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Difference between revisions of "ensfiles.pl"
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used to specify the ensemble directory. If no further arguments are given | used to specify the ensemble directory. If no further arguments are given | ||
it will list all ensemble files associated with the given tag.<BR> | it will list all ensemble files associated with the given tag.<BR> | ||
| + | |||
The option <B>-cluster</B> may be used to list only the files from | The option <B>-cluster</B> may be used to list only the files from | ||
| − | a specific cluster if | + | a specific cluster if [[enscluster.pl]] was run |
previously to perform the clustering. The utility | previously to perform the clustering. The utility | ||
| − | + | [[showcluster.pl]] is available to list all identified | |
clusters. Normally cluster information is read for the tag for which the | clusters. Normally cluster information is read for the tag for which the | ||
list of files is obtained. If clustering information is only available for | list of files is obtained. If clustering information is only available for | ||
a different tag in the same ensemble of structures this tag may be given with | a different tag in the same ensemble of structures this tag may be given with | ||
<B>-ctag</B> so that the corresponding cluster file is used instead.<BR> | <B>-ctag</B> so that the corresponding cluster file is used instead.<BR> | ||
| + | |||
The file list may be sorted according to values of | The file list may be sorted according to values of | ||
an associated ensemble property if the property tag is given with <B>-sort</B>.<BR> | an associated ensemble property if the property tag is given with <B>-sort</B>.<BR> | ||
| + | |||
The option <B>-list</B> is available to provide a file with indices to | The option <B>-list</B> is available to provide a file with indices to | ||
obtain file names for selected structures.<BR> | obtain file names for selected structures.<BR> | ||
| + | |||
Please note that by default the files are stored in compressed form | Please note that by default the files are stored in compressed form | ||
(gzip). This script, however, always returns the file names in | (gzip). This script, however, always returns the file names in | ||
| − | uncompressed form without the <font color=#508060>.gz</font> extension, whether the | + | uncompressed form without the <font color=#508060>.gz</font> extension, whether the files are compressed or not. |
| − | files are compressed or not. | + | |
== Options == | == Options == | ||
; -help : usage information | ; -help : usage information | ||
| − | + | ; -cluster level : clustering level for hierarchical clusters | |
| + | ; -ctag alttag : read clustering info from <TT>alttag.clusters</TT> | ||
| + | ; -dir directory : data directory | ||
| + | ; -list file : read index file of file names to be returned from file | ||
| + | ; -sort tag : sort file list by given property | ||
| + | ; -prop tag : write out property value along with file name | ||
== Examples == | == Examples == | ||
Latest revision as of 14:21, 30 July 2009
Usage
usage: ensfiles.pl [options] tag
options: [-cluster level]
[-ctag tag]
[-dir workdir]
[-list file]
[-sort proptag]
[-prop proptag]
Description
This script is used to extract a list of files from an ensemble structure.
It requires an ensemble tag as argument and -dir may be
used to specify the ensemble directory. If no further arguments are given
it will list all ensemble files associated with the given tag.
The option -cluster may be used to list only the files from
a specific cluster if enscluster.pl was run
previously to perform the clustering. The utility
showcluster.pl is available to list all identified
clusters. Normally cluster information is read for the tag for which the
list of files is obtained. If clustering information is only available for
a different tag in the same ensemble of structures this tag may be given with
-ctag so that the corresponding cluster file is used instead.
The file list may be sorted according to values of
an associated ensemble property if the property tag is given with -sort.
The option -list is available to provide a file with indices to
obtain file names for selected structures.
Please note that by default the files are stored in compressed form (gzip). This script, however, always returns the file names in uncompressed form without the .gz extension, whether the files are compressed or not.
Options
- -help
- usage information
- -cluster level
- clustering level for hierarchical clusters
- -ctag alttag
- read clustering info from alttag.clusters
- -dir directory
- data directory
- -list file
- read index file of file names to be returned from file
- -sort tag
- sort file list by given property
- -prop tag
- write out property value along with file name
Examples
ensfiles.pl -dir data sample
extracts all ensemble structures associated with the sample
tag.
data/0/1/sample.pdb data/0/2/sample.pdb data/0/3/sample.pdb data/0/4/sample.pdb data/0/5/sample.pdb data/0/6/sample.pdb data/0/7/sample.pdb data/0/8/sample.pdb data/0/9/sample.pdb data/0/10/sample.pdb ...
ensfiles.pl -dir data -cluster t.2 sample
extracts the ensemble files in cluster t.2 from
the sample set.
data/0/2/sample.pdb data/0/4/sample.pdb data/0/5/sample.pdb data/0/6/sample.pdb data/0/7/sample.pdb data/0/9/sample.pdb data/0/10/sample.pdb data/0/13/sample.pdb data/0/14/sample.pdb data/0/15/sample.pdb ...
ensfiles.pl -dir data -list sel.file sample
extracts the file names from the ensemble structures belonging to
the sample tag for the indices from sel.file.
data/0/1/sample.pdb data/0/5/sample.pdb data/0/6/sample.pdb data/0/7/sample.pdb data/0/9/sample.pdb