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Trace File Location

Gap4 does not store the trace data within the gap4 database. Instead it stores the filename of the trace file. Usually the trace files are kept within the same directory as the gap4 database. If this is not the case gap4 needs to know where they are.

To make sure that gap4 can still display the traces we need to specify any alternative locations where traces may be found. The "Trace File Location" command (which is available from the gap4 Options menu) performs this task. It brings up a dialogue asking for the directory names. If there is just one directory to specify, its name should be typed in. If there are several directories to search through, they must all be typed in, separated by the colon character (":"). To include a directory name that contains a colon, use a double colon.

For example, on windows to specify two directories, use (eg) "F::\tfiles1:G::\tfiles2".

In addition to specifying directories, RAWDATA may also be used to indicate that the trace files come from a variety of other sources using the general format SOURCETYPE=path. These can be combined with directories if desired. For example ".:/trace_cache:TAR=/traces/archived.tar".

TAR=filename.tar
Searches for the trace name in the Unix tar archive named filename.tar. If filename.tar.index exists and is of the format created using the index_tar program then the trace name will be looked up in the index instead of sequentially scanning through the tar file. In order to speed up accessing of traces within the tar file a command line utility named index_tar may be used. This produces a text index containing the filenames held within the tar and their offsets within it. Programs will then use this index file to provide a fast way of accessing the trace. The syntax for index_tar is: index_tar tar_filename > tar_filename.index. (For example "index_tar traces.tar > traces.tar.index".)
SFF=filename.sff
Searches for the trace name in a 454 SFF archive named filename.sff. SFF files have their own binary-sorted index which allows for random access.
HASH=archive.hash
This method supersedes the TAR= accessor. Tar files may be "hashed" using the hash_tar tool. Similarly 454 SFF archives may be hashed using hash_sff. In theory any type of archive may be indexed as a ".hash" provided that the traces are stored uncompressed (or compressed only using their own methods, such as with ZTR) so that random access is possible within the archive. The Hash file contains a precomputed binary index of all the traces contained within it stored in such a way that random access is very fast.
URL=url
This uses the external wget tool (not supplied as part of the Staden Package) to fetch a given url. Anywhere that %s occurs within the specified url will be replaced by the trace name. Hence, for example, URL=http://trace.server.org/cgi-bin/lookup.pl?trace=%s could be used to fetch named traces from a remote site. There are plans for such URL access to be made available via the Ensembl TraceArchive.

If the gap4 database has been opened with write-access this directory location will be stored as a database RAWD note (see section Special Note Types), which is read by gap4 when it opens the database. The demonstration data supplied with the package includes an example database (named DEMO.0) that has a RAWD note to specify that traces are fetched from a tar file within the same directory.

An alternative way of specifying the trace file location is by setting the RAWDATA environment variable. On Unix and Windows NT this is straightforward (although system and shell specific). However on Windows 95 this may prove difficult (and at least require a reboot), so manually setting the environment variable is no longer recommended.


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Last generated on 25 November 2011.