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
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gensprep
gensprep(8) ICU 50.1.2 Manual gensprep(8)NAME
gensprep - compile StringPrep data from files filtered by filterRFC3454.pl
SYNOPSIS
gensprep [ -h, -?, --help ] [ -v, --verbose ] [ -c, --copyright ] [ -s, --sourcedir source ] [ -d, --destdir destination ]
DESCRIPTION
gensprep reads filtered RFC 3454 files and compiles their information into a binary form. The resulting file, <name>.icu, can then be read
directly by ICU, or used by pkgdata(8) for incorporation into a larger archive or library.
The files read by gensprep are described in the FILES section.
OPTIONS -h, -?, --help
Print help about usage and exit.
-v, --verbose
Display extra informative messages during execution.
-c, --copyright
Include a copyright notice into the binary data.
-s, --sourcedir source
Set the source directory to source. The default source directory is specified by the environment variable ICU_DATA.
-d, --destdir destination
Set the destination directory to destination. The default destination directory is specified by the environment variable ICU_DATA.
ENVIRONMENT
ICU_DATA Specifies the directory containing ICU data. Defaults to /usr/share/icu/50.1.2/. Some tools in ICU depend on the presence of the
trailing slash. It is thus important to make sure that it is present if ICU_DATA is set.
FILES
The following files are read by gensprep and are looked for in the source /misc for rfc3454_*.txt files and in source /unidata for Normal-
izationCorrections.txt.
rfc3453_A_1.txt Contains the list of unassigned codepoints in Unicode version 3.2.0....
rfc3454_B_1.txt Contains the list of code points that are commonly mapped to nothing....
rfc3454_B_2.txt Contains the list of mappings for casefolding of code points when Normalization form NFKC is specified....
rfc3454_C_X.txt Contains the list of code points that are prohibited for IDNA.
NormalizationCorrections.txt
Contains the list of code points whose normalization has changed since Unicode Version 3.2.0.
VERSION
50.1.2
COPYRIGHT
Copyright (C) 2000-2002 IBM, Inc. and others.
SEE ALSO pkgdata(8)ICU MANPAGE 18 March 2003 gensprep(8)