Sponsored Content
Top Forums Shell Programming and Scripting awk to print field from lookup file in output Post 302980141 by Akshay Hegde on Wednesday 24th of August 2016 12:17:20 PM
Old 08-24-2016
Code:
[akshay@localhost tmp]$ awk '                   
    NR == FNR {min[$1]=$3; max[$1]=$4; o[$1]=$5; next}
    {                
        for (id in min) 
            if (min[id] < $2 && $2 < max[id]) {
                print $0, id, o[id]
                break              
            }
    }                                     
'  search lookup
7    48311388    rs672601345    G    GG    .    .    dbSNP_147;TSA=insertion;E_Phenotype_or_Disease;CLIN_pathogenic 21 ABCA13;AX746840
22    94487198    rs672601312    G    T    .    .    dbSNP_147;TSA=SNV;E_Phenotype_or_Disease;E_ExAC;CLIN_pathogenic;AA=G 22 ABCA4

OR

Code:
[akshay@localhost tmp]$ awk '                   
    NR == FNR {i=$1 OFS $5; min[i]=$3; max[i]=$4; next}
    {                
        for (id in min) 
            if (min[id] < $2 && $2 < max[id]) {
                print $0, id       
                break              
            }
    }                                     
'  search lookup
7    48311388    rs672601345    G    GG    .    .    dbSNP_147;TSA=insertion;E_Phenotype_or_Disease;CLIN_pathogenic 21 ABCA13;AX746840
22    94487198    rs672601312    G    T    .    .    dbSNP_147;TSA=SNV;E_Phenotype_or_Disease;E_ExAC;CLIN_pathogenic;AA=G 22 ABCA4

This User Gave Thanks to Akshay Hegde For This Post:
 

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

using awk or sed to print output from one file

dear i have one file regarding >abshabja>sdksjbs>sknakna>snajxcls so i want to be output like >abshabja >sjkabjb >sknakna >snajxcls Any using awk or sed will help thanks (2 Replies)
Discussion started by: cdfd123
2 Replies

2. Shell Programming and Scripting

awk command : To print the output to a file

half of the problem is already solved with the help of bartus11 suggestion I have a txt file having rows and coulmns, i want to perform some operation on a specific coulmn starting from a specific line. 50.000000 1 1 1 1000.00000 1000.00000 ... (5 Replies)
Discussion started by: shashi792
5 Replies

3. UNIX for Dummies Questions & Answers

Multiple Column print after lookup using NR==FNR (awk)

foo.txt FAMID IID AFF SEX Group AgeCat Dis1 Dis2 Dis3 Dis4 Dis5 Dis6 Dis6 AMD0001 Mayo_49542 1 2 AMD 8 1 1 1 1 1 1 1 AMD0002 Mayo_49606 1 1 AMD 3 1 1 1 1 ... (7 Replies)
Discussion started by: genehunter
7 Replies

4. Shell Programming and Scripting

Awk script to run a sql and print the output to an output file

Hi All, I have around 900 Select Sql's which I would like to run in an awk script and print the output of those sql's in an txt file. Can you anyone pls let me know how do I do it and execute the awk script? Thanks. (4 Replies)
Discussion started by: adept
4 Replies

5. UNIX for Dummies Questions & Answers

Help with AWK - Compare a field in a file to lookup file and substitute if only a match

I have the below 2 files: 1) Third field from file1.txt should be compared to the first field of lookup.txt. 2) If match found then third field, file1.txt should be substituted with the second field from lookup.txt. 3)Else just print the line from file1.txt. File1.txt:... (4 Replies)
Discussion started by: venalla_shine
4 Replies

6. Shell Programming and Scripting

File field to replace lookup from another file

Hi All, I don't know how to fast do this field replace that need lookup from another file to form the update result:confused: I want to do it by general shell script Can anyone help to solve it ? Thanks for your kindly reply in advance. CK (0 Replies)
Discussion started by: ckwong99
0 Replies

7. UNIX for Dummies Questions & Answers

Lookup field in map file

Hi, I have two questions which I would massively appreciate help with. 1. I am trying to insert a field into a file similar to the vlookup function in excel. In column 2 is a gene id for which i would like to insert the full name in the adjacent column. I have a map file (map.file) which... (1 Reply)
Discussion started by: genehersh
1 Replies

8. Shell Programming and Scripting

Lookup field values in two fixed format file in UNIX - not working

I have 2 fixed length files input#1 & input#2. I want to match the rows based on the value in position 37-50 in both files (pos 37-50 will have same value in both files). If any matching record is found then cut the value against company code & Invoice number from input file #1 (position 99 until... (3 Replies)
Discussion started by: Lingaraju
3 Replies

9. Shell Programming and Scripting

awk to lookup stored variable in file and print matching line

The bash bash below extracts the oldest folder from a directory and stores it in filename That result will match a line in bold in input. In the matching line there is an_xxx digit in italics that (once the leading zero is removed) will match a line in link. That is the lint to print in output.... (2 Replies)
Discussion started by: cmccabe
2 Replies

10. Shell Programming and Scripting

Using awk to print output based on first field.

Hi Folks, I have one requirement, There is one file, which contains two fields. Based on first field, I need to print an output. Example will be more suitable. Input file like this. abc 5 abc 10 xyz 6 xyz 9 xyz 10 mnp 10 mnp 12 mnp 6 (2 Replies)
Discussion started by: Raza Ali
2 Replies
A2P(1)							 Perl Programmers Reference Guide						    A2P(1)

NAME
a2p - Awk to Perl translator SYNOPSIS
a2p [options] [filename] DESCRIPTION
A2p takes an awk script specified on the command line (or from standard input) and produces a comparable perl script on the standard output. OPTIONS Options include: -D<number> sets debugging flags. -F<character> tells a2p that this awk script is always invoked with this -F switch. -n<fieldlist> specifies the names of the input fields if input does not have to be split into an array. If you were translating an awk script that processes the password file, you might say: a2p -7 -nlogin.password.uid.gid.gcos.shell.home Any delimiter can be used to separate the field names. -<number> causes a2p to assume that input will always have that many fields. -o tells a2p to use old awk behavior. The only current differences are: o Old awk always has a line loop, even if there are no line actions, whereas new awk does not. o In old awk, sprintf is extremely greedy about its arguments. For example, given the statement print sprintf(some_args), extra_args; old awk considers extra_args to be arguments to "sprintf"; new awk considers them arguments to "print". "Considerations" A2p cannot do as good a job translating as a human would, but it usually does pretty well. There are some areas where you may want to examine the perl script produced and tweak it some. Here are some of them, in no particular order. There is an awk idiom of putting int() around a string expression to force numeric interpretation, even though the argument is always integer anyway. This is generally unneeded in perl, but a2p can't tell if the argument is always going to be integer, so it leaves it in. You may wish to remove it. Perl differentiates numeric comparison from string comparison. Awk has one operator for both that decides at run time which comparison to do. A2p does not try to do a complete job of awk emulation at this point. Instead it guesses which one you want. It's almost always right, but it can be spoofed. All such guesses are marked with the comment ""#???"". You should go through and check them. You might want to run at least once with the -w switch to perl, which will warn you if you use == where you should have used eq. Perl does not attempt to emulate the behavior of awk in which nonexistent array elements spring into existence simply by being referenced. If somehow you are relying on this mechanism to create null entries for a subsequent for...in, they won't be there in perl. If a2p makes a split line that assigns to a list of variables that looks like (Fld1, Fld2, Fld3...) you may want to rerun a2p using the -n option mentioned above. This will let you name the fields throughout the script. If it splits to an array instead, the script is probably referring to the number of fields somewhere. The exit statement in awk doesn't necessarily exit; it goes to the END block if there is one. Awk scripts that do contortions within the END block to bypass the block under such circumstances can be simplified by removing the conditional in the END block and just exiting directly from the perl script. Perl has two kinds of array, numerically-indexed and associative. Perl associative arrays are called "hashes". Awk arrays are usually translated to hashes, but if you happen to know that the index is always going to be numeric you could change the {...} to [...]. Iteration over a hash is done using the keys() function, but iteration over an array is NOT. You might need to modify any loop that iterates over such an array. Awk starts by assuming OFMT has the value %.6g. Perl starts by assuming its equivalent, $#, to have the value %.20g. You'll want to set $# explicitly if you use the default value of OFMT. Near the top of the line loop will be the split operation that is implicit in the awk script. There are times when you can move this down past some conditionals that test the entire record so that the split is not done as often. For aesthetic reasons you may wish to change index variables from being 1-based (awk style) to 0-based (Perl style). Be sure to change all operations the variable is involved in to match. Cute comments that say "# Here is a workaround because awk is dumb" are passed through unmodified. Awk scripts are often embedded in a shell script that pipes stuff into and out of awk. Often the shell script wrapper can be incorporated into the perl script, since perl can start up pipes into and out of itself, and can do other things that awk can't do by itself. Scripts that refer to the special variables RSTART and RLENGTH can often be simplified by referring to the variables $`, $& and $', as long as they are within the scope of the pattern match that sets them. The produced perl script may have subroutines defined to deal with awk's semantics regarding getline and print. Since a2p usually picks correctness over efficiency. it is almost always possible to rewrite such code to be more efficient by discarding the semantic sugar. For efficiency, you may wish to remove the keyword from any return statement that is the last statement executed in a subroutine. A2p catches the most common case, but doesn't analyze embedded blocks for subtler cases. ARGV[0] translates to $ARGV0, but ARGV[n] translates to $ARGV[$n-1]. A loop that tries to iterate over ARGV[0] won't find it. ENVIRONMENT
A2p uses no environment variables. AUTHOR
Larry Wall <larry@wall.org> FILES
SEE ALSO
perl The perl compiler/interpreter s2p sed to perl translator DIAGNOSTICS
BUGS
It would be possible to emulate awk's behavior in selecting string versus numeric operations at run time by inspection of the operands, but it would be gross and inefficient. Besides, a2p almost always guesses right. Storage for the awk syntax tree is currently static, and can run out. perl v5.12.5 2012-10-11 A2P(1)
All times are GMT -4. The time now is 10:37 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy