read regex from ID file, print regex and line below from source file
I have a file of protein sequences with headers (my source file). Based on a list of IDs (which are included in some of the headers), I'd like to print out only the specified sequences, with only the ID as header.
In other words, I'd like to search source.txt for the terms in IDs.txt, and print the ID as well as the sequence. Ideally the process would continue even if an ID is not found in the source file. All headers in source.txt are of similar format.
I am able to pull out the sequences based on the ID one-by-one, but this is slow and doesn't give me the header.
I also tried extracting the entire header and the sequence by modifying a script I had for a sequence file with different header type, but again it's one-by-one it only prints the header.
As is probably clear, I'm still pretty low on the learning curve. Any help would be really appreciated!
Hello,
I have a file which has user information. Each user has 2 variables with the same name like
Email: testuser1
Email: testuser1@test.com
Email: testuser2
Email: testuser2@test.com
My intention is to delete the ones without the '@' symbol. When I run this statement awk '/^Email:/&&!/@/'... (6 Replies)
I have a .csv file which is seperated with (;)
inputfile
---------
ZZZZ;AAAA;BBB;CCCC;DDD;EEE;
YYYY;BBBB;CCC;DDDD;EEE;FFF;
...
...
reading file line by line till end of file.
while reading each line output format should be .
i need to print only specific columns let say 5th... (2 Replies)
I have a file that looks like this:
cat includes
CORP-CRASHTEST-BU
e:\crashplan\
CORP-TEST
/usr/openv/java
/usr/openv/logs
/usr/openv/man
CORP-LABS_TEST
/usr/openv/java
/usr/openv/logs
/usr/openv/man
What I want to do is make three new files with just those selections. So the three... (4 Replies)
Good day,
I have a list of regular expressions in file1. For each match in file2, print the containing line and the line after.
file1:
file2:
Output:
I can match a regex and print the line and line after
awk '{lines = $0} /Macrosiphum_rosae/ {print lines ; print lines } '
... (1 Reply)
Hi experts,
I have a file with regexes which is used for automatic searches on several files (40+ GB).
To do some postprocessing with the grep result I need the matching line as well as the match itself.
I know that the latter could be achieved with grep's -o option. But I'm not aware of a... (2 Replies)
I have a file1.txt with several 100k lines, each of which has a column 9 containing one of 60 "label" identifiers. Using an labels.txt file containing a list of labels, I'd like to extract 200 random lines from file1.txt for each of the labels in index.txt.
Using a contrived mini-example:
$ cat... (8 Replies)
I have a line that I need to parse through and extract a pattern that occurs multiple times in it.
Example line:
getInfoCall: info received please proceed, getInfoCall: info received please proceed, getInfoCall: info received please proceed, getInfoCall: info received please proceed,... (4 Replies)
Hello.
I have been looking high and low for the solution for this. I seems there should be a simple answer, but alas.
I have a big xml file, and I need to extract certain information from specific items. The information I need can be found between a specific set of tags. let's call them... (2 Replies)
I'm trying to get some exclusions into our sendmail regular expression for the K command. The following configuration & regex works:
LOCAL_CONFIG
#
Kcheckaddress regex -a@MATCH
+<@+?\.++?\.(us|info|to|br|bid|cn|ru)
LOCAL_RULESETS
SLocal_check_mail
# check address against various regex... (0 Replies)
Discussion started by: RobbieTheK
0 Replies
LEARN ABOUT DEBIAN
tie::hash::regex
Tie::Hash::Regex(3pm) User Contributed Perl Documentation Tie::Hash::Regex(3pm)NAME
Tie::Hash::Regex - Match hash keys using Regular Expressions
SYNOPSIS
use Tie::Hash::Regex;
my %h;
tie %h, 'Tie::Hash::Regex';
$h{key} = 'value';
$h{key2} = 'another value';
$h{stuff} = 'something else';
print $h{key}; # prints 'value'
print $h{2}; # prints 'another value'
print $h{'^s'}; # prints 'something else'
print tied(%h)->FETCH(k); # prints 'value' and 'another value'
delete $h{k}; # deletes $h{key} and $h{key2};
or (new! improved!)
my $h : Regex;
DESCRIPTION
Someone asked on Perlmonks if a hash could do fuzzy matches on keys - this is the result.
If there's no exact match on the key that you pass to the hash, then the key is treated as a regex and the first matching key is returned.
You can force it to leap straight into the regex checking by passing a qr'ed regex into the hash like this:
my $val = $h{qr/key/};
"exists" and "delete" also do regex matching. In the case of "delete" all vlaues matching your regex key will be deleted from the hash.
One slightly strange thing. Obviously if you give a hash a regex key, then it's possible that more than one key will match (consider
c<$h{qw/./}>). It might be nice to be able to do stuff like:
my @vals = $h{$pat};
to get all matching values back. Unfortuately, Perl knows that a given hash key can only ever return one value and so forces scalar context
on the "FETCH" call when using the tied interface. You can get round this using the slightly less readable:
my @vals = tied(%h)->FETCH($pat);
ATTRIBUTE INTERFACE
From version 0.06, you can use attributes to define your hash as being tied to Tie::Hash::Regex. You'll need to install the module
Attribute::Handlers.
METHODS
FETCH
Get a value from the hash. If there isn't an exact match try a regex match.
EXISTS
See if a key exists in the hash. If there isn't an exact match try a regex match.
DELETE
Delete a key from the hash. If there isn't an exact match try a regex match.
AUTHOR
Dave Cross <dave@mag-sol.com>
Thanks to the Perlmonks <http://www.perlmonks.org> for the original idea and to Jeff "japhy" Pinyan for some useful code suggestions.
COPYRIGHT
Copyright (C) 2001-8, Magnum Solutions Ltd. All Rights Reserved.
LICENSE
This script is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
SEE ALSO perl(1).
perltie(1).
Tie::RegexpHash(1)perl v5.10.0 2008-06-30 Tie::Hash::Regex(3pm)