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
svn::dump
SVN::Dump(3pm) User Contributed Perl Documentation SVN::Dump(3pm)NAME
SVN::Dump - A Perl interface to Subversion dumps
SYNOPSIS
#!/usr/bin/perl
use strict;
use warnings;
use SVN::Dump;
my $file = shift;
my $dump = SVN::Dump->new( { file => $file } );
# compute some stats
my %type;
my %kind;
while ( my $record = $dump->next_record() ) {
$type{ $record->type() }++;
$kind{ $record->get_header('Node-action') }++
if $record->type() eq 'node';
}
# print the results
print "Statistics for dump $file:
",
" version: ", $dump->version(), "
",
" uuid: ", $dump->uuid(), "
",
" revisions: ", $type{revision}, "
",
" nodes: ", $type{node}, "
";
print map { sprintf " - %-7s: %d
", $_, $kind{$_} } sort keys %kind;
DESCRIPTION
This module is an alpha release. The interfaces will probably change in the future, as I slowly learn my way inside the SVN dump format.
An "SVN::Dump" object represents a Subversion dump.
This module follow the semantics used in the reference document (the file notes/fs_dumprestore.txt in the Subversion source tree):
o A dump is a collection of records ("SVN::Dump::Record" objects).
o A record is composed of a set of headers (a "SVN::Dump::Headers" object), a set of properties (a "SVN::Dump::Property" object) and an
optional bloc of text (a "SVN::Dump::Text" object).
o Some special records ("delete" records with a "Node-kind" header) recursively contain included records.
Each class has a "as_string()" method that prints its content in the dump format.
The most basic thing you can do with "SVN::Dump" is simply copy a dump:
use SVN::Dump;
my $dump = SVN::Dump->new( 'mydump.svn' );
print $dump->as_string(); # only print the dump header
while( $rec = $dump->next_record() ) {
print $rec->as_string();
}
After the operation, the resulting dump should be identical to the original dump.
METHODS
"SVN::Dump" provides the following methods:
new( \%args )
Return a new "SVN::Dump" object.
The argument list is a hash reference.
If the "SVN::Dump" object will read information from a file, the arguments "file" is used (as usal, "-" means "STDIN"); if the dump is
read from a filehandle, "fh" is used.
Extra options will be passed to the "SVN::Dump::Reader" object that is created.
If the "SVN::Dump" isn't used to read information, the parameters "version" and "uuid" can be used to initialise the values of the
"SVN-fs-dump-format-version" and "UUID" headers.
next_record()
Return the next record read from the dump. This is a "SVN::Dump::Record" object.
version()
format()
Return the dump format version, if the version record has already been read, or if it was given in the constructor.
uuid()
Return the dump UUID, if there is an UUID record and it has been read, or if it was given in the constructor.
as_string()
Return a string representation of the dump specific blocks (the "format" and "uuid" blocks only).
SEE ALSO
"SVN::Dump::Reader", "SVN::Dump::Record".
The reference document for Subversion dumpfiles is at: <http://svn.apache.org/repos/asf/subversion/trunk/notes/dump-load-format.txt>
COPYRIGHT
Copyright 2006-2011 Philippe Bruhat (BooK), All Rights Reserved.
LICENSE
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
perl v5.10.1 2011-03-22 SVN::Dump(3pm)