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Revision as of 23:33, 13 February 2012 by Kyook (talk | contribs) (Created page with '==package dump script== tazendra /home/acedb/work/allele_phenotype/use_package.pl use_package.pl is a perl script that uses the perl module( ), to generate an error file and tw…')
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package dump script

tazendra /home/acedb/work/allele_phenotype/use_package.pl

use_package.pl is a perl script that uses the perl module( ), to generate an error file and two .ace files (since May 2011)- one for phenotypes and one for molecule-phenotype.


  • does not dump record when value in Curation status is "down right disgusted", this acts as our no dump toggle
  • when there is no value for phenotype -this will stop non-curated NBP data from being dumped
  • will dump if phenotype is present regardless of curator

requested changes


  • add a constraint - for rearrangement objects, dump all phenotype information except molecule values (molecule data should not be annotated for rearrangements so this is just a fail safe in case it does happen).
  • in addition to the varphene.ace output file, please output a separate file called mol_phene.ace, which contains:
  • molecule variation phenotype
  • molecule strain phenotype
  • molecule transgene phenotype


Add fields to OA - add to TAB2 at the bottom in the following order

  • rescued_by_transgene - multiontology from transgene tables, autocomplete on transgene name
  • legacy information - parsed from legacy data- all entries with [celegans] -
  • ease of scoring - drop down list
  • male mating efficiency - drop down list
  • hermaphrodite mating efficiency - drop down list

Add three more fields to dump script

  • mating_efficiency
    • lines with mating_efficiency values do not need a value in phenotype (app_phenotype)
    • should have value in curator, variation, person, mating efficiency
  • ease_of_scoring
  • rescued_by_transgene

--kjy 23:33, 13 February 2012 (UTC)

Phenotype OA postgres tables

postgres tables
app_allele_status app_finished_hst app_not_hst app_range_hst
app_allele_status_hst app_func app_obj_remark app_range_start
app_anat_term app_func_hst app_obj_remark_hst app_range_start_hst
app_anat_term_hst app_genotype app_paper app_remark
app_caused_by app_genotype_hst app_paper_hst app_rnai_brief
app_caused_by_hst app_go_sug app_paper_remark app_rnai_brief_hst
app_caused_by_other app_go_sug_hst app_paper_remark_hst app_species
app_caused_by_other_hst app_haplo app_pat_effect app_species_hst
app_child_of app_haplo_hst app_pat_effect_hst app_strain
app_child_of_hst app_heat_degree app_penetrance app_strain_hst
app_cold_degree app_heat_degree_hst app_penetrance_hst app_suggested
app_cold_degree_hst app_heat_sens app_percent app_suggested_definition
app_cold_sens app_heat_sens_hst app_percent_hst app_suggested_definition_hst
app_cold_sens_hst app_intx_desc app_person app_suggested_hst
app_control_isolate app_intx_desc_hst app_person_hst app_sug_ref
app_control_isolate_hst app_laboratory app_phenotype app_sug_ref_hst
app_curation_status app_laboratory_hst app_phenotype_hst app_temperature
app_curation_status_hst app_lifestage app_phen_remark app_temperature_hst
app_curator app_lifestage_hst app_phen_remark_hst app_tempname
app_curator_hst app_mat_effect app_preparation_hst app_tempname_hst
app_delivered app_mat_effect_hst app_quality app_term
app_delivered_hst app_molecule app_quality_hst app_term_hst
app_entity app_molecule_hst app_quantity app_treatment
app_entity_hst app_nature app_quantity_hst app_treatment_hst
app_filereaddate app_nature_hst app_quantity_remark app_type
app_filereaddate_hst app_nbp app_quantity_remark_hst app_type_hst
app_finalname app_nbp_hst app_range_end app_wbgene
app_finalname_hst app_not app_range_end_hst app_wbgene_hst