Export the result sequence with the backbone sequence on double click

Export the result sequence with the backbone sequence on double click

There is a table with results has been implemented in UGENE-7278. Now this table should be improved.

When you double click on the result, this result should be exported to the other file. The result should contain the sequence of the corresponding region and the backbone sequence (it will be stored in PCRPrimerDesignForDNAAssemblyTask::backboneSequence, but, this class member may be empty - that means, that there is no backbone sequence).

Check "Select areas for priming search" -> "Insert to backbone bearings". If "5' insert to 5' backbone" is checked, then you should "connect" 5' end of direct strand of the insert (A, B1, B2 or B3 forward/reverse sequences, depends on which of them user clicks on) and 5' end of reverse-comlement strand of backbone (PCRPrimerDesignForDNAAssemblyTask::backboneSequence).

In the following examples the annotated inserts are highlighted with bold, the backbone is highlighted with underlined.

Example for A/B1/B2/B3 forward:

                              Direct:     5'     AC    3'
Insert:                                            —
                       Rev-compl:     3'     TG    5'

 

                               Direct:     5'     GT    3'
Backbone:                                      —
                       Rev-compl:      3'    CA    5'

                    

                               Direct:      5'     GT*AC*     3'
Result:                                            -------
                       Rev-compl:       3'    +CA+TG   5'

See the attached file "gfp_a_forward_primer.gb". Other examples are very similar, so I won't attach file for them.

 

Example for A/B1/B2/B3 reverse:

                              Direct:     5'     AC    3'
Insert:                                            —
                       Rev-compl:    3'     TG    5'

 

                               Direct:     5'     GT    3'
Backbone:                                     ---
                       Rev-compl:     3'     CA     5'

                    

                               Direct:      5'    AC+GT+    3'
Result:                                           ------
                       Rev-compl:      3'    *TG*CA    5'

 

Now, if "5' insert to 3' backbone" is checked, then you should "connect" 5' end of direct strand of the insert (A, B1, B2 or B3 forward/reverse sequences, depends on which of them user clicks on) and 3' end of direct strand of backbone (PCRPrimerDesignForDNAAssemblyTask::backboneSequence).

 

Example for A/B1/B2/B3 forward:

                              Direct:     5'     AC    3'
Insert:                                            —
                       Rev-compl:     3'     TG    5'

 

                               Direct:     5'     GT    3'
Backbone:                                      —
                       Rev-compl:      3'    CA    5'

                    

                               Direct:      5'    GTAC   3'
Result:                                           -------
                       Rev-compl:       3'    CATG   5'

 

Example for A/B1/B2/B3 reverse:

                              Direct:     5'     AC    3'
Insert:                                            —
                       Rev-compl:    3'     TG    5'

 

                               Direct:     5'     GT    3'
Backbone:                                     ---
                       Rev-compl:     3'     CA     5'

                    

                               Direct:      5'    ACGT    3'
Result:                                           ------
                       Rev-compl:      3'    TGCA    5'
 
 
In the result file should be in GenBank format and the backbone and the fragment should be marked as annotations (don't forget, that the reverse fragments should be annotated on the reverse-complement strand). The fragment should have the same name as in the result table, like "A forward", "B1 Reverse", etc. The Annotation Table should have name like "A Forward annotations", the annotation group name - "A Forward". Of course, if the other result is exported, the result file should have the corresponding marks (A Reverse, etc). The result file should have the name corresponding to the following template: ${ORIGINAL-FILE-NAME}_${FRAGMENT-NAME_IN_LOWER_CASE}_res.gb. Example: "gfp_a_forward_res.gb". The example of the result file you can find in the attachments.