situation : i have 4 Unix Sco servers, one Windows 2000 server, and an ADSL internet connection. All the servers, that is the 4 unix and the windows server have real static IPs supplied by my ISP. the servers are connected to a Switch , the switch is connected to an... (2 Replies)
Discussion started by: BAM
2 Replies

2. Programming

A challenging problem involving symbolic links.

Hello, I'm working on an application that bridges together several applications involved in creating a video workflow for editing with digital cinema cameras. The main platform is MacOSX. Because of the nature of some of the utilities for working with this video footage I must spoof filenames... (2 Replies)
Discussion started by: ibloom
2 Replies

3. Shell Programming and Scripting

Very Challenging Problem. Please read fully.

Hi, This is the Third thread i'm putting here for the same problem. :( Actually, i'm trying a script like this.. but its taking a long time.. about 3 days to complete fully.. #!/bin/ksh if then exit 1 fi while read i do while read j do field7=`echo $j|cut -d "|"... (12 Replies)
Discussion started by: RRVARMA
12 Replies

4. Shell Programming and Scripting

awk array problem

hi i am trying to perform some calculations with awk and arrays. i have this so far: awk 'NR==FNR{ for(i=1; i<=NF; i++) {array+=$i} tot++;next} {for(i=1; i<=NF; i++) {avg=array/tot} {diff=(array - avg)}} {for(i=1; i<=NF; i++) {printf("%5.8f\n",diff)}}' "$count".txt "$count".ttt >... (4 Replies)
Discussion started by: npatwardhan
4 Replies

5. Shell Programming and Scripting

Problem with lookup values on AWK associative array

I'm at wits end with this issue and my troubleshooting leads me to believe it is a problem with the file formatting of the array referenced by my script: awk -F, '{if (NR==FNR) {a=$4","$3","$2}\ else {print a "," $0}}' WBTSassignments1.txt RNCalarms.tmp On the WBTSassignments1.txt file... (2 Replies)
Discussion started by: JasonHamm
2 Replies

6. Shell Programming and Scripting

AWK Array problem

Dear All, I am facing problem to get right output through awk program I have file in which “B” value is appearing multiple time and I need to capture all these values. My script is BEGIN { FS=" " } { if ( substr($1,1,5) == "START" ) { i =... (2 Replies)
Discussion started by: arvindng
2 Replies

7. Shell Programming and Scripting

awk array problem

Hi, Im trying to count bats flying through an infrared beam array. One of the experts here helped me a few months ago but now I am having a problem that is stumping me. here is the original code that works (with two differnt patterns in array): # this has been changed to operate under the... (15 Replies)
Discussion started by: cmp260
15 Replies

8. Shell Programming and Scripting

Using awk array problem

I am trying to map values in the input file, where 2nd column depends on the specific value in the 1st column. When 1st column is A place 1 into 2nd column, when it is B, place 2, when C place 3, otherwise no change. My input: U |100|MAIN ST |CLMN1|1 A |200|GREEN LN |CLMN2|2 1 |12... (4 Replies)
Discussion started by: migurus
4 Replies

9. Shell Programming and Scripting

Problem with awk array when loading from shell variable

Hi, I have a problem with awk array when iam trying to use awk in solaris box as below..Iam unable to figure out the problem.. Need your help. is there any alternative to make it in arrays from variable values nawk 'BEGIN {SUBSEP=" "; split("101880|110045 101887|110045 101896|110045... (9 Replies)
Discussion started by: cskumar
9 Replies

10. Shell Programming and Scripting

Index problem in associate array in awk

I am trying to reformat the table by filling any missing rows. The final table will have consecutive IDs in the first column. My problem is the index of the associate array in the awk script. infile: S01 36407 53706 88540 S02 69343 87098 87316 S03 50133 59721 107923... (4 Replies)
Discussion started by: yifangt
4 Replies
PASTE(1)						    BSD General Commands Manual 						  PASTE(1)

NAME
paste -- merge corresponding or subsequent lines of files SYNOPSIS
paste [-s] [-d list] file ... DESCRIPTION
The paste utility concatenates the corresponding lines of the given input files, replacing all but the last file's newline characters with a single tab character, and writes the resulting lines to standard output. If end-of-file is reached on an input file while other input files still contain data, the file is treated as if it were an endless source of empty lines. The options are as follows: -d list Use one or more of the provided characters to replace the newline characters instead of the default tab. The characters in list are used circularly, i.e., when list is exhausted the first character from list is reused. This continues until a line from the last input file (in default operation) or the last line in each file (using the -s option) is displayed, at which time paste begins selecting characters from the beginning of list again. The following special characters can also be used in list: newline character tab character \ backslash character Empty string (not a null character). Any other character preceded by a backslash is equivalent to the character itself. -s Concatenate all of the lines of each separate input file in command line order. The newline character of every line except the last line in each input file is replaced with the tab character, unless otherwise specified by the -d option. If '-' is specified for one or more of the input files, the standard input is used; standard input is read one line at a time, circularly, for each instance of '-'. EXIT STATUS
The paste utility exits 0 on success, and >0 if an error occurs. EXAMPLES
List the files in the current directory in three columns: ls | paste - - - Combine pairs of lines from a file into single lines: paste -s -d ' ' myfile Number the lines in a file, similar to nl(1): sed = myfile | paste -s -d ' ' - - Create a colon-separated list of directories named bin, suitable for use in the PATH environment variable: find / -name bin -type d | paste -s -d : - SEE ALSO
cut(1), lam(1) STANDARDS
The paste utility is expected to be IEEE Std 1003.2 (``POSIX.2'') compatible. HISTORY
A paste command appeared in Version 32V AT&T UNIX. BSD
June 25, 2004 BSD
All times are GMT -4. The time now is 07:49 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy