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Full Discussion: Extract specific content from data and rename its header problem asking
Top Forums Shell Programming and Scripting Extract specific content from data and rename its header problem asking Post 302407018 by alister on Wednesday 24th of March 2010 11:11:13 AM
Old 03-24-2010
Quote:
Originally Posted by malcomex999
You can modify alister code like this...
Code:
awk 'FNR==NR {if (/^>/) p=substr($0,2); 
else a[p]=a[p] $0; next} 
{printf(">%s_0.%02u\n%s\n", $1, ++i[$1], substr(a[$1], $2, ($2>=$3?$3:$3-$2+1)))}' f1 f2

Hi, malcomeex999:

That tweak is incorrect, if I understand the modification to f2 correctly. If the second field is greater than the third, then it instead of being treated as the beginning index of the substring, it should be considered the end index (and the interpretation of the third field should be complementarily swapped). The correct solution requires that the second argument to substr() be modified as well, since in the case of $2 > $3, it should be $3 not $2.

By the way, malcomeex999 and rdcwayx, thank you very much for your bit awards. It's appreciated Smilie


Hi, patrick87:

One solution to handle both cases (even if they appear within the same file2):
Code:
awk 'FNR==NR {if (/^>/) p=substr($0,2); else a[p]=a[p] $0; next}
     {if ($2>$3) {t=$2; $2=$3; $3=t}; printf(">%s_0.%02u\n%s\n", $1, ++i[$1], substr(a[$1], $2, $3-$2+1))}' f1 f2

It works identically to my earlier solution except that it tests the second and third fields in f2. If the first index is greater than the second, their values are swapped before the substr() call.

Regards,
Alister
 

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LEARN ABOUT DEBIAN

git-annex-shell

git-annex-shell(1)					      General Commands Manual						git-annex-shell(1)

NAME

       git-annex-shell - Restricted login shell for git-annex only SSH access

SYNOPSIS

       git-annex-shell [-c] command [params ...]

DESCRIPTION

       git-annex-shell is a restricted shell, similar to git-shell, which can be used as a login shell for SSH accounts.

       Since  its  syntax  is  identical to git-shell's, it can be used as a drop-in replacement anywhere git-shell is used. For example it can be
       used as a user's restricted login shell.

COMMANDS

       Any command not listed below is passed through to git-shell.

       Note that the directory parameter should be an absolute path, otherwise it is assumed to be relative to the user's home directory. Also the
       first "/~/" or "/~user/" is expanded to the specified home directory.

       configlist directory
	      This outputs a subset of the git configuration, in the same form as git config --list

       inannex directory [key ...]
	      This checks if all specified keys are present in the annex, and exits zero if so.

       dropkey directory [key ...]
	      This drops the annexed data for the specified keys.

       recvkey directory key
	      This runs rsync in server mode to receive the content of a key, and stores the content in the annex.

       sendkey directory key
	      This runs rsync in server mode to transfer out the content of a key.

       commit directory
	      This commits any staged changes to the git-annex branch.	It also runs the annex-content hook.

OPTIONS

       Most options are the same as in git-annex. The ones specific to git-annex-shell are:

       --uuid=UUID
	      git-annex uses this to specify the UUID of the repository it was expecting git-annex-shell to access, as a sanity check.

HOOK

       After  content is received or dropped from the repository by git-annex-shell, it runs a hook, .git/hooks/annex-content (or hooks/annex-con-
       tent on a bare repository). The hook is not currently passed any information about what changed.

ENVIRONMENT

       GIT_ANNEX_SHELL_READONLY

	      If set, disallows any command that could modify the repository.

       GIT_ANNEX_SHELL_LIMITED
	      If set, disallows running git-shell to handle unknown commands.

SEE ALSO

       git-annex(1)

       git-shell(1)

AUTHOR

       Joey Hess <joey@kitenet.net>

       <http://git-annex.branchable.com/>

																git-annex-shell(1)
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