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base repository: FDA-ARGOS/data.argosdb
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base: v1.1
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head repository: FDA-ARGOS/data.argosdb
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compare: v1.2
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  • 8 commits
  • 88 files changed
  • 3 contributors

Commits on Feb 7, 2023

  1. update assembly_qc_ncbi_.py 

    Also created assemblyQC_ncbi_all.tsv
    @HadleyKing
    HadleyKing committed Feb 7, 2023
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  2. Fixes #162

    @kerchner @HadleyKing
    kerchner authored and HadleyKing committed Feb 7, 2023
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  3. ngsQC_NCBI.tsv 

    Fix #144
	new file:   lib/add_lineage.py
	modified:   lib/efetch_bioproject_runs.sh
	modified:   lib/eutils_SRAcurl_experiments.sh
	new file:   lib/get_linage.py
	deleted:    lib/linage.py
	new file:   lib/sra_run_info_parser.py
    @HadleyKing
    HadleyKing committed Feb 7, 2023
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  4. Add ngsQC to data_files 

    Fix #144
	new file:   data_files/ngsQC_NCBI.tsv
    @HadleyKing
    HadleyKing committed Feb 7, 2023
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  5. Sort assemblyQC_ncbi 

    Changes to be committed:
    @HadleyKing
    HadleyKing committed Feb 7, 2023
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  6. ngsQC_ncbi_update 

    	modified:   data_files/assemblyQC_NCBI.tsv
	new file:   data_files/assemblyQC_NCBI_orig.tsv
	deleted:    data_files/assemblyQC_ncbi_all.tsv
	modified:   data_files/ngsQC_NCBI.tsv
    @HadleyKing
    HadleyKing committed Feb 7, 2023
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  7. update NCBI files 

    Fix #144
Fix #145
Changes to be committed:
	modified:   data_files/assemblyQC_NCBI.tsv
	modified:   data_files/ngsQC_NCBI.tsv
    @HadleyKing
    HadleyKing committed Feb 7, 2023
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  8. V1.2 (#205) 

    * update assembly_qc_ncbi_.py
Also created assemblyQC_ncbi_all.tsv

* T124 biosample meta (#191)

* resolved merge conflict

* revert in order to facilitate rebasing

* Repair after rebase

* Adding README

* revert in order to facilitate rebasing

* More forgiving xpath

* Fix for #131

Changes to be committed:
	deleted:    Untitled Diagram.drawio
	new file:   data_files/draft_galaxy_BCO_example.json
	new file:   data_files/extsion_example.json
	modified:   lib/galaxy_converter.py
	deleted:    test.tsv

* Improved documentation for galaxy_converter
Changes to be committed:
	new file:   data_files/final_galaxy_bco_result.json
	modified:   lib/galaxy_converter.py

* Remove failing CI actions

* resolved merge conflict

* revert in order to facilitate rebasing

* Repair after rebase

* Adding README

* revert in order to facilitate rebasing

* More forgiving xpath

* Assembly QC Data flow

1st piece for #135

Changes to be committed:
	new file:   docs/DataFlow.pptx
	new file:   docs/DataFlow_assemblyQC_NCBI.pdf

* Loop through a text file of biosample ids, create a single TSV file

* Added lineage grab; reordered tsv columns to adhere to schema v1.0

Co-authored-by: [email protected] <[email protected]>

* Fixes #162

* ngsQC_NCBI.tsv

Fix #144
	new file:   lib/add_lineage.py
	modified:   lib/efetch_bioproject_runs.sh
	modified:   lib/eutils_SRAcurl_experiments.sh
	new file:   lib/get_linage.py
	deleted:    lib/linage.py
	new file:   lib/sra_run_info_parser.py

* Add ngsQC to data_files

Fix #144
	new file:   data_files/ngsQC_NCBI.tsv

* Sort assemblyQC_ncbi
Changes to be committed:

* ngsQC_ncbi_update
	modified:   data_files/assemblyQC_NCBI.tsv
	new file:   data_files/assemblyQC_NCBI_orig.tsv
	deleted:    data_files/assemblyQC_ncbi_all.tsv
	modified:   data_files/ngsQC_NCBI.tsv

* update NCBI files

Fix #144
Fix #145
Changes to be committed:
	modified:   data_files/assemblyQC_NCBI.tsv
	modified:   data_files/ngsQC_NCBI.tsv

* Ngs qc ncbi update (#202)

* ngsQC_NCBI.tsv

Fix #144
	new file:   lib/add_lineage.py
	modified:   lib/efetch_bioproject_runs.sh
	modified:   lib/eutils_SRAcurl_experiments.sh
	new file:   lib/get_linage.py
	deleted:    lib/linage.py
	new file:   lib/sra_run_info_parser.py

* Add ngsQC to data_files

Fix #144
	new file:   data_files/ngsQC_NCBI.tsv

* Sort assemblyQC_ncbi
Changes to be committed:

* ngsQC_ncbi_update
	modified:   data_files/assemblyQC_NCBI.tsv
	new file:   data_files/assemblyQC_NCBI_orig.tsv
	deleted:    data_files/assemblyQC_ncbi_all.tsv
	modified:   data_files/ngsQC_NCBI.tsv

* update NCBI files

Fix #144
Fix #145
Changes to be committed:
	modified:   data_files/assemblyQC_NCBI.tsv
	modified:   data_files/ngsQC_NCBI.tsv

* 1st commit
	new file:   data_dictionary/v1.2/README.txt
	new file:   data_dictionary/v1.2/core_property_list.txt
	new file:   data_dictionary/v1.2/non-core_property_list.txt
	new file:   data_dictionary/v1.2/property_definition.txt
	new file:   data_dictionary/v1.2/release_notes.txt

* Run schema generation

For #201
Changes to be committed:
	renamed:    data_dictionary/v1.2/README.txt -> data_dictionary/v1.2/README.tsv
	new file:   data_dictionary/v1.2/core_property_list.tsv
	deleted:    data_dictionary/v1.2/core_property_list.txt
	new file:   data_dictionary/v1.2/non-core_property_list.tsv
	deleted:    data_dictionary/v1.2/non-core_property_list.txt
	renamed:    data_dictionary/v1.2/property_definition.txt -> data_dictionary/v1.2/property_definition.tsv
	renamed:    data_dictionary/v1.2/release_notes.txt -> data_dictionary/v1.2/release_notes.tsv
	new file:   schema/v1.2/core/assemblyQC.json
	new file:   schema/v1.2/core/assemblyQC_NCBI.json
	new file:   schema/v1.2/core/biosampleMeta.json
	new file:   schema/v1.2/core/ngsQC.json
	new file:   schema/v1.2/core/ngsQC_NCBI.json
	new file:   schema/v1.2/core/siteQC.json
	new file:   schema/v1.2/non-core/SRA_biosample.json
	new file:   schema/v1.2/non-core/ngs_ID_list.json
	new file:   schema/v1.2/non-core/sars-cov-2_lineage_mutations.json
	new file:   schema/v1.2/non-core/uniprot-proteome_*.json

* Testing data files

* Testign data files
Changes to be committed:
	new file:   tests/v1.1/test_files/NC_045512_SARS-CoV-2_Wuhan.fasta
	new file:   tests/v1.1/test_files/PRJNA231221_AssemblyUpdated.tsv
	new file:   tests/v1.1/test_files/SRA_biosample.tsv
	new file:   tests/v1.1/test_files/SRA_ngsQC.tsv
	new file:   tests/v1.1/test_files/UP000001014_99287.fasta
	new file:   tests/v1.1/test_files/UP000001014_99287_DNA.fasta
	new file:   tests/v1.1/test_files/UP000009255_211044.fasta
	new file:   tests/v1.1/test_files/UP000009255_211044_DNA.fasta
	new file:   tests/v1.1/test_files/UP000009255_proteome_genome_metadata.csv
	new file:   tests/v1.1/test_files/UP000180448_33727.fasta
	new file:   tests/v1.1/test_files/UP000180448_33727_DNA.fasta
	new file:   tests/v1.1/test_files/UP000464024_2697049.fasta
	new file:   tests/v1.1/test_files/UP000464024_2697049_DNA.fasta
	new file:   tests/v1.1/test_files/assemblyQC-Pond.tsv
	new file:   tests/v1.1/test_files/assemblyQC_HL.tsv
	new file:   tests/v1.1/test_files/assemblyQC_NCBI.tsv
	new file:   tests/v1.1/test_files/biosampleMeta-Crandall.tsv
	new file:   tests/v1.1/test_files/biosampleMeta_HL.tsv
	new file:   tests/v1.1/test_files/core_property_list.tsv
	new file:   tests/v1.1/test_files/ngsQC_Crandall.tsv
	new file:   tests/v1.1/test_files/ngsQC_HL.tsv
	new file:   tests/v1.1/test_files/ngs_id_list.tsv
	new file:   tests/v1.1/test_files/non-core_property_list.tsv
	new file:   tests/v1.1/test_files/property_definition.tsv
	new file:   tests/v1.1/test_files/sars-cov-2_lineage_mutations.tsv
	new file:   tests/v1.1/test_files/siteQC_HL.tsv
	new file:   tests/v1.1/test_files/uniprot-proteome_UP000001014.csv
	new file:   tests/v1.1/test_files/uniprot-proteome_UP000180448.csv
	new file:   tests/v1.1/test_files/uniprot-proteome_UP000464024.csv

---------

Co-authored-by: [email protected] <[email protected]>
    @HadleyKing @kerchner
    HadleyKing and kerchner authored Feb 7, 2023
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