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
bcp
BCP(1) Boost C++ Libraries Documentation BCP(1)NAME
bcp - extract subsets of Boost
SYNOPSIS
bcp --list [options] module-list
bcp [options] module-list output-path
bcp --report [options] module-list html-file
bcp --help
DESCRIPTION
Copies all the files, including dependencies, found in module-list to output-path. output-path must be an existing path.
With --list, prints the list of all the files in module-list, including dependencies.
With --report, writes the HTML report to html-file.
With --help, prints a quick usage reminder.
It is useful for Boost authors who want to distribute their library separately from Boost and for Boost users who want to distribute a sub-
set of Boost with their application.
module-list
When the --scan option is not used, a list of Boost files or library names to copy. It can be:
- The name of a tool: for example "build" will find "tools/build".
- The name of a library: for example "regex".
- The title of a header: for example "scoped_ptr" will find "boost/scoped_ptr.hpp".
- The name of a header: for example "scoped_ptr.hpp" will find "boost/scoped_ptr.hpp".
- The name of a file: for example "boost/regex.hpp".
When the --scan option is used, a list of (probably non-boost) files to scan for Boost dependencies, the files in the module list are not
therefore copied/listed.
File dependencies
C++ source files are scanned for #includes, all #includes present in the Boost source tree will then be scanned for their dependencies and
so on.
C++ source files are associated with the name of a library, if that library has source code (and possibly build data), then include that
source in the dependencies.
C++ source files are checked for dependencies on Boost.Test (for example to see if they use cpp_main as an entry point).
HTML files are scanned for immediate dependencies (images and style sheets, but not links).
HTML report contains:
- all the licenses in effect, plus the files using each license, and the copyright holders using each license
- any files with no recognizable license (please report these to the Boost mailing lists)
- any files with no recognizable copyright holders (please report these to the Boost mailing lists)
- all the copyright holders and the files on which they hold copyright
- file dependency information - indicates the reason for the inclusion of any particular file in the dependencies found
OPTIONS --boost=path
sets the location of the Boost tree to path
--scan treat the module list as a list of (possibly non-boost) files to scan for Boost dependencies
--cvs only copy files under CVS version control
--unix-lines
make sure that all copied files use Unix style line endings
EXAMPLES
bcp scoped_ptr /foo
Copies boost/scoped_ptr.hpp and dependencies to /foo.
bcp boost/regex.hpp /foo
Copies boost/regex.hpp and all dependencies including the regex source code (in libs/regex/src) and build files (in
libs/regex/build) to /foo. Does not copy the regex documentation, test or example code.
bcp regex /foo
Copies the full regex lib (in libs/regex) including dependencies (such as the Boost.Test source required by the regex test programs)
to /foo.
bcp regex config build /foo
Copies the full regex lib (in libs/regex) plus the config lib (libs/config) and the build system (tools/build) to /foo including all
the dependencies.
bcp --scan --boost=/boost foo.cpp bar.cpp boost
Scans the [non-boost] files foo.cpp and bar.cpp for Boost dependencies and copies those dependencies to the sub-directory boost.
bcp --report regex.hpp boost-regex-report.html
Creates a HTML report called boost-regex-report.html for the Boost module regex.hpp.
AUTHORS
Author of bcp is John Maddock.
Author of this manpage is Domenico Andreoli, who copied stuff from bcp --help and the HTML documentation.
Boost C++ Libraries March 2006 BCP(1)