Assuming that all of the file consists of the two records (alternating) that you have posted, then this will print the portion of the first record you've pointed out, and the entire next record.
If there are other records in the file this won't work.
Last edited by agama; 08-25-2012 at 08:43 PM..
Reason: fixed missing semicolon
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
bp_mask_by_search
BP_MASK_BY_SEARCH(1p) User Contributed Perl Documentation BP_MASK_BY_SEARCH(1p)NAME
mask_by_search - mask sequence(s) based on its alignment results
SYNOPSIS
mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa
DESCRIPTION
Mask sequence based on significant alignments of another sequence. You need to provide the report file and the entire sequence data which
you want to mask. By default this will assume you have done a TBLASTN (or TFASTY) and try and mask the hit sequence assuming you've
provided the sequence file for the hit database. If you would like to do the reverse and mask the query sequence specify the -t/--type
query flag.
This is going to read in the whole sequence file into memory so for large genomes this may fall over. I'm using DB_File to prevent keeping
everything in memory, one solution is to split the genome into pieces (BEFORE you run the DB search though, you want to use the exact file
you BLASTed with as input to this program).
Below the double dash (--) options are of the form --format=fasta or --format fasta or you can just say -f fasta
By -f/--format I mean either are acceptable options. The =s or =n or =c specify these arguments expect a 'string'
Options:
-f/--format=s Search report format (fasta,blast,axt,hmmer,etc)
-sf/--sformat=s Sequence format (fasta,genbank,embl,swissprot)
--hardmask (booelean) Hard mask the sequence
with the maskchar [default is lowercase mask]
--maskchar=c Character to mask with [default is N], change
to 'X' for protein sequences
-e/--evalue=n Evalue cutoff for HSPs and Hits, only
mask sequence if alignment has specified evalue
or better
-o/--out/
--outfile=file Output file to save the masked sequence to.
-t/--type=s Alignment seq type you want to mask, the
'hit' or the 'query' sequence. [default is 'hit']
--minlen=n Minimum length of an HSP for it to be used
in masking [default 0]
-h/--help See this help information
AUTHOR - Jason Stajich
Jason Stajich, jason-at-bioperl-dot-org.
perl v5.14.2 2012-03-02 BP_MASK_BY_SEARCH(1p)