10-19-2014
10 More Discussions You Might Find Interesting
1. UNIX for Dummies Questions & Answers
Hello all,
I have a test file that has the format:
.....
O
3.694950 -.895050 1.480000
O
5.485050 .895050 1.480000
Ti
-4.590000 4.590000 2.960000
Ti
-2.295000 ... (5 Replies)
Discussion started by: aarondesk
5 Replies
2. Shell Programming and Scripting
hello folks
i have a file that have data like
/test/aa/123
/test/aa/xyz
/test/bb/xyz
/test/bb/123
in above lines i just wants to grep "aa" and "bb".
Thanks,
Bash (4 Replies)
Discussion started by: learnbash
4 Replies
3. Shell Programming and Scripting
can someone help me in the awk part...little confuse on that part.
The problem is this: what input each utility gets and what it does with data and what output is provides to the next utility)
history | awk '{a++}END{for(i in a){print a " " i}}' | sort -rn | grep '^'
Thanks (4 Replies)
Discussion started by: Learnerabc
4 Replies
4. Shell Programming and Scripting
I have a file and need to only select users that have a shell of “/bin/bash” in the line using awk or sed please help (4 Replies)
Discussion started by: boyboy1212
4 Replies
5. Shell Programming and Scripting
Hi Expert,
Kindly request for your expertise in this matter.
I have below output:
12.125.124.173,xx1.common.com
12.125.124.174,xx2.common.com
12.125.124.175,xx3.common.com
12.125.124.176,
12.125.124.177,
12.125.124.178,
12.125.124.179,xx4.common.com
12.125.124.180,xx5.common.com... (8 Replies)
Discussion started by: regmaster
8 Replies
6. Shell Programming and Scripting
Pseudo name=hdiskpower54
Symmetrix ID=000190101757
Logical device ID=0601
state=alive; policy=SymmOpt; priority=0; queued-IOs=0
==============================================================================
---------------- Host --------------- - Stor - -- I/O Path - -- Stats ---
### HW... (7 Replies)
Discussion started by: Daniel Gate
7 Replies
7. Homework & Coursework Questions
Use and complete the template provided. The entire template must be completed. If you don't, your post may be deleted!
1. The problem statement, all variables and given/known data:
1. Print the number of people that are in the /etc/passwd file with the name of George
2. Sort by name and... (8 Replies)
Discussion started by: Jagst3r21
8 Replies
8. Shell Programming and Scripting
Hi,
Trying to sort grep result based on timestamp of the filename.
I have the following result and want to sort them on timestampgrep -i 'ERROR' *log*2013*
s_m_xxx_xxx_xxx_xxx_xxxx.log.20130906092431:TRANSF_1_1_1> DBG_21216 Finished transformations for Source Qualifier . Total errors ... (5 Replies)
Discussion started by: bobbygsk
5 Replies
9. Homework & Coursework Questions
1. The problem statement, all variables and given/known data:
So i'll probably get told off for this but I have a few problems and rather than clog up the whole forum I'll post them here. Please bare in mind I am a complete novice when it comes to all this and so if you help please treat me like a... (4 Replies)
Discussion started by: jamesb18
4 Replies
10. Shell Programming and Scripting
Hi Gurus,
I have two big files. I need to compare the different. currently, I am using
sort file1 > file1_temp;
sort file2 > file2_tmp
diff file1_tmp file2_tmp
I can use command
grep -v -f file1 file2
just wondering which way is fast to compare two big files.
Thanks... (4 Replies)
Discussion started by: ken6503
4 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)