06-23-2010
Trimming sequences based on specific pattern
My files look like this
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCTTGGTGTGTATCATTTCTGGGAAGCCCTACGCCCCGGGGC
>GHXCZCC01APUO5
T-ATGTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCAGCCCTACCCGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTA---AGCTGGATTTTCTGGGACGCCCCGGGGAGCCCTA
>GHXCZCC01AQSRP
TTGTTGCCAGCTAGCTGAGCCCTAGATTTTCTGGGGCCCCGGGG
>GHXCZCC01AQSRP
TTGATGTTGCCCAGCCCTATAGCTGGATTTTCTGGGACGCCCCGGGGTGC
And I need to cut the sequences at the last "A" found in the following 'pattern' -highlighted for easier identification, the pattern is the actual file is not highlighted.
The expected result should look like this
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCTTGGTGTGTATCATTTCTGGGAAGCCCTA
>GHXCZCC01APUO5
T-ATGTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCAGCCCTA
>GHXCZCC01AQSRP
TTGATGTTA---AGCTGGATTTTCTGGGACGCCCCGGGGAGCCCTA
>GHXCZCC01AQSRP
TTGTTGCCAGCTAGCTGAGCCCTA
>GHXCZCC01AQSRP
TTGATGTTGCCCAGCCCTA
Thus, all the sequences would end with
AGCCCTA but whatever is to the left of that particular pattern and the identifiers (>GHXCZCC01AJ8CJ) should be kept intact.
Thanks in advance
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LEARN ABOUT CENTOS
shell-quote
SHELL-QUOTE(1) User Contributed Perl Documentation SHELL-QUOTE(1)
NAME
shell-quote - quote arguments for safe use, unmodified in a shell command
SYNOPSIS
shell-quote [switch]... arg...
DESCRIPTION
shell-quote lets you pass arbitrary strings through the shell so that they won't be changed by the shell. This lets you process commands
or files with embedded white space or shell globbing characters safely. Here are a few examples.
EXAMPLES
ssh preserving args
When running a remote command with ssh, ssh doesn't preserve the separate arguments it receives. It just joins them with spaces and
passes them to "$SHELL -c". This doesn't work as intended:
ssh host touch 'hi there' # fails
It creates 2 files, hi and there. Instead, do this:
cmd=`shell-quote touch 'hi there'`
ssh host "$cmd"
This gives you just 1 file, hi there.
process find output
It's not ordinarily possible to process an arbitrary list of files output by find with a shell script. Anything you put in $IFS to
split up the output could legitimately be in a file's name. Here's how you can do it using shell-quote:
eval set -- `find -type f -print0 | xargs -0 shell-quote --`
debug shell scripts
shell-quote is better than echo for debugging shell scripts.
debug() {
[ -z "$debug" ] || shell-quote "debug:" "$@"
}
With echo you can't tell the difference between "debug 'foo bar'" and "debug foo bar", but with shell-quote you can.
save a command for later
shell-quote can be used to build up a shell command to run later. Say you want the user to be able to give you switches for a command
you're going to run. If you don't want the switches to be re-evaluated by the shell (which is usually a good idea, else there are
things the user can't pass through), you can do something like this:
user_switches=
while [ $# != 0 ]
do
case x$1 in
x--pass-through)
[ $# -gt 1 ] || die "need an argument for $1"
user_switches="$user_switches "`shell-quote -- "$2"`
shift;;
# process other switches
esac
shift
done
# later
eval "shell-quote some-command $user_switches my args"
OPTIONS
--debug
Turn debugging on.
--help
Show the usage message and die.
--version
Show the version number and exit.
AVAILABILITY
The code is licensed under the GNU GPL. Check http://www.argon.org/~roderick/ or CPAN for updated versions.
AUTHOR
Roderick Schertler <roderick@argon.org>
perl v5.16.3 2010-06-11 SHELL-QUOTE(1)