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Further Pregap Configuration

Pregap can be further tuned by adding extra configuration parameters in the .pregaprc file. Common changes include changing the arguments to the external programs used and changing how pregap obtains the reading name from a file. The following section ( See section Integration with External Databases.) describes the SCF and Experiment File filename generation and the entry name calculations.

To configure the clip program to clip using different parameters set the clip_args variable. To request clipping starting from base 50 (instead of the default at 70) use clip_args="${clip_args} -s 50". See the clip manual page (see section Clip) for full details of the parameters available. Note that the clip program (as can all the external programs used) can be replaced for any other program by redefining the clip variable (eg clip=our_clip). The replacement program will be called with the the clip_args specified and the name of the Experiment File to clip. Clip programs that work on a trace file must read the name of this trace file from the Experiment File.

In particular, to use trace_clip instead of clip simply add clip="trace_clip" to the `.pregapc' file. The trace_clip program (see section Trace_clip) performs the same task as clip except uses the trace data instead of the called sequence. In general it should do a better task, but needs setting up correctly before hand. The scale_trace_clip program (see section Scale_trace_clip) can be used to derive some arguments for trace_clip which should then be set using the clip_args variable.

Startup parameters may also be specified for Trev. By default these will be "-restrict -edits 0". Setting the trev_args variable will override these defaults, but please make sure the default arguments are still included. For example, to start trev at a specified position and size on the screen with a slightly larger than normal magnification use trev_args="${trev_args} -geometry 900x300+100+100 -xmag 200".See section Trev.

The vector_clip and repe programs used by Pregap require several argument parameters to fine tune their searching algorithms. Generally these do not need to be changed. Consult the vector_clip and repe (see section Screening Against Vector Sequences) documentation for full details on the meaning of these questions. To see the answers to these questions used by pregap look at the system-pregaprc file. A brief table of the questions and pregap variables follows.

Note that these variables still start with vepe_. This is simply to keep backwards compatibility. Pregap now uses vector_clip instead of vepe, but still reads the vepe_ parameters.

--vector_clip -s: mark sequencing vector--
vepe_svec_word_length     Word Length
vepe_svec_diagonal        Number of diagonals to combine
vepe_svec_score           Cutoff score
vepe_svec_min_length      Minimum length or percentage of vector. See vector_clip manual page

--vector_clip -c: mark cloning vector--
vepe_cvec_word_length     Word Length
vepe_cvec_diagonal        Number of diagonals to combine
vepe_cvec_score           Cutoff score

--vector_clip -r: check for vector rearrangements--
vepe_avec_min_match       Minimum match length

--Repe--
repe_repeat_file          Input file of repeat file names
repe_score                Cutoff score
repe_tag_type             Four letter tag type

Finally, it is sometimes useful to derive the experiment file name and reading name from the ABI filename rather than the sample named contained within it. This can now be done by answering the "Use ABI sample names?" question, however the previous method of implementing this is still instructive for people requiring yet another way of deriving their reading names. Answering yes to the question simply executes the abi_filenames command which redefines the abi_SCF_com, abi_Exp_com and abi_Ent_com variables as follows.

abi_SCF_com='echo "${file}.scf"'
abi_Exp_com='echo "${file}.exp"'
abi_Ent_com='echo "${file}" | sed "s/ /_/g"'

If this has been made the default mode of operation, it can be switched back by adding the use_sample_names=no command to the .pregaprc file.

To use a different filename derivation than used by abi_filenames add use_sample_names=pregaprc and your own definitions of the above three _com commands to the .pregaprc file.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap_6.html