I have a very long list of file (see input below). I only need the first "chunk" of the line before the space and omit the rest. Also, the > sign needs to be excluded. Can anyone help me please?
Thank you so much!
INPUT:
OUTPUT:
Last edited by Scott; 10-09-2013 at 06:51 PM..
Reason: Added Code Tags [6th time]
Hey guys,
I have this file generated by me... i want to create some HTML output from it.
The problem is that i am really confused about how do I go about reading the file.
The file is in the following format:
TID1 Name1 ATime=xx AResult=yyy AExpected=yyy BTime=xx BResult=yyy... (8 Replies)
Hello,
somewhere in a shell script, i am storing the output of "ls" into a variable. My question is how can i parse this variable to get each filepath. I don't want to create a temporary file to write down all the filenames and then parse it..
is there a easy way out..
here is what... (3 Replies)
Hi
I wanted to print/store just a specific element of the list . I have got the list as an output of grep command.
here is code snap below :
end_no=`egrep -ni '!return code: 0|return code other than 0' temp.log | cut -d':' -f1`
this will return the line numbers in end_no. I just... (2 Replies)
Hi folks,
I have a list of XML files with entries like this one:
<Item Name="Author" Type="String">Stark F</Item>
<Item Name="Author" Type="String">Pfannstiel J</Item>
<Item Name="Author" Type="String">Klaiber I</Item>
<Item Name="Author" Type="String">Raabe T</Item>
and what I would like... (1 Reply)
Hello I am trying to develop a shell script that takes a text file such as this...
E-mail@ Soc.Sec.No. *--------Name-----------* Class *School.Curriculum.Major.* Campus.Phone
JCC2380 XXX-XX-XXXX CAREY, JULIE C JR-II BISS CPSC BS INFO TECH 412/779-9445
JAC1936 XXX-XX-XXXX... (7 Replies)
Hi
I have a vcf file with 20000 lines, it looks like this-
23 122691 . C 1345.09 PASS
33 122961 . C 833.45 PASS
43 122970 . A 689.75 PASS
53 123009 . T 118.99 PASS
63 123033 . T 46.85 PASS
73 123042 . A 127.51 PASS
83 123060 . T 299.64 PASS
93 123081 . T 299.64 PASS... (3 Replies)
Most of the code I've seen is been listing processes or capturing process ids, etc. But here's what I need to do. Preferably in Korn shell.
1. do a ps -ef |grep tns |grep -v grep
in order to get a list or Oracle listeners that are running.
2. parse the line into components which... (7 Replies)
I have a requirement where I need parse through files in a directory which have a specific pattern and then check whether the file has been processed or not. The exit condition is any file that has been processed will have an entry in database. If it is processed i.e., if an entry is present for... (4 Replies)
Hi there,
Here is my checklist of items,
4.1.1 Alerter
4.1.2 Client Services for Netware
4.1.3 Clipbook
4.1.4 Fax Service
4.1.5 File Replication
4.1.6 File Services for Macintosh
4.1.7 FTP Publishing Service
4.1.8 Help and Support
4.1.9 HTTP SSL
4.1.10 IIS Admin Service ... (1 Reply)
Discussion started by: alvinoo
1 Replies
LEARN ABOUT DEBIAN
bio::alignio::nexus
Bio::AlignIO::nexus(3pm) User Contributed Perl Documentation Bio::AlignIO::nexus(3pm)NAME
Bio::AlignIO::nexus - NEXUS format sequence input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.
use Bio::AlignIO;
my $in = Bio::AlignIO->new(-format => 'nexus',
-file => 'aln.nexus');
while( my $aln = $in->next_aln ) {
# do something with the alignment
}
DESCRIPTION
This object can transform Bio::Align::AlignI objects to and from NEXUS data blocks. See method documentation for supported NEXUS features.
ACKNOWLEDGEMENTS
Will Fisher has written an excellent standalone NEXUS format parser in Perl, readnexus. A number of tricks were adapted from it.
FEEDBACK
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 - Heikki Lehvaslaiho
Email: heikki-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : $alignio = Bio::AlignIO->new(-format => 'nexus', -file => 'filename');
Function: returns a new Bio::AlignIO object to handle clustalw files
Returns : Bio::AlignIO::clustalw object
Args : -verbose => verbosity setting (-1,0,1,2)
-file => name of file to read in or with ">" - writeout
-fh => alternative to -file param - provide a filehandle
to read from/write to
-format => type of Alignment Format to process or produce
Customization of nexus flavor output
-show_symbols => print the symbols="ATGC" in the data definition
(MrBayes does not like this)
boolean [default is 1]
-show_endblock => print an 'endblock;' at the end of the data
(MyBayes does not like this)
boolean [default is 1]
next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: Returns the next alignment in the stream.
Supports the following NEXUS format features:
- The file has to start with '#NEXUS'
- Reads in the name of the alignment from a comment
(anything after 'TITLE: ') .
- Sequence names can be given in a taxa block, too.
- If matchchar notation is used, converts
them back to sequence characters.
- Does character conversions specified in the
NEXUS equate command.
- Sequence names of type 'Homo sapiens' and
Homo_sapiens are treated identically.
Returns : L<Bio::Align::AlignI> object
Args :
write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: Writes the $aln object into the stream in interleaved NEXUS
format. Everything is written into a data block.
SimpleAlign methods match_char, missing_char and gap_char must be set
if you want to see them in the output.
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
flag
Title : flag
Usage : $obj->flag($name,$value)
Function: Get/Set a flag value
Returns : value of flag (a scalar)
Args : on set, new value (a scalar or undef, optional)
perl v5.14.2 2012-03-02 Bio::AlignIO::nexus(3pm)