Ingest: Derive url and use accession fields during ingest

ingest/defaults/config.yaml

@@ -45,8 +45,8 @@ curate:
   # The original field names should match the ncbi_datasets_fields provided above.
   # This is the first step in the pipeline, so any references to field names in the configs below should use the new field names
   field_map:
-    accession: genbank_accession
-    accession-rev: genbank_accession_rev
+    accession: accession
+    accession_version: accession_version
     isolate-lineage: strain
     sourcedb: database
     geo-region: region
@@ -62,7 +62,7 @@ curate:
   # Currently accepts any characters because we do not have a clear standard for strain names across pathogens
   strain_regex: '^.+$'
   # Back up strain name field to use if 'strain' doesn't match regex above
-  strain_backup_fields: ['genbank_accession']
+  strain_backup_fields: ['accession']
   # List of date fields to standardize to ISO format YYYY-MM-DD
   date_fields: ['date', 'release_date', 'update_date']
   # List of expected date formats that are present in the date fields provided above
@@ -89,15 +89,17 @@ curate:
   # The path should be relative to the ingest directory
   annotations: "defaults/annotations.tsv"
   # The ID field in the metadata to use to merge the manual annotations
-  annotations_id: 'genbank_accession'
+  annotations_id: 'accession'
   # The ID field in the metadata to use as the sequence id in the output FASTA file
-  output_id_field: 'genbank_accession'
+  output_id_field: 'accession'
   # The field in the NDJSON record that contains the actual genomic sequence
   output_sequence_field: 'sequence'
+  # The field in the NDJSON record that contains the actual GenBank accession
+  genbank_accession: 'accession'
   # The list of metadata columns to keep in the final output of the curation pipeline.
   metadata_columns: [
-    'genbank_accession',
-    'genbank_accession_rev',
+    'accession',
+    'accession_version',
     'strain',
     'date',
     'region',
@@ -111,4 +113,5 @@ curate:
     'sra_accessions',
     'authors',
     'institution',
+    'url',
   ]

ingest/rules/curate.smk

@@ -102,9 +102,30 @@ rule curate:
         """
 
 
+rule add_metadata_columns:
+    """Add columns to metadata
+    Notable columns:
+    - [NEW] url: URL linking to the NCBI GenBank record ('https://www.ncbi.nlm.nih.gov/nuccore/*').
+    """
+    input:
+        metadata = "data/all_metadata.tsv"
+    output:
+        metadata = temp("data/all_metadata_added.tsv")
+    params:
+        accession=config['curate']['genbank_accession']
+    shell:
+        """
+        csvtk mutate2 -t \
+          -n url \
+          -e '"https://www.ncbi.nlm.nih.gov/nuccore/" + ${params.accession}' \
+          {input.metadata} \
+        > {output.metadata}
+        """
+
+
 rule subset_metadata:
     input:
-        metadata="data/all_metadata.tsv",
+        metadata="data/all_metadata_added.tsv",
     output:
         subset_metadata="results/metadata.tsv",
     params:

ingest/rules/fetch_from_ncbi.smk

@@ -66,8 +66,8 @@ rule format_ncbi_dataset_report:
             --elide-header \
             | csvtk fix-quotes -Ht \
             | csvtk add-header -t -n {params.ncbi_datasets_fields:q} \
-            | csvtk rename -t -f accession -n accession-rev \
-            | csvtk -t mutate -f accession-rev -n accession -p "^(.+?)\." \
+            | csvtk rename -t -f accession -n accession_version \
+            | csvtk -t mutate -f accession_version -n accession -p "^(.+?)\." \
             | csvtk del-quotes -t \
             | tsv-select -H -f accession --rest last \
             > {output.ncbi_dataset_tsv}
@@ -89,7 +89,7 @@ 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_version \
             --seq-field sequence \
             --unmatched-reporting warn \
             --duplicate-reporting warn \

phylogenetic/example_data/metadata.tsv

@@ -1,35 +1,35 @@
-strain	virus	genbank_accession	date	region	country	division	city	db	segment	authors
-PAN/CDC_259359_V1_V3/2015	zika	KX156774	2015-12-18	North America	Panama	Panama	Panama	genbank	genome	Shabman et al
-COL/FLR_00024/2015	zika	MF574569	2015-12-XX	South America	Colombia	Colombia	Colombia	genbank	genome	Pickett et al
-PRVABC59	zika	KU501215	2015-12-XX	North America	Puerto Rico	Puerto Rico	Puerto Rico	genbank	genome	Lanciotti et al
-COL/FLR_00008/2015	zika	MF574562	2015-12-XX	South America	Colombia	Colombia	Colombia	genbank	genome	Pickett et al
-Colombia/2016/ZC204Se	zika	KY317939	2016-01-06	South America	Colombia	Colombia	Colombia	genbank	genome	Quick et al
-ZKC2/2016	zika	KX253996	2016-02-16	Oceania	American Samoa	American Samoa	American Samoa	genbank	genome	Wu et al
-VEN/UF_1/2016	zika	KX702400	2016-03-25	South America	Venezuela	Venezuela	Venezuela	genbank	genome	Blohm et al
-DOM/2016/BB_0059	zika	KY785425	2016-04-04	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al
-BRA/2016/FC_6706	zika	KY785433	2016-04-08	South America	Brazil	Brazil	Brazil	genbank	genome	Metsky et al
-DOM/2016/BB_0183	zika	KY785420	2016-04-18	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al
-EcEs062_16	zika	KX879603	2016-04-XX	South America	Ecuador	Ecuador	Ecuador	genbank	genome	Marquez et al
-HND/2016/HU_ME59	zika	KY785418	2016-05-13	North America	Honduras	Honduras	Honduras	genbank	genome	Metsky et al
-DOM/2016/MA_WGS16_011	zika	KY785484	2016-06-06	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al
-DOM/2016/BB_0433	zika	KY785441	2016-06-13	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al
-USA/2016/FL022	zika	KY075935	2016-07-22	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al
-SG_027	zika	KY241697	2016-08-27	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al
-SG_074	zika	KY241744	2016-08-28	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al
-SG_056	zika	KY241726	2016-08-28	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al
-USA/2016/FLUR022	zika	KY325473	2016-08-31	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al
-Aedes_aegypti/USA/2016/FL05	zika	KY075937	2016-09-09	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al
-SG_018	zika	KY241688	2016-09-13	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al
-USA/2016/FLWB042	zika	KY325478	2016-09-26	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al
-COL/PRV_00028/2015	zika	MF574578	2016-12-XX	South America	Colombia	Colombia	Colombia	genbank	genome	Pickett et al
-Thailand/1610acTw	zika	MF692778	2016-10-XX	Southeast Asia	Thailand	Thailand	Thailand	genbank	genome	Lin et al
-1_0087_PF	zika	KX447509	2013-12-XX	Oceania	French Polynesia	French Polynesia	French Polynesia	genbank	genome	Pettersson et al
-1_0199_PF	zika	KX447519	2013-11-XX	Oceania	French Polynesia	French Polynesia	French Polynesia	genbank	genome	Pettersson et al
-1_0181_PF	zika	KX447512	2013-12-XX	Oceania	French Polynesia	French Polynesia	French Polynesia	genbank	genome	Pettersson et al
-Brazil/2015/ZBRC301	zika	KY558995	2015-05-13	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al
-Brazil/2015/ZBRA105	zika	KY558989	2015-02-23	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al
-Brazil/2016/ZBRC16	zika	KY558991	2016-01-19	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al
-V8375	zika	KU501217	2015-11-01	North America	Guatemala	Guatemala	Guatemala	genbank	genome	Lanciotti et al
-Nica1_16	zika	KX421195	2016-01-19	North America	Nicaragua	Nicaragua	Nicaragua	genbank	genome	Tabata et al
-Brazil/2015/ZBRC303	zika	KY558997	2015-05-14	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al
-SMGC_1	zika	KX266255	2016-02-14	Oceania	American Samoa	American Samoa	American Samoa	genbank	genome	Bi et al
+strain	virus	accession	date	region	country	division	city	db	segment	authors	url
+PAN/CDC_259359_V1_V3/2015	zika	KX156774	2015-12-18	North America	Panama	Panama	Panama	genbank	genome	Shabman et al	https://www.ncbi.nlm.nih.gov/nuccore/KX156774
+COL/FLR_00024/2015	zika	MF574569	2015-12-XX	South America	Colombia	Colombia	Colombia	genbank	genome	Pickett et al	https://www.ncbi.nlm.nih.gov/nuccore/MF574569
+PRVABC59	zika	KU501215	2015-12-XX	North America	Puerto Rico	Puerto Rico	Puerto Rico	genbank	genome	Lanciotti et al	https://www.ncbi.nlm.nih.gov/nuccore/KU501215
+COL/FLR_00008/2015	zika	MF574562	2015-12-XX	South America	Colombia	Colombia	Colombia	genbank	genome	Pickett et al	https://www.ncbi.nlm.nih.gov/nuccore/MF574562
+Colombia/2016/ZC204Se	zika	KY317939	2016-01-06	South America	Colombia	Colombia	Colombia	genbank	genome	Quick et al	https://www.ncbi.nlm.nih.gov/nuccore/KY317939
+ZKC2/2016	zika	KX253996	2016-02-16	Oceania	American Samoa	American Samoa	American Samoa	genbank	genome	Wu et al	https://www.ncbi.nlm.nih.gov/nuccore/KX253996
+VEN/UF_1/2016	zika	KX702400	2016-03-25	South America	Venezuela	Venezuela	Venezuela	genbank	genome	Blohm et al	https://www.ncbi.nlm.nih.gov/nuccore/KX702400
+DOM/2016/BB_0059	zika	KY785425	2016-04-04	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al	https://www.ncbi.nlm.nih.gov/nuccore/KY785425
+BRA/2016/FC_6706	zika	KY785433	2016-04-08	South America	Brazil	Brazil	Brazil	genbank	genome	Metsky et al	https://www.ncbi.nlm.nih.gov/nuccore/KY785433
+DOM/2016/BB_0183	zika	KY785420	2016-04-18	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al	https://www.ncbi.nlm.nih.gov/nuccore/KY785420
+EcEs062_16	zika	KX879603	2016-04-XX	South America	Ecuador	Ecuador	Ecuador	genbank	genome	Marquez et al	https://www.ncbi.nlm.nih.gov/nuccore/KX879603
+HND/2016/HU_ME59	zika	KY785418	2016-05-13	North America	Honduras	Honduras	Honduras	genbank	genome	Metsky et al	https://www.ncbi.nlm.nih.gov/nuccore/KY785418
+DOM/2016/MA_WGS16_011	zika	KY785484	2016-06-06	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al	https://www.ncbi.nlm.nih.gov/nuccore/KY785484
+DOM/2016/BB_0433	zika	KY785441	2016-06-13	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al	https://www.ncbi.nlm.nih.gov/nuccore/KY785441
+USA/2016/FL022	zika	KY075935	2016-07-22	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al	https://www.ncbi.nlm.nih.gov/nuccore/KY075935
+SG_027	zika	KY241697	2016-08-27	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al	https://www.ncbi.nlm.nih.gov/nuccore/KY241697
+SG_074	zika	KY241744	2016-08-28	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al	https://www.ncbi.nlm.nih.gov/nuccore/KY241744
+SG_056	zika	KY241726	2016-08-28	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al	https://www.ncbi.nlm.nih.gov/nuccore/KY241726
+USA/2016/FLUR022	zika	KY325473	2016-08-31	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al	https://www.ncbi.nlm.nih.gov/nuccore/KY325473
+Aedes_aegypti/USA/2016/FL05	zika	KY075937	2016-09-09	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al	https://www.ncbi.nlm.nih.gov/nuccore/KY075937
+SG_018	zika	KY241688	2016-09-13	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al	https://www.ncbi.nlm.nih.gov/nuccore/KY241688
+USA/2016/FLWB042	zika	KY325478	2016-09-26	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al	https://www.ncbi.nlm.nih.gov/nuccore/KY325478
+COL/PRV_00028/2015	zika	MF574578	2016-12-XX	South America	Colombia	Colombia	Colombia	genbank	genome	Pickett et al	https://www.ncbi.nlm.nih.gov/nuccore/MF574578
+Thailand/1610acTw	zika	MF692778	2016-10-XX	Southeast Asia	Thailand	Thailand	Thailand	genbank	genome	Lin et al	https://www.ncbi.nlm.nih.gov/nuccore/MF692778
+1_0087_PF	zika	KX447509	2013-12-XX	Oceania	French Polynesia	French Polynesia	French Polynesia	genbank	genome	Pettersson et al	https://www.ncbi.nlm.nih.gov/nuccore/KX447509
+1_0199_PF	zika	KX447519	2013-11-XX	Oceania	French Polynesia	French Polynesia	French Polynesia	genbank	genome	Pettersson et al	https://www.ncbi.nlm.nih.gov/nuccore/KX447519
+1_0181_PF	zika	KX447512	2013-12-XX	Oceania	French Polynesia	French Polynesia	French Polynesia	genbank	genome	Pettersson et al	https://www.ncbi.nlm.nih.gov/nuccore/KX447512
+Brazil/2015/ZBRC301	zika	KY558995	2015-05-13	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al	https://www.ncbi.nlm.nih.gov/nuccore/KY558995
+Brazil/2015/ZBRA105	zika	KY558989	2015-02-23	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al	https://www.ncbi.nlm.nih.gov/nuccore/KY558989
+Brazil/2016/ZBRC16	zika	KY558991	2016-01-19	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al	https://www.ncbi.nlm.nih.gov/nuccore/KY558991
+V8375	zika	KU501217	2015-11-01	North America	Guatemala	Guatemala	Guatemala	genbank	genome	Lanciotti et al	https://www.ncbi.nlm.nih.gov/nuccore/KU501217
+Nica1_16	zika	KX421195	2016-01-19	North America	Nicaragua	Nicaragua	Nicaragua	genbank	genome	Tabata et al	https://www.ncbi.nlm.nih.gov/nuccore/KX421195
+Brazil/2015/ZBRC303	zika	KY558997	2015-05-14	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al	https://www.ncbi.nlm.nih.gov/nuccore/KY558997
+SMGC_1	zika	KX266255	2016-02-14	Oceania	American Samoa	American Samoa	American Samoa	genbank	genome	Bi et al	https://www.ncbi.nlm.nih.gov/nuccore/KX266255

