Parsing data using keys from one file


 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Parsing data using keys from one file
# 1  
Old 03-27-2012
Parsing data using keys from one file

I have 2 text files where I need to parse data from file 2 using the data from file 1. Below are my sample files
File 1 (tab delimited)
Code:
257 350
670 845
725 1025
767 820
...
....
....

file 2 (tab delimited)
Code:
220..450 TA AB650 ABCED
520..850 GA AB720 ABCDE
700..1100 TC AB820 ABCDE
1200..1356 AT AB920 ABCDE
..
...
...

I want to read the numbers (lower-upper limits) in file 1 and parse the row on file 2 that are equal to or within the limits based on column 1 in file2.

So the resultant output file will be like

Code:
257 350 220..450 TA AB650 ABCED
670 845 520..850 GA AB720 ABCDE
725 1025 700..1100 TC AB820 ABCDE
767 820 700..1100 TC AB820 ABCDE

Please let me know the best way to parse this using awk.

---------- Post updated at 08:50 PM ---------- Previous update was at 04:53 PM ----------

Didn't get any suggestions
# 2  
Old 03-28-2012
Here's a perl:

Code:
perl -ane 'open I, "< file2";
for (<I>) {
    if (/(\d+)\.\.(\d+)/) { $x=$1; $y=$2 }
    if ($x <= $F[0] && $y >= $F[1]) { print "@F $_" }
}
close I' file1

# 3  
Old 03-28-2012
Code:
awk -F'\t|[.][.]' 'NR==FNR{M[$1]=$2;next}{for(i in M)if($1<=i+0 && $2>=M[i])print i,M[i],$0}' OFS='\t'  file file2

Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Extract data according to keys from filename mentioned in file

Hello experts, I want to join a file with files whosE names are mentioned in one of the columns of the same file. File 1 t1,a,b,file number 1 t1,a,c,file number 1 t2,c,d,file number 2 t2,c,e,file number 2 t2,c,f,file number 2 t2,c,g,file number 2 t3,e,f,file number 3 file number 1... (3 Replies)
Discussion started by: ritakadm
3 Replies

2. Shell Programming and Scripting

Parsing file data

Hey Guys, I'm a novice at shell scripts and i need some help parsing file data. Basically, I want to write a script that retrieves URLs. Here is what I have so far. #!/bin/bash echo "Please enter start date (format: yyyy-mm-dd):\c" read STARTDATE echo "Please enter end date... (7 Replies)
Discussion started by: silverdust
7 Replies

3. Shell Programming and Scripting

Parsing C Data Tipes from Input File

Im really beginner in this case, maybe someone can help me find the answer: if my input file like this: void main(int a, int b){ int x; double y; printf("file"); } and i want output like this: int a int b int x double y A awk script that can parse only data tipe, im confused. what... (2 Replies)
Discussion started by: radynaraya
2 Replies

4. Shell Programming and Scripting

parsing data from a big file using keys from another smaller file

Hi, I have 2 files format of file 1 is: a1 b2 a2 c2 d1 f3 format of file 2 is (tab delimited): a1 1.2 0.5 0.06 0.7 0.9 1 0.023 a3 0.91 0.007 0.12 0.34 0.45 1 0.7 a2 1.05 2.3 0.25 1 0.9 0.3 0.091 b1 1 5.4 0.3 9.2 0.3 0.2 0.1 b2 3 5 7 0.9 1 9 0 1 b3 0.001 1 2.3 4.6 8.9 10 0 1 0... (10 Replies)
Discussion started by: Lucky Ali
10 Replies

5. Shell Programming and Scripting

parsing a portion of Data from a text file

Hi All, I need some help to effectively parse out a subset of results from a big results file. Below is an example of the text file. Each block that I need to parse starts with "Output of GENE for sequence file 100.fasta" (next block starts with another number). I have given the portion of... (8 Replies)
Discussion started by: Lucky Ali
8 Replies

6. Shell Programming and Scripting

parsing data and incorporating it into another file

Hi, I have a folder that contains many (multiple) files 1.fasta 2.fasta 3.fasta 4.fasta 5.fasta . . 100's of files Each such file have data in the following format for example: vi 1.fasta >AB_1 gi|15835212|ref|NP_296971.1| preprotein translocase subunit SecE... (3 Replies)
Discussion started by: Lucky Ali
3 Replies

7. Shell Programming and Scripting

parsing data and incorporating it into another file

Hi All I have two files: file 1 >AB_1 MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYDHPLAFDTDFM IQQLKELLAGRPVDIPIYDYKKHTRSNTTFRQDPQDVIIVEGILVLEDERLRDLMDIKLFVDTDDDIRII RRIKRDMMERGRSLESIIDQYTSVVKPMYHQFIEPSKRYADIVIPEGVSNVVAIDVINSKIASILGEV >AB_2... (5 Replies)
Discussion started by: Lucky Ali
5 Replies

8. Shell Programming and Scripting

urgent<parsing data from a excel file>

Hi all, I wud like to get ur assistance in retrieving lines containing l1.My excel dataset contains around 8000 lines.I converted it into a text tab delimiter file and got the lines containing l1,My output is a list of lines containing l1 saved in a outfile.Some of d lines from my outfile s... (5 Replies)
Discussion started by: sayee
5 Replies

9. Shell Programming and Scripting

Parsing the data in a file

Hi, I have file (FILE.tmp) having contents, FILE.tmp ======== filename=menudata records=0000000000037 ldbname=pinsys timestamp=2005/05/14-18:32:33 I want to parse it bring a new file which will look like, filename records ldbname timestamp... (2 Replies)
Discussion started by: Omkumar
2 Replies

10. Shell Programming and Scripting

Parsing file and extracting the useful data block

Greetings All!! I have a very peculiar problem where I have to parse a big text file and extract useful data out of it with starting and ending block pattern matching. e.g. I have a input file like this: sample data block1 sample data start useful data end sample data block2 sample... (5 Replies)
Discussion started by: arminder
5 Replies
Login or Register to Ask a Question