Variable modifiers in csh and bash: bash

Bash do not have variable modifiers, but it has a feature called Posix, which originates from ksh and seems to be more powerful, albeit somewhat more cryptic.

% is used to remove smallest suffix pattern. Like:

$ gatesfile=/home/gates/bin/foo.bar
$ echo ${gatesfile%.bar}
/home/gates/bin/foo

Of course you can append something to the end and forge the functionality of replace:

$ echo ${gatesfile%.bar}.x
/home/gates/bin/foo.x

%% is to remove largest suffix pattern:

$ gatesfile=posix/src/std
$ echo ${gatesfile%%/*}
posix

# is used to remove smallest prefix pattern, and ## is to remove largest prefix pattern

In summary, given:

a=/a/b/c/d
b=b.xxx

  +------------------------------------+
  |csh    bash           result        |
  +------------------------------------+
  |$a:h   ${a%/*}        /a/b/c        |
  |$a:t   ${a##*/}       d             |
  |$b:r   ${b%.*}        b             |
  |$b:e   ${b##*.}       xxx           |
  +------------------------------------+

Variable modifiers in csh and bash: csh

csh has a nice feature called variable modification to easily trim your variable for your needs. The modifiers work by appending to the variable interpolation with a ":". This feature is especially useful dealing with pathnames.

For example

% set gatesfile=/home/gates/bin/foo.bar
% echo $gatesfile
/home/gates/bin/foo.bar

In order to get the directory name, you only need this:

% echo $gatesfile:h
home/gates/bin

and for file name:

% echo $gatesfile:t
foo.bar

how about file base? Use combinations:

% echo $gatesfile:r:t
foo

Ok, here is all of the appendixes:

  +----------------------------------------------------------+
  |Modifier   Meaning               Example   Results        |
  +----------------------------------------------------------+
  |r          Root                  $a:r      a/b/c.d.e.f    |
  |e          Extension             $a:e      g              |
  |h          Head (or Directory)   $a:h      /a/b           |
  |t          Tail (or Filename)    $a:t      c.d.e.f.g      |
  +----------------------------------------------------------+

Linux Tips

use scp to copy files from lab to my home:

scp qz2126@adgate.cu-genome.org:~/oct2.RData ./

QSUB Tips

1, transfer variable
use -V, you can transfer all variables to the job, and use -v, you can specify a variable to transfer:

qsub -V -cwd -l mem=3G,time=72:00:00 -o $qoutF -e $qerrF $qsubF
qsub -cwd -v sparks=$sparksDir -o $qoutF -e $qerrF $qsubF

2, big jobs, for titan@lab

qrsh -l mem=30G,time=24:: -now n

3, binds to a specified queue/node

qrsh -q all.q@gaianode-8-85.local -now n

BLAST Tips

1, fastacmd

get DB info:

fastacmd -d $PDBBLST -I T

get sequence

fastacmd -d $PDBBLST -s 1a2k_A

get sequence with taxonomy info

fastacmd -d $BLASTDB/nr.fa -s XP_642131.1 -TT