Sponsored Content
Top Forums Shell Programming and Scripting Request to check:Fetch certain entries Post 302731357 by manigrover on Wednesday 14th of November 2012 10:30:50 PM
Old 11-14-2012
Changes in code to provide proper result with one additional fiield
Hi all


I am using following code to get results for brand name drug target name and generic name from my attached fiile



Code:
Code:
awk 'k>0 {if (a[k] && k==2) {print a[1]":"a[2]":"a[3]; a[1]=a[2]=a[3]="";} a[k]=a[k]?a[k]","$0:$0; k=0;} /^# Drug_Target_.*_Gene_Name/ {k=3;} /^# Generic/ {k=1;} /^# Brand_Name/ {k=2;} END {if (a[1]) print a[1]":"a[2]":"a[3];}' drugbank.txt >drugbank3.txt

But when I change the code to additional field Drug Type. It is not giving me proper results can anybody guide to make changes in this code to get drug type as well.

---------- Post updated at 10:30 PM ---------- Previous update was at 10:06 PM ----------

Hi

Its working now using the same code completely Smilie dont know why? can any body try on his or her system?Smilie

Last edited by Franklin52; 11-30-2012 at 04:43 AM.. Reason: Code tags
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Request to check:find out common entries

I have to compare 2 files which means 2 files with common entries in same column and separate those common entries in a diferent file as well right before those entries common so that I can separat common and Uncommon entries in rows in 2 different files. Is it possible For eg. one file ... (3 Replies)
Discussion started by: manigrover
3 Replies

2. Shell Programming and Scripting

Request to check:remove entries with N/A entries

Hi I have a file with numerous entries some entries are 1 mani 2 kavya 3 N/A 4 Praveeen 5 N/A and so on How to remove entries with N/A so the result will be 1 mani 2 kavya 3 Praveeen (6 Replies)
Discussion started by: manigrover
6 Replies

3. Shell Programming and Scripting

Request to check:remove entries more than once

Hi I have a file like this 1234 2345 567889 567889 2345 234899420 83743 2345 67890 67890 ................ so on I want to delete entries which are more than once like 2345, 567889 and 67890 so that these appear once (4 Replies)
Discussion started by: manigrover
4 Replies

4. Shell Programming and Scripting

Request to check:remove entries with blank spaces

Hi I want to remove entries with blank spaces in my input file: 123 234 456 678 56789 345346456 589 3454 345456 3454566............................ (2 Replies)
Discussion started by: manigrover
2 Replies

5. Shell Programming and Scripting

Request to check:remove entries with N/A mentioned

Hi I have a file with following entries 122 N/A 123 5654656 123423 43534543 4544 45435 435454 N/A i Have to remove entries with N/A so that only 123 5654656 123423 43534543 4544 45435 remain in output file can anybody guide for a code/unix/perl (2 Replies)
Discussion started by: manigrover
2 Replies

6. Shell Programming and Scripting

Request to check:remove entries more than once in different column

Hi I have a file 12m 345693460 12 1234 12 1234 34 345 34 345 And I want output fiel as 12m 345693460 12 1234 34 345 hw can it be done Thanks (1 Reply)
Discussion started by: manigrover
1 Replies

7. Shell Programming and Scripting

Request to check: Not printing all entries

Dear all, I am facing one problem in my input file there are many Entries which starts from *FIELD * AV (checked the attached file) I want all the entries in the output file which start from *FIELD * AV I have written this programm but its not printing all the entries with *FIELD... (4 Replies)
Discussion started by: manigrover
4 Replies

8. Shell Programming and Scripting

Request to check:count specific entries

Hi all I have an input file which contains so many entries like this: And, I want to count hw many among ASN in one column are converted to LYS in third coulmns. which means output shuld contain only "ASN number LYS" Kindly let me know wny programm for this My input is ASN 217 LYS... (2 Replies)
Discussion started by: manigrover
2 Replies

9. Shell Programming and Scripting

Extract certain entries from big file:Request to check

Hi all I have a big file which I have attached here. And, I have to fetch certain entries and arrange in 5 columns Name Drug DAP ID disease approved or notIn the attached file data is arranged with tab separated columns in this way: and other data is... (2 Replies)
Discussion started by: manigrover
2 Replies

10. Shell Programming and Scripting

Urgent request to consider:Search specific name in a file and fetch specific entries

Hi all, I have 2 files, One file contain data like this FHIT CS CHRM1 PDE3A PDE3B HSP90AA1 PTK2 HTR1A ESR1 PARP1 PLA2G1B These names are mentioned in the second file(Please see attached second file) as # Drug_Target_X_Gene_Name:(Where X can be any number (1-1000) (1 Reply)
Discussion started by: manigrover
1 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 v5.18.2 2014-01-06 A2P(1)
All times are GMT -4. The time now is 02:52 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy