Sponsored Content
Top Forums UNIX for Beginners Questions & Answers Match patterns between two files and extract certain range of strings Post 303041964 by vgersh99 on Monday 9th of December 2019 11:44:45 AM
Old 12-09-2019
a bit verbose, but a possible starter.
awk -f bunny.awk inputfile2.txt inputfile1.fa where bunny.awk is:
Code:
function printRec() {
   #print a[f], s[f], e[f]
   for ( i in s) {
      split(i,t, OFS)
      if (f == ">" t[1])
        print ">" i ORS substr(a[f],s[i],e[i]-s[i]+1)
   }
   f=""
   split("",a)
}
FNR==NR {
   idx=$1 OFS $2 OFS $3
   s[idx]=$2
   e[idx]=$3
   next
}
/>/ && f {
   printRec()
}
f { a[f]=(f in a)?a[f] $1:$1 }
/^>/ { f=$1 }
END { printRec() }

results in:
Code:
>l-WR24-1:1 1 71
GCCGGCGTCGCGGTTGCTCGCGCTCTGGGCGCTGGCGGCTGTGGCTCTACCCGGCTCCGGGGCGGAGGGCG
>l-ZF385A-2:1 33 105
TGAGCTTCGGGTCACCGCCCCTCCAGAGGCTGAGTACTCAGGACTCGTCAGACACCCAGGGGTGAGATGAGAC
>l-YJC-1:1 1 161
GTCCCGCCCTCGCATGCGCCTGGTGGTCACCGCGGACGACTTTGGTTACTGCCCGCGACGCGATGAGGGTATCGTGGAGGCCTTTCTGGCCGGGGCTGTGACCAGCGTGTCCCTGCTGGTCAACGGTGCGGCCACGGAGAGCGCGGCGGAGCTGGCCCGCA
>l-YJC-1:1 1 165
GTCCCGCCCTCGCATGCGCCTGGTGGTCACCGCGGACGACTTTGGTTACTGCCCGCGACGCGATGAGGGTATCGTGGAGGCCTTTCTGGCCGGGGCTGTGACCAGCGTGTCCCTGCTGGTCAACGGTGCGGCCACGGAGAGCGCGGCGGAGCTGGCCCGCAGGCA


Last edited by vgersh99; 12-09-2019 at 12:51 PM..
This User Gave Thanks to vgersh99 For This Post:
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

print range between two patterns if it contains a pattern within the range

I want to print between the range two patterns if a particular pattern is present in between the two patterns. I am new to Unix. Any help would be greatly appreciated. e.g. Pattern1 Bombay Calcutta Delhi Pattern2 Pattern1 Patna Madras Gwalior Delhi Pattern2 Pattern1... (2 Replies)
Discussion started by: joyan321
2 Replies

2. Shell Programming and Scripting

script to match patterns in 2 different files.

I am new to shell scripting and need some help. I googled, but couldn't find a similar scenario. Basically, I need to rename a datafile. This is the scenario - I have a file, readonly.txt that has 2 columns - file# and name. I have another file,missing_files.txt that has id and name. Both the... (3 Replies)
Discussion started by: mathews
3 Replies

3. Shell Programming and Scripting

Find files that do not match specific patterns

Hi all, I have been searching online to find the answer for getting a list of files that do not match certain criteria but have been unsuccessful. I have a directory that has many jpg files. What I need to do is get a list of the files that do not match both of the following patterns (I have... (21 Replies)
Discussion started by: nikos-koutax
21 Replies

4. Shell Programming and Scripting

Extract patterns and copy them in different files

Hi All, I have a file which looks like this: Name1;A01 Name2;A01.047 Name3;A01.047.025 Newname1;B01 NewName2;B01.056.32 NewName3;B04.09.43 NewNewName1;C01.03 NewNewName2;C01.034.44As you can see, in the file there is some name and followed by the name is some identifier. These... (5 Replies)
Discussion started by: shoaibjameel123
5 Replies

5. Shell Programming and Scripting

How to extract information from two files with data range

Hi, I want to make a query about extracting data from two files that both have data ranges. the data that i want to extract; when there is matching between file1 column 2 is equal to file2 column2 , and file1 column 3 and column 4 is within the range of file2 columns 3 and 4. I would like rows... (1 Reply)
Discussion started by: houkto
1 Replies

6. Shell Programming and Scripting

Using AWK to match CSV files with duplicate patterns

Dear awk users, I am trying to use awk to match records across two moderately large CSV files. File1 is a pattern file with 173,200 lines, many of which are repeated. The order in which these lines are displayed is important, and I would like to preserve it. File2 is a data file with 456,000... (3 Replies)
Discussion started by: isuewing
3 Replies

7. Shell Programming and Scripting

awk extract strings matching multiple patterns

Hi, I wasn't quite sure how to title this one! Here goes: I have some already partially parsed log files, which I now need to extract info from. Because of the way they are originally and the fact they have been partially processed already, I can't make any assumptions on the number of... (8 Replies)
Discussion started by: chrissycc
8 Replies

8. Shell Programming and Scripting

Extract multiple occurance of strings between 2 patterns

I need to extract multiple occurance strings between 2 different patterns in given line. For e.g. in below as input ------------------------------------------------------------------------------------- mike(hussey) AND mike(donald) AND mike(ryan) AND mike(johnson)... (8 Replies)
Discussion started by: sameermohite
8 Replies

9. Shell Programming and Scripting

Match strings in 2 different files

Hi, i am trying to match strings from 2 different files based on position like below:- file1 (tab delimited) f07270 lololol fff u12730 gggddd dddkkrr mmm file2 (not tab delimited) %f07270 APSLH bl%alalalalallaadsdsfdfdfdgsgfss %g13450 GDIDFLRIP%ILITEAPPRKgsfgsgsf %d08880... (11 Replies)
Discussion started by: redse171
11 Replies

10. Shell Programming and Scripting

Match to range in files

I am trying to create a script that will use the position in column A ($1) in 48850.txt and search for it in columns B ($2) in gene.txt. Then when it finds a match it copies the text in column A ($1) and places it in column C ($3) of 48850.txt. I have attached the files. Thank you :). The... (2 Replies)
Discussion started by: cmccabe
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 v5.12.1 2010-04-26 A2P(1)
All times are GMT -4. The time now is 11:06 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy