From ad34fa3f00b3db63b9174b6d09ffdf8c7f5169ec Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Fri, 19 Jan 2024 11:53:01 -0800 Subject: [PATCH 1/7] Move fetch_sequences.smk to fetch_from_ncbi.smk This is a more accurate name for the rule, since it fetches from NCBI and matches the pathogen-repo-template/ingest/ncbi_fetch_sequences.smk rule. --- ingest/Snakefile | 2 +- ingest/rules/{fetch_sequences.smk => fetch_from_ncbi.smk} | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) rename ingest/rules/{fetch_sequences.smk => fetch_from_ncbi.smk} (94%) diff --git a/ingest/Snakefile b/ingest/Snakefile index fb26cc1..8c916ce 100644 --- a/ingest/Snakefile +++ b/ingest/Snakefile @@ -54,7 +54,7 @@ rule all: _get_all_targets, -include: "rules/fetch_sequences.smk" +include: "rules/fetch_from_ncbi.smk" include: "rules/transform.smk" diff --git a/ingest/rules/fetch_sequences.smk b/ingest/rules/fetch_from_ncbi.smk similarity index 94% rename from ingest/rules/fetch_sequences.smk rename to ingest/rules/fetch_from_ncbi.smk index 2fef4b1..c775819 100644 --- a/ingest/rules/fetch_sequences.smk +++ b/ingest/rules/fetch_from_ncbi.smk @@ -7,6 +7,10 @@ defined in the config. If adding other sources, add a new rule upstream of rule `fetch_all_sequences` to create the file `data/{source}.ndjson` or the file must exist as a static file in the repo. +Fetch with NCBI Datasets (https://www.ncbi.nlm.nih.gov/datasets/) + - requires `ncbi_taxon_id` config + - Only returns metadata fields that are available through NCBI Datasets + Produces final output as sequences_ndjson = "data/sequences.ndjson" From 01154842e7559a8e771b28c363a3b28d9d529cf1 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Fri, 19 Jan 2024 16:51:33 -0800 Subject: [PATCH 2/7] Move transform.smk to curate.smk This matches the pathogen-repo-template/ingest/rules/curate.smk --- ingest/Snakefile | 2 +- ingest/config/defaults.yaml | 4 +- ingest/rules/{transform.smk => curate.smk} | 44 +++++++++++----------- 3 files changed, 25 insertions(+), 25 deletions(-) rename ingest/rules/{transform.smk => curate.smk} (66%) diff --git a/ingest/Snakefile b/ingest/Snakefile index 8c916ce..a99870a 100644 --- a/ingest/Snakefile +++ b/ingest/Snakefile @@ -55,7 +55,7 @@ rule all: include: "rules/fetch_from_ncbi.smk" -include: "rules/transform.smk" +include: "rules/curate.smk" if config.get("upload", False): diff --git a/ingest/config/defaults.yaml b/ingest/config/defaults.yaml index e7bd353..9610676 100644 --- a/ingest/config/defaults.yaml +++ b/ingest/config/defaults.yaml @@ -24,8 +24,8 @@ ncbi_datasets_fields: - submitter-affiliation - submitter-country -# Params for the transform rule -transform: +# Params for the curate rule +curate: # NCBI fields to rename to Nextstrain field names. # This is the first step in the pipeline, so any references to field names # in the configs below should use the new field names diff --git a/ingest/rules/transform.smk b/ingest/rules/curate.smk similarity index 66% rename from ingest/rules/transform.smk rename to ingest/rules/curate.smk index 2860fdd..6fedbbd 100644 --- a/ingest/rules/transform.smk +++ b/ingest/rules/curate.smk @@ -1,5 +1,5 @@ """ -This part of the workflow handles transforming the data into standardized +This part of the workflow handles curating the data into standardized formats and expects input file sequences_ndjson = "data/sequences.ndjson" @@ -9,7 +9,7 @@ This will produce output files as metadata = "results/metadata.tsv" sequences = "results/sequences.fasta" -Parameters are expected to be defined in `config.transform`. +Parameters are expected to be defined in `config.curate`. """ @@ -17,7 +17,7 @@ rule fetch_general_geolocation_rules: output: general_geolocation_rules="data/general-geolocation-rules.tsv", params: - geolocation_rules_url=config["transform"]["geolocation_rules_url"], + geolocation_rules_url=config["curate"]["geolocation_rules_url"], shell: """ curl {params.geolocation_rules_url} > {output.general_geolocation_rules} @@ -27,7 +27,7 @@ rule fetch_general_geolocation_rules: rule concat_geolocation_rules: input: general_geolocation_rules="data/general-geolocation-rules.tsv", - local_geolocation_rules=config["transform"]["local_geolocation_rules"], + local_geolocation_rules=config["curate"]["local_geolocation_rules"], output: all_geolocation_rules="data/all-geolocation-rules.tsv", shell: @@ -36,32 +36,32 @@ rule concat_geolocation_rules: """ -rule transform: +rule curate: input: sequences_ndjson="data/sequences.ndjson", all_geolocation_rules="data/all-geolocation-rules.tsv", - annotations=config["transform"]["annotations"], + annotations=config["curate"]["annotations"], output: metadata="results/metadata.tsv", sequences="results/sequences.fasta", log: - "logs/transform.txt", + "logs/curate.txt", params: - field_map=config["transform"]["field_map"], - strain_regex=config["transform"]["strain_regex"], - strain_backup_fields=config["transform"]["strain_backup_fields"], - date_fields=config["transform"]["date_fields"], - expected_date_formats=config["transform"]["expected_date_formats"], - articles=config["transform"]["titlecase"]["articles"], - abbreviations=config["transform"]["titlecase"]["abbreviations"], - titlecase_fields=config["transform"]["titlecase"]["fields"], - authors_field=config["transform"]["authors_field"], - authors_default_value=config["transform"]["authors_default_value"], - abbr_authors_field=config["transform"]["abbr_authors_field"], - annotations_id=config["transform"]["annotations_id"], - metadata_columns=config["transform"]["metadata_columns"], - id_field=config["transform"]["id_field"], - sequence_field=config["transform"]["sequence_field"], + field_map=config["curate"]["field_map"], + strain_regex=config["curate"]["strain_regex"], + strain_backup_fields=config["curate"]["strain_backup_fields"], + date_fields=config["curate"]["date_fields"], + expected_date_formats=config["curate"]["expected_date_formats"], + articles=config["curate"]["titlecase"]["articles"], + abbreviations=config["curate"]["titlecase"]["abbreviations"], + titlecase_fields=config["curate"]["titlecase"]["fields"], + authors_field=config["curate"]["authors_field"], + authors_default_value=config["curate"]["authors_default_value"], + abbr_authors_field=config["curate"]["abbr_authors_field"], + annotations_id=config["curate"]["annotations_id"], + metadata_columns=config["curate"]["metadata_columns"], + id_field=config["curate"]["id_field"], + sequence_field=config["curate"]["sequence_field"], shell: """ (cat {input.sequences_ndjson} \ From 5b1369ed9c32084ffcfb8f36bece33c89ab971a9 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Fri, 19 Jan 2024 17:09:42 -0800 Subject: [PATCH 3/7] ingest/curate: Make the field map config more user friendly Incorporating changes from the pathogen repo template: * https://github.com/nextstrain/pathogen-repo-template/commit/5e1b1efd30fc9875980fea4bb956877fec12af5c --- ingest/config/defaults.yaml | 31 ++++++++++++++++--------------- ingest/rules/curate.smk | 9 ++++++++- 2 files changed, 24 insertions(+), 16 deletions(-) diff --git a/ingest/config/defaults.yaml b/ingest/config/defaults.yaml index 9610676..41c3432 100644 --- a/ingest/config/defaults.yaml +++ b/ingest/config/defaults.yaml @@ -27,23 +27,24 @@ ncbi_datasets_fields: # Params for the curate rule curate: # NCBI fields to rename to Nextstrain field names. + # List of field names to change where the key is the original field name and + # the value is the new field name # 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', - 'isolate-lineage=strain', - 'sourcedb=database', - 'geo-region=region', - 'geo-location=location', - 'host-name=host', - 'isolate-collection-date=date', - 'release-date=release_date', - 'update-date=update_date', - 'sra-accs=sra_accessions', - 'submitter-names=authors', - 'submitter-affiliations=institution', - ] + field_map: + accession: genbank_accession + accession-rev: genbank_accession_rev + isolate-lineage: strain + sourcedb: database + geo-region: region + geo-location: location + host-name: host + isolate-collection-date: date + release-date: release_date + update-date: update_date + sra-accs: sra_accessions + submitter-names: authors + submitter-affiliations: institution # Standardized strain name regex # Currently accepts any characters because we do not have a clear standard for strain names strain_regex: '^.+$' diff --git a/ingest/rules/curate.smk b/ingest/rules/curate.smk index 6fedbbd..dee2813 100644 --- a/ingest/rules/curate.smk +++ b/ingest/rules/curate.smk @@ -36,6 +36,13 @@ rule concat_geolocation_rules: """ +def format_field_map(field_map: dict[str, str]) -> str: + """ + Format dict to `"key1"="value1" "key2"="value2"...` for use in shell commands. + """ + return " ".join([f'"{key}"="{value}"' for key, value in field_map.items()]) + + rule curate: input: sequences_ndjson="data/sequences.ndjson", @@ -47,7 +54,7 @@ rule curate: log: "logs/curate.txt", params: - field_map=config["curate"]["field_map"], + field_map=format_field_map(config["curate"]["field_map"]), strain_regex=config["curate"]["strain_regex"], strain_backup_fields=config["curate"]["strain_backup_fields"], date_fields=config["curate"]["date_fields"], From 446047e8d748527566961b956a9a1148866a0765 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Mon, 22 Jan 2024 12:00:55 -0800 Subject: [PATCH 4/7] Harmonize ingest/config/defaults.yaml with the pathogen repo template https://github.com/nextstrain/pathogen-repo-template/blob/b8ae886b25877a218ad50380fb44f8825d50aedb/ingest/config/defaults.yaml --- ingest/config/defaults.yaml | 73 ++++++++++++++++++++----------------- ingest/rules/curate.smk | 5 +-- 2 files changed, 41 insertions(+), 37 deletions(-) diff --git a/ingest/config/defaults.yaml b/ingest/config/defaults.yaml index 41c3432..10ada38 100644 --- a/ingest/config/defaults.yaml +++ b/ingest/config/defaults.yaml @@ -1,7 +1,15 @@ +# This configuration file should contain all required configuration parameters +# for the ingest workflow to run to completion. +# +# Define optional config parameters with their default values here so that users +# do not have to dig through the workflows to figure out the default values + # Sources of sequences to include in the ingest run sources: ['genbank'] -# Pathogen NCBI Taxonomy ID -ncbi_taxon_id: '64320' + +# Required to fetch from NCBI Datasets +ncbi_taxon_id: "64320" + # 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 @@ -24,13 +32,18 @@ ncbi_datasets_fields: - submitter-affiliation - submitter-country -# Params for the curate rule +# Config parameters related to the curate pipeline curate: - # NCBI fields to rename to Nextstrain field names. - # List of field names to change where the key is the original field name and - # the value is the new field name - # This is the first step in the pipeline, so any references to field names - # in the configs below should use the new field names + # URL pointed to public generalized geolocation rules + # For the Nextstrain team, this is currently + # 'https://raw.githubusercontent.com/nextstrain/ncov-ingest/master/source-data/gisaid_geoLocationRules.tsv' + geolocation_rules_url: 'https://raw.githubusercontent.com/nextstrain/ncov-ingest/master/source-data/gisaid_geoLocationRules.tsv' + # The path to the local geolocation rules within the pathogen repo + # The path should be relative to the ingest directory. + local_geolocation_rules: 'config/geolocation-rules.tsv' + # List of field names to change where the key is the original field name and the value is the new field name + # 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 @@ -46,47 +59,40 @@ curate: submitter-names: authors submitter-affiliations: institution # Standardized strain name regex - # Currently accepts any characters because we do not have a clear standard for strain names + # Currently accepts any characters because we do not have a clear standard for strain names across pathogens strain_regex: '^.+$' - # Back up strain name field if 'strain' doesn't match regex above + # Back up strain name field to use if 'strain' doesn't match regex above strain_backup_fields: ['genbank_accession'] - # List of date fields to standardize + # List of date fields to standardize to ISO format YYYY-MM-DD date_fields: ['date', 'release_date', 'update_date'] - # Expected date formats present in date fields + # List of expected date formats that are present in the date fields provided above # These date formats should use directives expected by datetime # See https://docs.python.org/3.9/library/datetime.html#strftime-and-strptime-format-codes expected_date_formats: ['%Y', '%Y-%m', '%Y-%m-%d', '%Y-%m-%dT%H:%M:%SZ'] - # Titlecase rules titlecase: - # Abbreviations not cast to titlecase, keeps uppercase + # List of string fields to titlecase + fields: ['region', 'country', 'division', 'location'] + # List of abbreviations not cast to titlecase, keeps uppercase abbreviations: ['USA'] # Articles that should not be cast to titlecase articles: [ 'and', 'd', 'de', 'del', 'des', 'di', 'do', 'en', 'l', 'la', 'las', 'le', 'los', 'nad', 'of', 'op', 'sur', 'the', 'y' ] - # List of string fields to titlecase - fields: ['region', 'country', 'division', 'location'] - # Authors field name + # Metadata field that contains the list of authors associated with the sequence authors_field: 'authors' - # Authors default value if authors value is empty + # Default value to use if the authors field is empty authors_default_value: '?' - # Field name for the generated abbreviated authors - abbr_authors_field: 'abbr_authors' - # General geolocation rules to apply to geolocation fields - geolocation_rules_url: 'https://raw.githubusercontent.com/nextstrain/ncov-ingest/master/source-data/gisaid_geoLocationRules.tsv' - # Local geolocation rules that are only applicable to zika data - # Local rules can overwrite the general geolocation rules provided above - local_geolocation_rules: 'config/geolocation-rules.tsv' - # User annotations file - annotations: 'config/annotations.tsv' - # ID field used to merge annotations + # Path to the manual annotations file + # The path should be relative to the ingest directory + annotations: "config/annotations.tsv" + # The ID field in the metadata to use to merge the manual annotations annotations_id: 'genbank_accession' - # Field to use as the sequence ID in the FASTA file - id_field: 'genbank_accession' - # Field to use as the sequence in the FASTA file - sequence_field: 'sequence' - # Final output columns for the metadata TSV + # The ID field in the metadata to use as the sequence id in the output FASTA file + output_id_field: 'genbank_accession' + # The field in the NDJSON record that contains the actual genomic sequence + output_sequence_field: 'sequence' + # The list of metadata columns to keep in the final output of the curation pipeline. metadata_columns: [ 'genbank_accession', 'genbank_accession_rev', @@ -104,4 +110,3 @@ curate: 'authors', 'institution', ] - diff --git a/ingest/rules/curate.smk b/ingest/rules/curate.smk index dee2813..f278fec 100644 --- a/ingest/rules/curate.smk +++ b/ingest/rules/curate.smk @@ -64,11 +64,10 @@ rule curate: titlecase_fields=config["curate"]["titlecase"]["fields"], authors_field=config["curate"]["authors_field"], authors_default_value=config["curate"]["authors_default_value"], - abbr_authors_field=config["curate"]["abbr_authors_field"], annotations_id=config["curate"]["annotations_id"], metadata_columns=config["curate"]["metadata_columns"], - id_field=config["curate"]["id_field"], - sequence_field=config["curate"]["sequence_field"], + id_field=config["curate"]["output_id_field"], + sequence_field=config["curate"]["output_sequence_field"], shell: """ (cat {input.sequences_ndjson} \ From 19c825971621637f3038f32679b37c82ced517b3 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Fri, 19 Jan 2024 17:23:03 -0800 Subject: [PATCH 5/7] More specific naming: merging in USVI sequences --- phylogenetic/Snakefile | 2 +- phylogenetic/rules/{usvi.smk => merge_sequences_usvi.smk} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename phylogenetic/rules/{usvi.smk => merge_sequences_usvi.smk} (100%) diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile index d40f00e..da7fdd9 100644 --- a/phylogenetic/Snakefile +++ b/phylogenetic/Snakefile @@ -4,8 +4,8 @@ rule all: input: auspice_json = "auspice/zika.json", -include: "rules/usvi.smk" include: "rules/prepare_sequences.smk" +include: "rules/merge_sequences_usvi.smk" include: "rules/construct_phylogeny.smk" include: "rules/annotate_phylogeny.smk" include: "rules/export.smk" diff --git a/phylogenetic/rules/usvi.smk b/phylogenetic/rules/merge_sequences_usvi.smk similarity index 100% rename from phylogenetic/rules/usvi.smk rename to phylogenetic/rules/merge_sequences_usvi.smk From 540f32d276db724b1dabdc12a6897ffbe8c81440 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Mon, 22 Jan 2024 11:41:50 -0800 Subject: [PATCH 6/7] Move USVI data to the data folder Document provenance of the USVI data that is merged into the Zika live site. --- phylogenetic/data/README.md | 101 + phylogenetic/data/metadata_usvi.tsv | 26 + phylogenetic/data/sequences_usvi.fasta | 4530 +++++++++++++++++ .../profiles/ci/copy_example_data.smk | 3 +- phylogenetic/rules/merge_sequences_usvi.smk | 47 +- 5 files changed, 4679 insertions(+), 28 deletions(-) create mode 100644 phylogenetic/data/README.md create mode 100644 phylogenetic/data/metadata_usvi.tsv create mode 100644 phylogenetic/data/sequences_usvi.fasta diff --git a/phylogenetic/data/README.md b/phylogenetic/data/README.md new file mode 100644 index 0000000..4de29fa --- /dev/null +++ b/phylogenetic/data/README.md @@ -0,0 +1,101 @@ +# Zika Data + +The primary source of data for this build is GenBank. However, there are instances where certain records, crucial for phylogenetic analysis, are not yet present in GenBank. This is particularly true for some USVI records, as detailed in a previous analysis documented at https://github.com/blab/zika-usvi/. + +### Integration of USVI data + +This Zika build incorporates data from https://github.com/blab/zika-usvi/. The sequences and metadata for USVI from that GitHub repository have undergone curation and were uploaded to https://github.com/nextstrain/fauna. Subsequently, they were downloaded as sequences and metadata, and a filter was applied to include only those records not yet submitted to NCBI GenBank. The resulting records are now available as a pair of metadata