BlastLocalColumnSearch_subset.yaml

id: d35172ce-5e4b-945a-631d-14e47c9a1fc6
name: Blast Local Column Search (subset)
description: Performs a BLAST search of user selected databases using queries from a sequence column. Pre-configured BLAST databases can be downloaded from https://tinyurl.com/3d38p356
category: Biopolymer
version: 1.2.0
serviceName: BlastLocalColumnSearch
serviceUri: glysade.python
executorId: Glysade.CPythonDataFxn
inputFields:
- control:
    id: sequenceColumn
    label: Select sequence column
    type: columnselect
    filters:
    - dataType: string
      contentType:
      - chemical/x-sequence
    - dataType: binary
      contentType: chemical/x-genbank
    validationRules:
    - type: required
      message: Must select column of sequences
    limitByControlId: limitByField
  request:
    id: sequenceColumn
    dataType: string
    selectorType: column
- control:
    id: idColumn
    label: ID Column (optional)
    type: columnselect
    multi: !!bool false
    filters:
    - dataType:
      - string
      - int
      contentType: []
    tooltip: ID column is not required for Genbank encoded sequences
    limitByControlId: limitByField
  request:
    id: idColumn
    dataType: string
    selectorType: column
- control:
    id: method
    label: Select method
    type: select
    options:
    - text: 'BLASTP: protein(q)-protein(d)'
      value: BLASTP
    - text: 'BLASTN: nucleotide(q)-nucleotide(d)'
      value: BLASTN
    - text: 'BLASTX: nucleotide(q)+translation-protein(d)'
      value: BLASTX
    - text: 'TBLASTN: protein(q)-nucleotide(d)+translation'
      value: TBLASTN
    - text: 'TBLASTX: nucleotide(q)+translation-nucleotide(d)+translation'
      value: TBLASTX
    validationRules:
    - type: required
  request:
    id: method
    dataType: string
    data: BLASTP
- control:
    id: databaseName
    label: Select database
    type: select
    options:
    - text: Human NCBI NR
      value: human_nr
    - text: Human Uniprot SwissProt
      value: up_sp_human
    - text: Human Uniprot Trembl
      value: up_tbl_human
    - text: Human PDB
      value: human_pdbaa
    - text: Human Patented Proteins
      value: human_pataa
    - text: Human IG Germline (Proteins)
      value: human_IG_germline
    - text: Human NCBI NT
      value: human_nt
    - text: Human EBI ENA
      value: ena_cd_human
    - text: Human Patented Nucleotides
      value: human_patnt
    - text: Mouse NCBI NR
      value: mouse_nr
    - text: Mouse PDB
      value: mouse_pdbaa
    - text: Mouse Patented Proteins
      value: mouse_pataa
    - text: Mouse NCBI NT
      value: mouse_nt
    - text: Mouse Patented Nucleotides
      value: mouse_patnt
    - text: Rat NCBI NR
      value: rat_nr
    - text: Rat PDB
      value: rat_pdbaa
    - text: Rat Patented Proteins
      value: rat_pataa
    - text: Rat NCBI NT
      value: rat_nt
    - text: Rat Patented Nucleotides
      value: rat_patnt
    validationRules:
    - type: required
  request:
    id: databaseName
    dataType: string
- control:
    id: maxHits
    label: Max hits
    type: text
    validationRules:
    - type: required
      message: Must enter a value between 1 and 5000
    - type: range
      min: !!int 1
      max: !!int 5000
      message: Max hits must be a value between 1 and 5000
  request:
    id: maxHits
    dataType: integer
    data: !!int 100
- control:
    id: blastDbPath
    label: Directory containing BLAST databases
    type: file
    mode: path
    pathType: folder
    validationRules:
    - type: required
      message: ''
  request:
    id: blastDbPath
    dataType: string
    data: C:\db\ncbi
- control:
    id: limitByField
    label: Apply data function to
    type: limitby
  request:
  - id: limitByField
    dataType: string
    field: limitBy
    data: none
  - id: limitByFieldMarking
    dataType: string
    field: marking
tags:
- color: '#337abc'
  text: sequence
- color: '#f7cb2d'
  text: search
ironPython: |
  ####################################################
  #  Copyright 2022 Glysade LLC, All Rights Reserved #
  ####################################################

  import sys,clr
  from Spotfire.Dxp.Data import DataTable, DataManager
  from Spotfire.Dxp.Application import PanelTypeIdentifiers
  from Spotfire.Dxp.Application import Panel
  import Spotfire.Dxp.Application.PanelCollection

  from System import AppDomain
  for asm in AppDomain.CurrentDomain.GetAssemblies():
      if asm.GetName().Name == 'Charts':
          clr.AddReference(asm.FullName)

  from Charts import ChartsModel
  model_type = ChartsModel

  #tableId pass in args
  dataTable = ResultTables[0]

  if not dataTable:
      raise Exception('target table not found')

  page = Document.Pages.AddNew('Blast (local) column query Results')
  panelsToHide = [PanelTypeIdentifiers.DataPanel, PanelTypeIdentifiers.DetailsOnDemandPanel]

  for panel in page.Panels:
      if panel.TypeId in panelsToHide:
          if panel.Visible:
              panel.Visible = False

  filteringScheme = Document.FilteringSchemes[0]
  page.FilterPanel.FilteringSchemeReference = filteringScheme

  tableVis = page.Visuals.AddNew[model_type]()
  tableVis.SetKeyValue('visualization','table-visualization')
  tableVis.DataTable = dataTable
  tableVis.ConfigureColumns()
  tableVis.Marking = Document.Data.Markings.DefaultMarkingReference

  tableVis.SetActiveVisual()
  page.AutoConfigure()
updateBehavior: manual
maximumOutputColumns: !!int 0
maximumOutputTables: !!int 1
chemistryFunction: !!bool false
allowedClients:
- Analyst
demoUrl: https://youtu.be/v7leIlBaiz4
minimumChartsVersion: 4.4.0.0
confirmSubmit: