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 MOJAVE
text::glob
Text::Glob(3) User Contributed Perl Documentation Text::Glob(3)NAME
Text::Glob - match globbing patterns against text
SYNOPSIS
use Text::Glob qw( match_glob glob_to_regex );
print "matched
" if match_glob( "foo.*", "foo.bar" );
# prints foo.bar and foo.baz
my $regex = glob_to_regex( "foo.*" );
for ( qw( foo.bar foo.baz foo bar ) ) {
print "matched: $_
" if /$regex/;
}
DESCRIPTION
Text::Glob implements glob(3) style matching that can be used to match against text, rather than fetching names from a filesystem. If you
want to do full file globbing use the File::Glob module instead.
Routines
match_glob( $glob, @things_to_test )
Returns the list of things which match the glob from the source list.
glob_to_regex( $glob )
Returns a compiled regex which is the equivalent of the globbing pattern.
glob_to_regex_string( $glob )
Returns a regex string which is the equivalent of the globbing pattern.
SYNTAX
The following metacharacters and rules are respected.
"*" - match zero or more characters
"a*" matches "a", "aa", "aaaa" and many many more.
"?" - match exactly one character
"a?" matches "aa", but not "a", or "aaa"
Character sets/ranges
"example.[ch]" matches "example.c" and "example.h"
"demo.[a-c]" matches "demo.a", "demo.b", and "demo.c"
alternation
"example.{foo,bar,baz}" matches "example.foo", "example.bar", and "example.baz"
leading . must be explictly matched
"*.foo" does not match ".bar.foo". For this you must either specify the leading . in the glob pattern (".*.foo"), or set
$Text::Glob::strict_leading_dot to a false value while compiling the regex.
"*" and "?" do not match /
"*.foo" does not match "bar/baz.foo". For this you must either explicitly match the / in the glob ("*/*.foo"), or set
$Text::Glob::strict_wildcard_slash to a false value with compiling the regex.
BUGS
The code uses qr// to produce compiled regexes, therefore this module requires perl version 5.005_03 or newer.
AUTHOR
Richard Clamp <richardc@unixbeard.net>
COPYRIGHT
Copyright (C) 2002, 2003, 2006, 2007 Richard Clamp. All Rights Reserved.
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
SEE ALSO
File::Glob, glob(3)perl v5.18.2 2017-10-06 Text::Glob(3)