phylogenetic/example_data/metadata_usvi.tsv

@@ -1,2 +1,2 @@
-genbank_accession	genbank_accession_rev	accession	strain	date	region	country	division	location	length	host	release_date	update_date	sra_accessions	authors	institution	url
-USVI/37/2016		VI37	USVI/37/2016	2016-10-06	North America	Usvi	Saint Croix	Saint Croix	10807	Homo sapiens				Black et al	FH	https://github.com/blab/zika-usvi/
+accession	accession_version	strain	date	region	country	division	location	length	host	release_date	update_date	sra_accessions	authors	institution	url
+VI37	VI37	USVI/37/2016	2016-10-06	North America	Usvi	Saint Croix	Saint Croix	10807	Homo sapiens				Black et al	FH	https://github.com/blab/zika-usvi/

phylogenetic/rules/merge_sequences_usvi.smk

@@ -21,35 +21,11 @@ This part of the workflow usually includes the following steps:
 
 """
 
-rule add_metadata_columns:
-    """Add columns to metadata
-
-    Notable columns:
-    - genbank_accession: GenBank accession for Auspice to generate a URL to the NCBI GenBank record.
-    - [NEW] accession: The GenBank accession. Added to go alongside USVI accession.
-    - [NEW] url: URL linking to the NCBI GenBank record ('https://www.ncbi.nlm.nih.gov/nuccore/*'). Added to go alongside USVI url.
-    """
-    input:
-        metadata = "data/metadata.tsv"
-    output:
-        metadata = "data/metadata_modified.tsv"
-    shell:
-        """
-        csvtk mutate2 -tl \
-          -n url \
-          -e '"https://www.ncbi.nlm.nih.gov/nuccore/" + $genbank_accession' \
-          {input.metadata} \
-        | csvtk mutate2 -tl \
-          -n accession \
-          -e '$genbank_accession' \
-        > {output.metadata}
-        """
-
 rule append_usvi:
     """Appending USVI sequences"""
     input:
         sequences = "data/sequences.fasta",
-        metadata = "data/metadata_modified.tsv",
+        metadata = "data/metadata.tsv",
         usvi_sequences = "data/sequences_usvi.fasta",
         usvi_metadata = "data/metadata_usvi.tsv"
     output: