fixup: NCBI Dataset field name transformations

nextstrain · Dec 5, 2023 · 95ac6fd · 95ac6fd
1 parent 870c938
commit 95ac6fd
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Showing 4 changed files with 106 additions and 137 deletions.
diff --git a/ingest/config/config.yaml b/ingest/config/config.yaml
@@ -2,8 +2,27 @@
 sources: ['genbank']
 # Pathogen NCBI Taxonomy ID
 ncbi_taxon_id: '64320'
-# Renames the NCBI dataset headers
-ncbi_field_map: 'source-data/ncbi-dataset-field-map.tsv'
+# The list of NCBI Datasets fields to include from NCBI Datasets output
+# These need to be the mneumonics of the NCBI Datasets fields, see docs for full list of fields
+# https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_virus-genome/#fields
+# Note: the "accession" field MUST be provided to match with the sequences
+ncbi_datasets_fields:
+  - accession
+  - sourcedb
+  - sra-accs
+  - isolate-lineage
+  - geo-region
+  - geo-location
+  - isolate-collection-date
+  - release-date
+  - update-date
+  - length
+  - host-name
+  - isolate-lineage-source
+  - biosample-acc
+  - submitter-names
+  - submitter-affiliation
+  - submitter-country
 
 # Params for the transform rule
 transform:

diff --git a/ingest/source-data/ncbi-dataset-field-map.tsv b/ingest/source-data/ncbi-dataset-field-map.tsv
diff --git a/ingest/workflow/snakemake_rules/fetch_sequences.smk b/ingest/workflow/snakemake_rules/fetch_sequences.smk
@@ -44,56 +44,23 @@ rule extract_ncbi_dataset_sequences:
         """
 
 
-def _get_ncbi_dataset_field_mnemonics(wildcards) -> str:
-    """
-    Return list of NCBI Dataset report field mnemonics for fields that we want
-    to parse out of the dataset report. The column names in the output TSV
-    are different from the mnemonics.
-
-    See NCBI Dataset docs for full list of available fields and their column
-    names in the output:
-    https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_virus-genome/#fields
-    """
-    fields = [
-        "accession",
-        "sourcedb",
-        "isolate-lineage",
-        "geo-region",
-        "geo-location",
-        "isolate-collection-date",
-        "release-date",
-        "update-date",
-        "length",
-        "host-name",
-        "isolate-lineage-source",
-        "bioprojects",
-        "biosample-acc",
-        "sra-accs",
-        "submitter-names",
-        "submitter-affiliation",
-    ]
-    return ",".join(fields)
-
-
 rule format_ncbi_dataset_report:
     # Formats the headers to match the NCBI mnemonic names
     input:
         dataset_package="data/ncbi_dataset.zip",
-        ncbi_field_map=config["ncbi_field_map"],
     output:
         ncbi_dataset_tsv=temp("data/ncbi_dataset_report.tsv"),
     params:
-        fields_to_include=_get_ncbi_dataset_field_mnemonics,
+        ncbi_datasets_fields=",".join(config["ncbi_datasets_fields"]),
     benchmark:
         "benchmarks/format_ncbi_dataset_report.txt"
     shell:
         """
         dataformat tsv virus-genome \
             --package {input.dataset_package} \
-            --fields {params.fields_to_include:q} \
-            | csvtk -tl rename2 -F -f '*' -p '(.+)' -r '{{kv}}' -k {input.ncbi_field_map} \
-            | csvtk -tl mutate -f accession-rev -n accession -p "^(.+?)\." \
-            | tsv-select -H -f accession --rest last \
+            --fields {params.ncbi_datasets_fields:q} \
+            --elide-header \
+            | csvtk add-header -t -n {params.ncbi_datasets_fields:q} \
             > {output.ncbi_dataset_tsv}
         """
 
@@ -113,7 +80,7 @@ rule format_ncbi_datasets_ndjson:
         augur curate passthru \
             --metadata {input.ncbi_dataset_tsv} \
             --fasta {input.ncbi_dataset_sequences} \
-            --seq-id-column accession-rev \
+            --seq-id-column accession \
             --seq-field sequence \
             --unmatched-reporting warn \
             --duplicate-reporting warn \

diff --git a/phylogenetic/config/dropped_strains.txt b/phylogenetic/config/dropped_strains.txt
@@ -1,87 +1,87 @@
-MG827392
-KX369547 # PF13/251013_18 # reference included in config/zika_reference.gb
-KY553111 # AFMC_U # too basal
-KY962729 # AFMC_S # too basal
-KY120353 # Boracay/16423 # too basal
-KU179098 # JMB_185 # too basal
-KU681082 # PHL/2012/CPC_0740 # too basal
+MG827392.1
+KX369547.1 # PF13/251013_18 # reference included in config/zika_reference.gb
+KY553111.1 # AFMC_U # too basal
+KY962729.1 # AFMC_S # too basal
+KY120353.1 # Boracay/16423 # too basal
+KU179098.1 # JMB_185 # too basal
+KU681082.1 # PHL/2012/CPC_0740 # too basal
 VIE/Bra/2016 # too basal
-KU853013 # Dominican_Republic/2016/PD2 # duplicate of other strain in dataset
-KU740184 # GD01 # duplicate of other strain in dataset
-KU761564 # GDZ16001 # duplicate of other strain in dataset
-KX893855 # VEN/UF_2/2016 # duplicate of other strain in dataset
-KY927808 # ZZ_1 # duplicate of other strain in dataset
-KY003154 # VR10599/Pavia/2016 # export with unknown origin
-KY003153 # 34997/Pavia/2016 # export with unknown origin
-MF574552 # COL/FLR_00001/2015 # duplicate of COL/FLR/2015
-MF574559 # COL/FLR_00002/2015 # duplicate of COL/FLR/2015
-MF574560 # COL/FLR_00003/2015 # duplicate of COL/FLR/2015
-MF574561 # COL/FLR_00004/2015 # duplicate of COL/FLR/2015
-MF574571 # COL/FLR_00005/2015 # duplicate of COL/FLR/2015
-MF574555 # COL/FLR_00006/2015 # duplicate of COL/FLR/2015
-MF574557 # COL/FLR_00007/2015 # duplicate of COL/FLR/2015
-MF574562 # COL/FLR_00008/2015 # duplicate of COL/FLR/2015
-MF574572 # COL/FLR_00009/2015 # duplicate of COL/FLR/2015
-MF574570 # COL/FLR_00010/2015 # duplicate of COL/FLR/2015
-MF574565 # COL/FLR_00011/2015 # duplicate of COL/FLR/2015
-MF574568 # COL/FLR_00012/2015 # duplicate of COL/FLR/2015
-MF574558 # COL/FLR_00013/2015 # duplicate of COL/FLR/2015
-MF574576 # COL/FLR_00014/2015 # duplicate of COL/FLR/2015
-MF574567 # COL/FLR_00015/2015 # duplicate of COL/FLR/2015
-MF574575 # COL/FLR_00016/2015 # duplicate of COL/FLR/2015
-MF574553 # COL/FLR_00017/2015 # duplicate of COL/FLR/2015
-MF574573 # COL/FLR_00018/2015 # duplicate of COL/FLR/2015
-MF574574 # COL/FLR_00019/2015 # duplicate of COL/FLR/2015
-MF574577 # COL/FLR_00020/2015 # duplicate of COL/FLR/2015
-MF574556 # COL/FLR_00021/2015 # duplicate of COL/FLR/2015
-MF574554 # COL/FLR_00022/2015 # duplicate of COL/FLR/2015
