User Interaction

Where pregap requires answers to questions it uses the following procedures in order:

1. Process the $PREGAPROOT/system-pregaprc file.
2. Process the $HOME/.pregaprc file. This overrides any definitions from step 1.
3. Process the .pregaprc file to override any definitions from steps 1 and 2.
4. If we still have no answer, then ask the user.

Questions asked can have default values. These can be adjusted by defining the <variable>_def (eg file_type_def=ABI) value. With this set the default is listed in square brackets and pressing return will take this value as the answer. With no default defined, pressing return will simply ask the question again until an input is supplied.

The supplied pregap and system-pregaprc use the following questions and default values.

File of filenames to be used:

This is a file containing a list (one entry per line) of trace files to process. It sets the fofn variable.

Trace file type (ABI, ALF, EXP, PLN or SCF) [ABI]:

Sets the file_type variable.

Use ABI sample names? [pregaprc]:

Only asked when the previous question is answered as 'ABI'. ABI files contain samplename information. By default pregap uses this information to derive the filenames of the SCF and Experiment files and the reading names to be used in Gap4. In some cases the sample name information is missing from the ABI file or is incorrect. In this case we can tell pregap to use the filename of the ABI file instead of the sample name for the derived filenames and reading name. Answering 'Yes' will tell pregap to use the ABI sample names; 'No' to use the filenames, and 'pregaprc' to use the existing pregaprc definitions. This sets the abi_SCF_com, abi_Exp_com and abi_Ent_com variables.

Quality clipping required? [Yes]:

Whether to clip the 3' end based on sequence quality. Currently this is a program to simply check the number of dashes in a sequence. This sets the do_qual_clip variable.

Interactive clipping required? [No]:

Only asked when the previous question is answered 'yes' to. The trace is displayed on the screen which allows interactive scrolling along the trace and setting of both the left and right cutoffs. This sets the qual_clip_interactive variable.

Locate and mark sequencing vector [Yes]:

Whether or not to perform sequence vector clipping. The necessary information to pass to vector_clip is obtained during the Augment Experiment File stage and from the vepe_svec_* variables. This sets the screen_sv variable.

Sequence vector file:

The filename of the sequencing vector to be used. Only asked when clipping the sequencing vector and both the SF and SF_com variables are undefined. This sets the SF variable.

Sequence vector cloning site:

The cloning site of the sequencing vector to be used. Only asked when clipping the sequencing vector and both the SC and SC_com variables are undefined. This sets the SC variable.

Sequence vector primer site (as offset from cloning site):

The primer site of the sequencing vector to be used. Note this must be relative to the cloning site specified above (which means it may also be a negative number). Only asked when clipping the sequencing vector and both the SP and SP_com variables are undefined. This sets the SP variable.

Locate and mark cloning vector [Yes]:

Whether or not to perform cloning vector clipping. The necessary information to pass to vector_clip is obtained during the Augment Experiment File stage and from the vepe_svec_* variables. This sets the screen_cv variable.

Cloning vector file:

The filename of the cloning vector to be used. Only asked when clipping the cloning vector and both the CF and CF_com variables are undefined. This sets the CF variable.

Screen against vector? [No]:

Whether to check for vector rearrangements. Only sequencing vector is screened against. It is not advisable to use this without screening for sequencing vector using vector_clip. This sets the screen_av variable.

Repeat tagging required? [No]:

Whether to use repe to mark the repeat segments (ALU by default) in the sequence files. This sets the tag_alu variable.

Search for mutations? [No]:

Whether to look for mutations by comparing each trace against a wild type trace. This sets the find_mutants variable.

Wild type trace file:

The wild type trace to use when looking for mutations. Only asked when the above question is answered as Yes and both the WT and WT_com variables are undefined. This sets the WT variable.

A summary of the variables governing user interaction are as follows. Note: the default values are dependent on your system-wide pregap defaults.

Variable                     Default value(*)   Possible values
-----------------------------------------------------------------------
fofn                         <undefined>        <anything>
fofn_def                     <undefined>        <anything>
                           
file_type                    <undefined>        ABI, ALF, EXP, PLN, SCF
file_type_def                ABI                ABI, ALF, EXP, PLN, SCF
                           
use_sample_names             <undefined>        Yes, No, pregaprc
use_sample_names_def         pregaprc           Yes, No, pregaprc

do_qual_clip                 <undefined>        Yes, No
do_qual_clip_def             Yes                Yes, No
                           
qual_clip_interactive        <undefined>        Yes, No
qual_clip_interactive_def    No                 Yes, No
                           
screen_sv                    <undefined>        Yes, No
screen_sv_def                No                 Yes, No
                           
SF_def                       <undefined>        <anything>
SC_def                       <undefined>        <any numeric>
SP_def                       <undefined>        <any numeric>
CF_def                       <undefined>        <anything>
                           
screen_cv                    <undefined>        Yes, No
screen_cv_def                No                 Yes, No
                           
screen_av                    <undefined>        Yes, No
screen_av_def                No                 Yes, No
                           
tag_alu                      <undefined>        Yes, No
tag_alu_def                  No                 Yes, No

find_mutants                 <undefined>        Yes, No
find_mutants_def             No                 No

WT_def                       <undefined>        <anything>

do_eba                       Yes                Yes, No

do_sort                      No                 Yes, No