CroMaSt: A workflow for assessing protein domain classification by cross-mapping of structural instances between domain databases and structural alignment

public public 1yr ago Version: v1.1 0 bookmarks
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cromast-a-workflow-for-assessing-protein-domain-cl
cromast-a-workflow-for-assessing-protein-domain-cl
cromast-a-workflow-for-assessing-protein-domain-cl
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CroMaSt: A workflow for assessing protein domain classification by cross-mapping of structural instances between domain databases and structural alignment CroMaSt ( Cro ss Ma pper of domain St ructural instances) is an automated iterative workflow to clarify the assignment of protein domains to a given domain type of interest, based on their 3D structure and by cross-mapping of domain structural instances between domain databases. CroMaSt (for Cross-Mapper of domain Structural instances) will classify all structural instances of a given domain type into 4 different categories ( Core , True , Domain-like , and Failed ).

Code Snippets

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- entryname: add_crossmapped2resmapped.py
  entry:
    $include: Python/add_crossmapped2resmapped.py
  writable: false
CWL From line 27 of Tools/add_crossmapped2resmapped.cwl 
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baseCommand:
  - python3
  - add_crossmapped2resmapped.py
CWL From line 98 of Tools/add_crossmapped2resmapped.cwl 
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- entryname: check_threshold.py
  entry:
    $include: Python/check_threshold.py
  writable: false
CWL From line 14 of Tools/check_threshold.cwl 
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baseCommand:
  - python3
  - check_threshold.py
CWL From line 99 of Tools/check_threshold.cwl 
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- entryname: compare_cath_pfam.py
  entry:
    $include: Python/compare_cath_pfam.py
  writable: false
CWL From line 22 of Tools/compare_cath_pfam.cwl 
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baseCommand:
- python3
- compare_cath_pfam.py
CWL From line 98 of Tools/compare_cath_pfam.cwl 
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- entryname: runtime_parm.json
  entry: |-
    {
    "filename": $(inputs.fam_tracker),
    "true_domain_file": $(inputs.true_domains),
    "core_domain_struct": $(inputs.core_domain_struct),
    "crossmap_pfam": $(inputs.crossmap_pfam),
    "crossmap_cath": $(inputs.crossmap_cath),
    "domain_like": $(inputs.domain_like),
    "failed_domain": $(inputs.failed_domains),
    "parm_file": $(inputs.in_paramfile),
    "pfam_lost_structs": $(inputs.pfam_lost),
    "cath_lost_structs": $(inputs.cath_lost)
    }
CWL From line 14 of Tools/create_param.cwl 
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- entryname: create_param.py
  entry:
    $include: Python/create_param.py
  writable: false
CWL From line 35 of Tools/create_param.cwl 
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baseCommand:
  - python3
  - create_param.py
CWL From line 116 of Tools/create_param.cwl 
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- entryname: get_family_ids.py
  entry:
    $include: Python/get_family_ids.py
  writable: false
CWL From line 24 of Tools/get_family_ids.cwl 
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baseCommand:
  - python3
  - get_family_ids.py
CWL From line 70 of Tools/get_family_ids.cwl 
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- entryname: list_true_domains.py
  entry: |-
    #!/usr/bin/env python3
    import json
    all_data = json.load(open('$(inputs.infile.path)', 'r'))
    new = [all_data["0"][a]['$(inputs.database)'] for a in all_data["0"]]
    tmp_dict = {"core": new}
    with open('$(inputs.outfile)', "w") as f:
        json.dump(tmp_dict, f, indent=2)
  writable: false
CWL JSON From line 21 of Tools/list_true_domains.cwl 
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baseCommand:
  - python3
  - list_true_domains.py
CWL From line 59 of Tools/list_true_domains.cwl 
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- entryname: map_unique_struct_cath2pfam.py
  entry:
    $include: Python/map_unique_struct_cath2pfam.py
  writable: false
CWL From line 28 of Tools/map_unique_struct_cath2pfam.cwl 
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baseCommand:
- python3
- map_unique_struct_cath2pfam.py
CWL From line 99 of Tools/map_unique_struct_cath2pfam.cwl 
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- entryname: map_unique_struct_pfam2cath.py
  entry:
    $include: Python/map_unique_struct_pfam2cath.py
  writable: false
CWL From line 28 of Tools/map_unique_struct_pfam2cath.cwl 
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baseCommand:
- python3
- map_unique_struct_pfam2cath.py
CWL From line 98 of Tools/map_unique_struct_pfam2cath.cwl 
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- entryname: merge_unmapped.py
  entry:
    $include: Python/merge_df2json.py
  writable: false
CWL From line 22 of Tools/merge_df2json.cwl 
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baseCommand:
  - python3
  - merge_unmapped.py
CWL From line 78 of Tools/merge_df2json.cwl 
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- entryname: pairwise_aligner.py
  entry:
    $include: Python/pairwise_aligner.py
  writable: false
CWL From line 21 of Tools/pairwise_aligner.cwl 
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baseCommand:
  - python3
  - pairwise_aligner.py
CWL From line 94 of Tools/pairwise_aligner.cwl
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/HrishiDhondge/CroMaSt.git
Name: cromast-a-workflow-for-assessing-protein-domain-cl
Version: v1.1
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Copyright: Public Domain
License: MIT License
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