Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Match patterns between two files and extract certain range of strings
Top Forums UNIX for Beginners Questions & Answers Match patterns between two files and extract certain range of strings Post 303041966 by RudiC on Monday 9th of December 2019 01:59:52 PM
Old 12-09-2019
Try also
Code:
awk '
NR==FNR         {PAT[$1,$2,$3]
                 next
                }
                {IX  = $1
                 L1  = length ($1) + 1
                 $1 = $1 "|"
                 $0 = $0
                 for (p in PAT) {split (p, T)
                                 if (IX == T[1]) print RS p ORS substr ($0, T[2]+L1, T[3]-T[2]+1)
                                }
                }
' SUBSEP="\t" inputfile2.txt   RS=">"  OFS="" inputfile1.fa

>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

If you really really need the output lines 60 chars in length, use
Code:
                 if (IX == T[1])    {print RS p
                                     TMP = substr ($0, T[2]+L1, T[3]-T[2]+1)
                                     PTR = 1
                                     while (PTR < length (TMP))    {print substr (TMP, PTR, 60)
                                                                    PTR += 60
                                                                   }
                                    }

Last edited by RudiC; 12-09-2019 at 03:20 PM..
These 3 Users Gave Thanks to RudiC For This Post:
bunny_merah19 jim mcnamara vgersh99
 

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

LEARN ABOUT MOJAVE

mail::spf::mech::ptr5.18

Mail::SPF::Mech::PTR(3) 				User Contributed Perl Documentation				   Mail::SPF::Mech::PTR(3)

NAME

       Mail::SPF::Mech::PTR - SPF record "ptr" mechanism class

DESCRIPTION

       An object of class Mail::SPF::Mech::PTR represents an SPF record mechanism of type "ptr".

   Constructors
       The following constructors are provided:

       new(%options): returns Mail::SPF::Mech::PTR
	   Creates a new SPF record "ptr" mechanism object.

	   %options is a list of key/value pairs representing any of the following options:

	   qualifier
	   domain_spec
	       See "new" in Mail::SPF::Mech.

       new_from_string($text, %options): returns Mail::SPF::Mech::PTR; throws Mail::SPF::ENothingToParse, Mail::SPF::EInvalidMech
	   Creates a new SPF record "ptr" mechanism object by parsing the string and any options given.

   Class methods
       The following class methods are provided:

       default_qualifier
       qualifier_pattern
	   See "Class methods" in Mail::SPF::Mech.

       name: returns string
	   Returns 'ptr'.

       name_pattern: returns Regexp
	   Returns a regular expression that matches a mechanism name of 'ptr'.

   Instance methods
       The following instance methods are provided:

       text
       qualifier
       params
       stringify
	   See "Instance methods" in Mail::SPF::Mech.

       domain_spec: returns Mail::SPF::MacroString
	   Returns the "domain-spec" parameter of the mechanism.

       match($server, $request): returns boolean
	   Checks whether the mechanism's target domain name, or a sub-domain thereof, is a "valid" domain name for the given request's IP address
	   (see "ip_address" in Mail::SPF::Request), and returns true if it does, or false otherwise.  See "valid_domain_for_ip_address" in
	   Mail::SPF::Util for how domains are validated.  See RFC 4408, 5.5, for the description of an equivalent algorithm.

SEE ALSO

       Mail::SPF, Mail::SPF::Record, Mail::SPF::Term, Mail::SPF::Mech

       <http://tools.ietf.org/html/rfc4408>

       For availability, support, and license information, see the README file included with Mail::SPF.

AUTHORS

       Julian Mehnle <julian@mehnle.net>, Shevek <cpan@anarres.org>

perl v5.18.2							    2017-10-06						   Mail::SPF::Mech::PTR(3)
All times are GMT -4. The time now is 01:43 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy