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Merge pull request #27 from common-workflow-language/custom-types
Custom Types Lesson
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‎_episodes/19-custom-types.md

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---
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title: "Custom Types"
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teaching: 10
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exercises: 0
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questions:
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- "How do I create and import my own custom types into a CWL description?"
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objectives:
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- "Learn how to write custom CWL object types."
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- "Learn how to import these custom objects into a tool description."
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keypoints:
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- "You can create your own custom types to load into descriptions."
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- "These custom types allow the user to configure the behaviour of a tool
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without tinkering directly with the tool description."
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- "Custom types are described in separate YAML files and imported as needed."
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---
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Sometimes you may want to write your own custom types for use and reuse in CWL
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descriptions. Use of such custom types can reduce redundancy between multiple
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descriptions that all use the same type, and also allow for additional
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customisation/configuration of a tool/analysis without the need to fiddle with
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the CWL description directly.
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The example below is a CWL description of the [InterProScan][ips] tool for
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simultaneously searching protein sequences against a wide variety of resources.
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It is a good example of a number of good practices in CWL.
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*custom-types.cwl*
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~~~
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{% include cwl/custom-types.cwl %}
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~~~
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{: .source}
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*custom-types.yml*
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~~~
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{% include cwl/custom-types.yml %}
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~~~
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{: .source}
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On line 34, in `inputs:applications`, a list of applications to be used in the
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search are imported as a custom object:
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```
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inputs:
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proteinFile:
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type: File
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inputBinding:
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prefix: --input
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applications:
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type: InterProScan-apps.yml#apps[]?
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inputBinding:
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itemSeparator: ','
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prefix: --applications
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```
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{: .source}
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The reference to a custom type is a combination of the name of the file in which
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the object is defined (`InterProScan-apps.yml`) and the name of the object
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within that file (`apps`) that defines the custom type. The square brackets `[]`
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mean that an array of the preceding type is expected, in this case the `apps`
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type from the imported `InterProScan-apps.yaml` file
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The contents of the YAML file describing the custom type are given below:
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~~~
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{% include cwl/InterProScan-apps.yml %}
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~~~
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{: .source}
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In order for the custom type to be used in the CWL description, it must be
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imported. Imports are described in `requirements:SchemaDefRequirement`, as
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below in the example `custom-types.cwl` description:
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```
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requirements:
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ResourceRequirement:
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ramMin: 10240
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coresMin: 3
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SchemaDefRequirement:
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types:
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- $import: InterProScan-apps.yml
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```
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{: .source}
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Note also that the author of this CWL description has also included
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`ResourceRequirement`s, specifying the minimum amount of RAM and number of cores
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required for the tool to run successfully, as well as details of the version of
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the software that the description was written for and other useful metadata.
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These features are discussed further in other chapters of this user guide.
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[ips]: https://github.com/ebi-pf-team/interproscan

‎_includes/cwl/InterProScan-apps.yml

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type: enum
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name: apps
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symbols:
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- TIGRFAM
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- SFLD
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- SUPERFAMILY
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- Gene3D
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- Hamap
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- Coils
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- ProSiteProfiles
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- SMART
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- CDD
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- PRINTS
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- PIRSF
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- ProSitePatterns
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- Pfam
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- ProDom
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- MobiDBLite

‎_includes/cwl/custom-types.cwl

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cwlVersion: v1.0
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class: CommandLineTool
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label: "InterProScan: protein sequence classifier"
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doc: |
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Version 5.21-60 can be downloaded here:
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https://github.com/ebi-pf-team/interproscan/wiki/HowToDownload
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Documentation on how to run InterProScan 5 can be found here:
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https://github.com/ebi-pf-team/interproscan/wiki/HowToRun
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requirements:
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ResourceRequirement:
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ramMin: 10240
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coresMin: 3
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SchemaDefRequirement:
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types:
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- $import: InterProScan-apps.yml
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hints:
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SoftwareRequirement:
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packages:
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interproscan:
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specs: [ "https://identifiers.org/rrid/RRID:SCR_005829" ]
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version: [ "5.21-60" ]
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inputs:
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proteinFile:
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type: File
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inputBinding:
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prefix: --input
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applications:
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type: InterProScan-apps.yml#apps[]?
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inputBinding:
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itemSeparator: ','
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prefix: --applications
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baseCommand: interproscan.sh
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arguments:
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- valueFrom: $(inputs.proteinFile.nameroot).i5_annotations
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prefix: --outfile
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- valueFrom: TSV
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prefix: --formats
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- --disable-precalc
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- --goterms
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- --pathways
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- valueFrom: $(runtime.tmpdir)
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prefix: --tempdir
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outputs:
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i5Annotations:
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type: File
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format: iana:text/tab-separated-values
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outputBinding:
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glob: $(inputs.proteinFile.nameroot).i5_annotations
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$namespaces:
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iana: https://www.iana.org/assignments/media-types/
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s: http://schema.org/
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$schemas:
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- https://schema.org/docs/schema_org_rdfa.html
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s:license: "https://www.apache.org/licenses/LICENSE-2.0"
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s:copyrightHolder: "EMBL - European Bioinformatics Institute"

‎_includes/cwl/custom-types.yml

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proteinFile:
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class: File
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path: test_proteins.fasta

‎_includes/cwl/test_proteins.fasta

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>Q97R95
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MKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALG
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FKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQAL
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SVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNS
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DPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICSSLKSDS
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MIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWVDKGAAEALSQYGKSLLLSGI
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VEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDMLRSQKAKGVLIYRDDWISITP
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EIQLLFTEF
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>A2VDN9
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MEVKGKKKLTGKGTKMSQEKSKFHKNNDSGSSKTFPKKVVKEGGPKITSKNFEKTATKPGKKGVKQFKNKQQGDRIPKNK
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FQQANKFNQKRKFQPDSKSDESAAKKPKWDEFKKKKKELKQSRQLSDKTNYDIVIRAKQIWEILRRKDCDKEKRVKLMSD
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LQKLIQGKIKTIAFAHDSTRVIQCYIQFGNEEQRKQAFEELRGDLVELSKAKYSRNIVKKFLMYGSKAQIAEIIRSFKGH
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VRKLLRHAEASAIVEYAYNDKAILEQRNMLTEELYGNTFQLYKSADHPTLDKVLEVQPEKLELIMDEMKQILTPMAQKEA
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VIKHSLVHKVFLDFFTYAPPKLRSEMIEAIREAVVYLAHTHDGARVAMYCLWHGTPKDRKVIVKTMKTYIEKVANGQYSH
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LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEVLQKGDGNAHSKKDTEIRRRE
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LLESISPALLSYLQGHAQEVVLDKSACVLVADILGTATGDVQPAMDAVASLAAAELHPGGKDGELHIAEHPAGHLVLKWL
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IEQDKKMKERGREGCFAKTLIERVGVKNLKSWASVNRGAIILSSLLQSSDQEVANKVKAGLKSLIPALEKSKNTSKGIEM
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LLEKLTA
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>A2YIW7
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MAAEEGVVIACHNKDEFDAQMTKAKEAGKVVIIDFTASWCGPCRFIAPVFAEYAKKFPGAVFLKVDVDELKEVAEKYNVE
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AMPTFLFIKDGAEADKVVGARKDDLQNTIVKHVGATAASASA
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>P22298
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GRGLLPFVLLALGIXAPWAVEGAENALKGGACPPRKIVQCLRYEKPKCTSDWQCPDKKKC
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CRDTCAIKCLNPVAITNPVKVKPGKCPVVYGQCMMLNPPNHCKTDSQCLGDLKCCKSMCG
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KVCLTPVKA
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>A0B6J9
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MSKIGKSIRLERIIDRKTRKTVIVPMDHGLTVGPIPGLIDLAAAVDKVAEGGANAVLGHM
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GLPLYGHRGYGKDVGLIIHLSASTSLGPDANHKVLVTRVEDAIRVGADGVSIHVNVGAED
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EAEMLRDLGMVARRCDLWGMPLLAMMYPRGAKVRSEHSVEYVKHAARVGAELGVDIVKTN
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YTGSPETFREVVRGCPAPVVIAGGPKMDTEADLLQMVYDAMQAGAAGISIGRNIFQAENP
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TLLTRKLSKIVHEGYTPEEAARLKL
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>P02939
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MNRTKLVLGAVILGSTLLAGCSSNAKIDQLSTDVQTLNAKVDQLSNDVTAIRSDVQAAKD
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DAARANQRLDNQAHSYRK

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