Sorry for such a dreadful title, but I'm not sure how to be more descriptive. I'm hoping some of the more gurutastic out there can take a look at a solution I came up with to a problem, and advice if there are better ways to have gone about it.
To make a long story short around 20K pieces of... (2 Replies)
Hi all
Sorry for the basic question, but i am writing a shell script to get around a slightly flaky binary that ships with one of our servers. This particular utility randomly generates the correct information and could work first time or may work on the 12th or 100th attempt etc !.... (4 Replies)
Please help me to automatically assign the output of awk command to the variables cs3, cs4, cs5 and cs6 using a for loop. The below code is not working.
for i in 3 4 5 6
do
cs$i=`awk -F"|" 'BEGIN{sum=0}{sum=sum+$'$i'}END{printf("%d\n", sum)}' css`
done
echo $cs3 $cs4 $cs5 $cs6 (9 Replies)
I am new to unix and trying to make a script for writing all my command into another file and use that file to run all commands
I am trying to use for loop with echo command to generate a command based script for writing the file with all the command sequentially w.r.t for loop.
I want... (6 Replies)
Hi,
I have the following folder structure:
TST500-1000
TST500-2000
TST500-3000
TST700-1000
TST700-2000
TST700-3000
TST900-1000
TST900-2000
TST900-3000
I would like to store the numbers in the first column (considering "-" as column separator) into a variable then the numbers in... (3 Replies)
I'm relatively new to bash scripting and am trying to use awk inside a bash for loop but am having a problem with the variables.
for i in $(seq 30 5 60)
do
# Define variables up and down in AWK
eval $(awk 'BEGIN{ print "up=$((i+1))"}' < /dev/null)
eval $(awk 'BEGIN{ print... (2 Replies)
I'm taking a unix class and need to countdown to 0 from whatever number the user inputs. I know how to do this with a while or until loop but using the for loop is throwing me off....
I know I can use an if-then statement in my for loop but can I include a while loop in my for loop? (3 Replies)
Hi there guys!
I was trying to do:
while read line; do
if ; then
read -p "Press Enter to continue..."
cont=0
fi
echo $line
let cont++
done < file.txt
However, I have read that the read -p would not work in a while loop...
I was wondering if there is any other way to... (2 Replies)
I have created one file that contains all the necessary info in it to create a download link. In each of the lines /results/analysis/output/Home/Auto_user_S5-00580-6-Medexome_67_032/plugin_out/FileExporter_out.67... (8 Replies)
I am trying to check whether particular host and port are responding or not. I am using below script to check. but node_port array that i am using in loop is getting replaced with previous iteration value. Script and output is given.
Please help me to understanding why node_port values are... (5 Replies)
Discussion started by: tmalik79
5 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)