                    EXAMPLE SOUTHERN BLOT PROBE DESIGN
                    ----------------------------------


1) CREATE DATABASE TABLES
2) CREATE PROBE SEARCH
3) RUN PROBE SEARCH
4) ANALYSE THE RESULTS
5) GET PROBE SEARCH CPU TIME                (OPTIONAL)
6) DELETE AN INDIVIDUAL SEARCH JOBS RESULTS (OPTIONAL)
7) DELETE A WHOLE PROBE SEARCH              (OPTIONAL)


WEB OUTPUT IS IN: southern_blot_design/docs/output



1) LINUX> ./create_probe_search_db_tables --host=host
 --user=user --pass=pass --db=southern_blot_design

Connected to mysql on: host, port 3306

Made table: 'conf'
Made table: 'external_db'
Made table: 'hit'
Made table: 'hit_xref'
Made table: 'job'
Made table: 'job_error'
Made table: 'job_sequence'
Made table: 'probe'
Made table: 'probe_sequence'
Made table: 'sequence'
Made table: 'sequence_hit'
Made table: 'xref'


2) LINUX> ./create_probe_search
 --config_file=create_probe_search_NCBI_m37.ini --probe_name=test
 --probe_description=testing --chromosome=2 --start=25209733
 --end=25212733 --end_bias=5prime

Ensembl database --
Connected to host: ensembldb.ensembl.org, as user: anonymous
Database         : mus_musculus_core_47_37

GeneTargeting analysis database --
Connected to host: host, as user: user
Database       : southern_blot_design

Stored genome ExternalDB     : mouse_NCBIM37 (with id: 1)
Stored exonerate search Conf : Exonerate mouse_NCBIM37 (with id: 1)

Coordinates checkout OK with chromosome length

Designing probe in this region:
REF              : Bio::EnsEMBL::Slice
name             : chromosome:NCBIM37:2:25209733:25212733:1
seq_region_name  : 2
seq_region_length: 181748087
strand           : 1
start            : 25209733
end              : 25212733
length           : 3001

Stored as DNAProbe 'test' (with id: 1)
Design window length: 3001
Designing sequences with 5' bias in window

Probe size: 1300, step size: 130
Probe size: 1250, step size: 125
Probe size: 1200, step size: 120
Probe size: 1150, step size: 115
Probe size: 1100, step size: 110
Probe size: 1050, step size: 105
Probe size: 1000, step size: 100
Probe size: 950, step size: 95
Probe size: 900, step size: 90
Probe size: 850, step size: 85
Probe size: 800, step size: 80
Probe size: 750, step size: 75
Probe size: 700, step size: 70
Probe size: 650, step size: 65
Probe size: 600, step size: 60
Probe size: 550, step size: 55
Probe size: 500, step size: 50

-----------------------------------------

Total jobs created: 23
Total sequences stored for searching: 458


3) LINUX> ./submit_probe_search --config_file=submit_probe_search.ini
  --probe_name=test

Connected to host: host, as user: user
Database       : southern_blot_design

Using GeneTargetingBaseDir: '/software/southern_blot_design'
Submission host ok : 'bc-16-1-01'
Using default queue: 'normal'
Using default lsf output dir: '/lsf_out'

Fetched 23 job ids for probe: 'test'
Job <225646> is submitted to queue <normal>.
Submitted job id=1
Job <225647> is submitted to queue <normal>.
Submitted job id=2
Job <225648> is submitted to queue <normal>.
Submitted job id=3
Job <225649> is submitted to queue <normal>.
<SNIP>
Submitted job id=20
Job <225666> is submitted to queue <normal>.
Submitted job id=21
Job <225667> is submitted to queue <normal>.
Submitted job id=22
Job <225668> is submitted to queue <normal>.
Submitted job id=23

Total skipped  : 0/23 jobs
Total submitted: 23/23 jobs


4) LINUX> ./analyse_probe_search --config_file=analyse_probe_search.ini
  --probe_name=test

./analyse_probe_search : Mon Aug 24 15:09:21 2009

GeneTargeting analysis database --
Connected to host: host, as user: user
Database       : southern_blot_design

Analysing probe: test
  assembly      : NCBIM37
  bias          : 5prime
  chromosome    : 2
  description   : testing
  end           : 25212733
  id            : 1
  name          : test
  start         : 25209733
  strand        : 1
  -------------
Generating image
  - done
Generating primers
Primer3 parameters used
------------------

  PRIMER_GC_CLAMP     : 1
  PRIMER_MAX_GC       : 50
  PRIMER_MAX_SIZE     : 22
  PRIMER_MAX_TM       : 60
  PRIMER_MIN_GC       : 40
  PRIMER_MIN_SIZE     : 20
  PRIMER_MIN_TM       : 55
  PRIMER_NUM_RETURN   : 5
  PRIMER_OPT_SIZE     : 21
  PRIMER_SALT_CONC    : 50
  -------------------
Wrote: /output/test_probe_search_primers.html
Wrote: /output/test_probe_search.html


5) LINUX> ./get_probe_search_cpu_time
  --config_file=get_probe_search_cpu_time.ini --probe_name=test

./get_probe_search_cpu_time : Mon Aug 24 15:13:24 2009

GeneTargeting analysis database --
Connected to host: host, as user: user
Database       : southern_blot_design

Total cpu time: 3011.4 sec.
Total cpu time: 0.8 hrs


6) LINUX> ./delete_job_results
  --config_file=delete_job_results.ini --job_id=1

GeneTargeting analysis database --
Connected to host: host, as user: user
Database       : southern_blot_design

Fetched job id=1,  state='success'
  - fetched 20 sequence ids
  - job state reset to 'created'


deleted_job_errors         : 0
deleted_sequence_hit_links : 33
fetched_sequences          : 20
jobs_processed             : 1


7) LINUX> ./delete_probe_search --config_file=delete_probe_search.ini
  --probe_name=test

GeneTargeting analysis database --
Connected to host: host, as user: user
Database       : southern_blot_design

Fetched 23 Jobs to be deleted

deleted_job_errors           : 0
deleted_job_sequence_links   : 458
deleted_jobs                 : 23
deleted_probe_sequence_links : 458
deleted_probes               : 1
deleted_sequence_hit_links   : 582
deleted_sequences            : 458
