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
bio::seqio::tab
Bio::SeqIO::tab(3pm) User Contributed Perl Documentation Bio::SeqIO::tab(3pm)NAME
Bio::SeqIO::tab - nearly raw sequence file input/output stream. Reads/writes id" "sequence"
"
SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
DESCRIPTION
This object can transform Bio::Seq objects to and from tabbed flat file databases.
It is very useful when doing large scale stuff using the Unix command line utilities (grep, sort, awk, sed, split, you name it). Imagine
that you have a format converter 'seqconvert' along the following lines:
my $in = Bio::SeqIO->newFh(-fh => *STDIN , '-format' => $from);
my $out = Bio::SeqIO->newFh(-fh=> *STDOUT, '-format' => $to);
print $out $_ while <$in>;
then you can very easily filter sequence files for duplicates as:
$ seqconvert < foo.fa -from fasta -to tab | sort -u |
seqconvert -from tab -to fasta > foo-unique.fa
Or grep [-v] for certain sequences with:
$ seqconvert < foo.fa -from fasta -to tab | grep -v '^S[a-z]*control' |
seqconvert -from tab -to fasta > foo-without-controls.fa
Or chop up a huge file with sequences into smaller chunks with:
$ seqconvert < all.fa -from fasta -to tab | split -l 10 - chunk-
$ for i in chunk-*; do seqconvert -from tab -to fasta < $i > $i.fa; done
# (this creates files chunk-aa.fa, chunk-ab.fa, ..., each containing 10
# sequences)
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHORS
Philip Lijnzaad, p.lijnzaad@med.uu.nl
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args :
write_seq
Title : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object
perl v5.14.2 2012-03-02 Bio::SeqIO::tab(3pm)