-MF574566 # COL/FLR_00023/2015 # duplicate of COL/FLR/2015
-MF574569 # COL/FLR_00024/2015 # duplicate of COL/FLR/2015
-MF574563 # COL/FLR_00025/2015 # duplicate of COL/FLR/2015
-MF574564 # COL/FLR_00026/2015 # duplicate of COL/FLR/2015
-MF574581 # COL/FLR_00034/2015 # duplicate of COL/FLR/2015
-MF574588 # COL/FLR_00035/2015 # duplicate of COL/FLR/2015
-MF574582 # COL/FLR_00036/2015 # duplicate of COL/FLR/2015
-MF574586 # COL/FLR_00038/2015 # duplicate of COL/FLR/2015
-MF574584 # COL/FLR_00040/2015 # duplicate of COL/FLR/2015
-MF574583 # COL/FLR_00041/2015 # duplicate of COL/FLR/2015
-MF574580 # COL/FLR_00042/2015 # duplicate of COL/FLR/2015
-MF574579 # COL/PRV_00027/2015 # misdated
-MF574578 # COL/PRV_00028/2015 # misdated
-MF574585 # COL/PAN_00029/2015 # misdated
-MF574587 # COL/PAN_00030/2015 # misdated
-KY785436 # BRA/2016/FC_DQ12D1 # large indel
-KY559010 # Brazil/2016/ZBRX8 # large indel
-KY559011 # Brazil/2016/ZBRX11 # large indel
-KX986761 # CX17 # large indel
-MF801405 # MEX/2016/mex27 # large indel
-MF801424 # MEX/2016/mex50 # large indel
-MF801377 # SLV/2016/ElSalvador_1055 # large indel
+KU853013.1 # Dominican_Republic/2016/PD2 # duplicate of other strain in dataset
+KU740184.1 # GD01 # duplicate of other strain in dataset
+KU761564.1 # GDZ16001 # duplicate of other strain in dataset
+KX893855.1 # VEN/UF_2/2016 # duplicate of other strain in dataset
+KY927808.1 # ZZ_1 # duplicate of other strain in dataset
+KY003154.1 # VR10599/Pavia/2016 # export with unknown origin
+KY003153.1 # 34997/Pavia/2016 # export with unknown origin
+MF574552.1 # COL/FLR_00001/2015 # duplicate of COL/FLR/2015
+MF574559.1 # COL/FLR_00002/2015 # duplicate of COL/FLR/2015
+MF574560.1 # COL/FLR_00003/2015 # duplicate of COL/FLR/2015
+MF574561.1 # COL/FLR_00004/2015 # duplicate of COL/FLR/2015
+MF574571.1 # COL/FLR_00005/2015 # duplicate of COL/FLR/2015
+MF574555.1 # COL/FLR_00006/2015 # duplicate of COL/FLR/2015
+MF574557.1 # COL/FLR_00007/2015 # duplicate of COL/FLR/2015
+MF574562.1 # COL/FLR_00008/2015 # duplicate of COL/FLR/2015
+MF574572.1 # COL/FLR_00009/2015 # duplicate of COL/FLR/2015
+MF574570.1 # COL/FLR_00010/2015 # duplicate of COL/FLR/2015
+MF574565.1 # COL/FLR_00011/2015 # duplicate of COL/FLR/2015
+MF574568.1 # COL/FLR_00012/2015 # duplicate of COL/FLR/2015
+MF574558.1 # COL/FLR_00013/2015 # duplicate of COL/FLR/2015
+MF574576.1 # COL/FLR_00014/2015 # duplicate of COL/FLR/2015
+MF574567.1 # COL/FLR_00015/2015 # duplicate of COL/FLR/2015
+MF574575.1 # COL/FLR_00016/2015 # duplicate of COL/FLR/2015
+MF574553.1 # COL/FLR_00017/2015 # duplicate of COL/FLR/2015
+MF574573.1 # COL/FLR_00018/2015 # duplicate of COL/FLR/2015
+MF574574.1 # COL/FLR_00019/2015 # duplicate of COL/FLR/2015
+MF574577.1 # COL/FLR_00020/2015 # duplicate of COL/FLR/2015
+MF574556.1 # COL/FLR_00021/2015 # duplicate of COL/FLR/2015
+MF574554.1 # COL/FLR_00022/2015 # duplicate of COL/FLR/2015
+MF574566.1 # COL/FLR_00023/2015 # duplicate of COL/FLR/2015
+MF574569.1 # COL/FLR_00024/2015 # duplicate of COL/FLR/2015
+MF574563.1 # COL/FLR_00025/2015 # duplicate of COL/FLR/2015
+MF574564.1 # COL/FLR_00026/2015 # duplicate of COL/FLR/2015
+MF574581.1 # COL/FLR_00034/2015 # duplicate of COL/FLR/2015
+MF574588.1 # COL/FLR_00035/2015 # duplicate of COL/FLR/2015
+MF574582.1 # COL/FLR_00036/2015 # duplicate of COL/FLR/2015
+MF574586.1 # COL/FLR_00038/2015 # duplicate of COL/FLR/2015
+MF574584.1 # COL/FLR_00040/2015 # duplicate of COL/FLR/2015
+MF574583.1 # COL/FLR_00041/2015 # duplicate of COL/FLR/2015
+MF574580.1 # COL/FLR_00042/2015 # duplicate of COL/FLR/2015
+MF574579.1 # COL/PRV_00027/2015 # misdated
+MF574578.1 # COL/PRV_00028/2015 # misdated
+MF574585.1 # COL/PAN_00029/2015 # misdated
+MF574587.1 # COL/PAN_00030/2015 # misdated
+KY785436.1 # BRA/2016/FC_DQ12D1 # large indel
+KY559010.1 # Brazil/2016/ZBRX8 # large indel
+KY559011.1 # Brazil/2016/ZBRX11 # large indel
+KX986761.1 # CX17 # large indel
+MF801405.1 # MEX/2016/mex27 # large indel
+MF801424.1 # MEX/2016/mex50 # large indel
+MF801377.1 # SLV/2016/ElSalvador_1055 # large indel
 VI20_12plex # USVI/20/2016 # large indel
 USVI/21/2016 # large indel
 VI23_12plex # USVI/23/2016 # large indel
 VI27_1d # USVI/27/2016 # large indel
 VI30_1d # USVI/30/2016 # large indel
 VI32_12plex # USVI/32/2016 # large indel
-KY126351 # Thailand/1605aTw # excess divergence
-KU744693 # VE_Ganxian # excess divergence
-KY328290 # ZK_YN001 # excess divergence
-KY415986 # Haiti/0029/2014 # contamination present
-KY415987 # Haiti/0033/2014 # contamination present
-KY415990 # Haiti/0036/2014 # contamination present
-KY415988 # Haiti/0054/2014 # contamination present
-KY415989 # Haiti/0074/2014 # contamination present
-KY415991 # Haiti/0097/2014 # contamination present
-MF384325 # mosquito/Haiti/1682/2016 # contamination present
-ZF36_36S # contamination present
-MK105975 # MR766 # lab strain
-KX856011 # Aedes_sp/MEX_I_44/2016 # duplicate of Aedes_aegypti/MEX/MEX_I_44/2016
-MK028857 # Puerto_Rico/2015/PRVABC59 # duplicate of PRVABC59
-MN025403 # V15555 # highly diverged
-MT505349 # DK # lab strain
-MT505350 # DK23 # lab strain
-MW680969 # rGZ02a/2018 # highly diverged
-MW680970 # rGZ02p/2018 # highly diverged
-OK054351 # V211784 # highly diverged
-MT478034 # LMM/AG5643
-OL414716 # Faranah/18
+KY126351.1 # Thailand/1605aTw # excess divergence
+KU744693.1 # VE_Ganxian # excess divergence
+KY328290.1 # ZK_YN001 # excess divergence
+KY415986.1 # Haiti/0029/2014 # contamination present
+KY415987.1 # Haiti/0033/2014 # contamination present
+KY415990.1 # Haiti/0036/2014 # contamination present
+KY415988.1 # Haiti/0054/2014 # contamination present
+KY415989.1 # Haiti/0074/2014 # contamination present
+KY415991.1 # Haiti/0097/2014 # contamination present
+MF384325.1 # mosquito/Haiti/1682/2016 # contamination present
+ZF36_36S.1 # contamination present
+MK105975.1 # MR766 # lab strain
+KX856011.1 # Aedes_sp/MEX_I_44/2016 # duplicate of Aedes_aegypti/MEX/MEX_I_44/2016
+MK028857.1 # Puerto_Rico/2015/PRVABC59 # duplicate of PRVABC59
+MN025403.1 # V15555 # highly diverged
+MT505349.1 # DK # lab strain
+MT505350.1 # DK23 # lab strain
+MW680969.1 # rGZ02a/2018 # highly diverged
+MW680970.1 # rGZ02p/2018 # highly diverged
+OK054351.1 # V211784 # highly diverged
+MT478034.1 # LMM/AG5643
+OL414716.1 # Faranah/18