Thanks, agama, but with the following command I get the following error:
awk: syntax error at source line 1
context is
/^>gi/ { printf( ">%s\n", $4 ); getline >>> print <<< ; }
awk: illegal statement at source line 1
I have written a script to test some isdn links in my network and I am trying to format the output to be more readable. Each line of the output has a different number of digits as follows...
Sitename , spid1 12345678901234 1234567890 1234567 , spid2 1234567890 1234567890 1234567
Sitename , ... (1 Reply)
Hello:
I'm trying to extracta a matching substring from a string using regular expression. I need to extract the date part of any giving string.
All input string will have date in YYYYMMDD format in them, but it can be anywhere in the string.
Eg.
The_Mummy20080125_New... (2 Replies)
could anybody tell me how i can add/append a new line using regular expression in vi on AIX?
i've tried several ways before, but all of them failed. e.g.
:%s/$/\n/
:%s/^/\v\r/
:( (1 Reply)
Hi All,
@months = qw(Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec);
$day=091023;
$day_combine = $day;
$day_combine =~ s/({2})({2})({2})/20$1-$months-$3/;
Instead of three lines, is possible to combine the last two lines into a single line? means no need assign $day to $day_combine... (2 Replies)
Hi I just started on GNU Grep with regex and am finding it very challenging and need to ask for help already...
here is the problem, I have a page (MYFILE) which consists of the following....
<div>
<input type="hidden" name="__EVENTTARGET" id="__EVENTTARGET" value="" />
<input type="hidden"... (2 Replies)
Hi all ,
I have a string in my weblog xheader v6-day-2011:xx:yy:zz:qq:qq:ww:ee:rr
My requirement is to lookup the sting v6-day-2011 in this header and if found would like to extract the V6 ip part .
v6-day-2011 is always constant for a ipv6 entry so i would like to extract every thing... (4 Replies)
Hi all,
How am I read a file, find the match regular expression and overwrite to the same files.
open DESTINATION_FILE, "<tmptravl.dat" or die "tmptravl.dat";
open NEW_DESTINATION_FILE, ">new_tmptravl.dat" or die "new_tmptravl.dat";
while (<DESTINATION_FILE>)
{
# print... (1 Reply)
hi
i am trying to extract some specific data out of a text file using regular expressions with shell script
that is using a multiline grep .. and the tool i am using is pcregrep so that i can get compatibility with perl's regular expressions
for a sample data like this, i am trying to grab... (6 Replies)
Discussion started by: vemkiran
6 Replies
LEARN ABOUT DEBIAN
alien_hunter
ALIEN_HUNTER(1) User Commands ALIEN_HUNTER(1)NAME
alien_hunter - Interpolated Variable Order Motifs for identification of horizontally acquired DNA
SYNOPSIS
alien_hunter <sequence.file> <output.file> [Options]
DESCRIPTION
Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated
Variable Order Motifs (IVOMs). An IVOM approach exploits compositional biases using variable order motif distributions and captures more
reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd
order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted
regions. The predictions (embl format) can be automatically loaded into Artemis genome viewer freely available at:
http://www.sanger.ac.uk/Software/Artemis/.
INPUT: raw genomic sequence PREDICTION: HGT regions based on Interpolated Variable Order Motifs (IVOMs) arguments:
<sequence.file>
raw genomic sequence
<output.file>
filename for output data
Optional arguments:
-a to load the prediction file into Artemis
-c optimize predicted boundaries with a change-point detection 2 state 2nd order HMM
Output files:
<output.file>
predictions (tab file) in embl format
<output.file>.opt
optimized (HMM) predictions (tab file) in embl format
<output.file>.plot
predictions in Artemis User Plot format to be loaded manually using Graph -> Add User Plot...
<output.file>.opt.plot
optimized (HMM) predictions in Artemis User Plot format to be loaded manually using Graph -> Add User Plot...
<output.file>.sco
the scores over all the sliding windows - for score distribution check
Note: Predictions that overlap with rRNA operon are mentioned in the note qualifier
SEE ALSO
The manuscript describing the alien_hunter algorithm is available from Bioinformatics: Interpolated variable order motifs for identifica-
tion of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Vernikos GS, Parkhill J Bioinformatics. 2006;. PMID:
16837528
AUTHOR
This manual page was written by Andreas Tille <tille@debian.com> for the Debian(TM) system (but may be used by others). This man page is
released under the same conditions as the software, that is GPL.
alien_hunter 1.7 October 2009 ALIEN_HUNTER(1)