and sequences files in this directory. + +The process of merging the USVI data into the GenBank dataset is facilitated through the `append_usvi` rule. + +Steps to create the `metadata_usvi.tsv` and `sequences_usvi.fasta` files were as follows: + +1. Sequences were uploaded to the fauna database following [these instructions](https://github.com/nextstrain/fauna/blob/f9e7955cb4381d5e881c337e005778ed43b7c56c/builds/ZIKA.md#fred-hutch-sequences). +2. Sequences were downloaded from the fauna database following [these instructions](https://github.com/nextstrain/fauna/blob/5d5a1f3faf06805a5f31e91df2c76b06e6f3bf6a/builds/ZIKA.md#download-from-fauna-parse-compress-and-push-to-s3) and saved as `zika.fasta` +3. Sequences were ingested from GenBank following [these instructions](../README.md) and saved as `sequences.fasta` +4. [NCBI Blastn](https://www.ncbi.nlm.nih.gov/books/NBK279690/) was used to identify fauna sequences that were not one hundred percent identical to GenBank sequences using the following commnads: + + +```bash +GENBANK_SEQUENCES=sequences.fasta +FAUNA_SEQUENCES=zika.fasta + +# Create a local blast database +makeblastdb \ +  -in ${GENBANK_SEQUENCES} \   +  -dbtype nucl + +# Blast fauna against GenBank +blastn \ + -db ${GENBANK_SEQUENCES} \ + -query ${FAUNA_SEQUENCES} \ + -num_alignments 1 \ + -outfmt 6 \ + -out blast_output.txt + +# USVI strains that +# + match at 100% +# + match at least a 5000nt region (to filter out short substring matches) +cat blast_output.txt \ +| awk -F'\t' '$1~"USVI" && $3>=100 && $4>5000 , OFS="\t" {print $1}' \ +> USVI_100_match.txt + +less USVI_100_match.txt +# USVI/5/2016|zika|MW165881|2016-10-17|north_america|usvi|saint_thomas|saint_thomas|genbank|genome|Santiago +# USVI/43/2016|zika|MW165884|2016-07-19|north_america|usvi|saint_thomas|saint_thomas|genbank|genome|Santiago +# USVI/4/2016|zika|MW165880|2016-10-14|north_america|usvi|saint_thomas|saint_thomas|genbank|genome|Santiago +# USVI/35/2016|zika|MW165883|2016-09-08|north_america|usvi|saint_thomas|saint_thomas|genbank|genome|Santiago +# USVI/25/2016|zika|MW165882|2016-09-27|north_america|usvi|saint_thomas|saint_thomas|genbank|genome|Santiago + +# USVI strains that are not in the 100 match list +cat blast_output.txt \ +| awk -F'\t' '$1~"USVI" , OFS="\t" {print}' \ +| grep -Fvf USVI_100_match.txt \ +| awk -F'\t' '{print $1}' \ +| sort \ +| uniq \ +> USVI_not_match.txt + +head USVI_not_match.txt +# USVI/1/2016|zika|VI1_1d|2016-09-28|north_america|usvi|saint_croix|saint_croix|fh|genome|Black +# USVI/11/2016|zika|VI11|2016-03-22|north_america|usvi|saint_thomas|saint_thomas|fh|genome|Black +# USVI/12/2016|zika|VI12|2016-11-04|north_america|usvi|saint_croix|saint_croix|fh|genome|Black +# USVI/13/2016|zika|VI13|2016-08-13|north_america|usvi|saint_thomas|saint_thomas|fh|genome|Black +# USVI/19/2016|zika|VI19_12plex|2016-11-21|north_america|usvi|saint_croix|saint_croix|fh|genome|Black +# ... +``` + +5. Pull out the corresponding `metadata_usvi.tsv` and `sequences_usvi.fasta` using a combination of [smof](https://github.com/incertae-sedis/smof) and [augur parse](https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/parse.html) + +```bash +# Pulls out sequences based on a match against header strings +smof grep -f USVI_not_match.txt zika.fasta > usvi.fasta + +# Splits file into metadata_usvi.tsv and sequences_usvi.fasta +augur parse \ + --sequences usvi.fasta \ + --output-sequences sequences_usvi.fasta \ + --output-metadata raw_metadata_usvi.tsv \ + --fields strain virus accession date region country division location institution segment authors url title journal paper_url \ + --prettify-fields region country division location + +augur parse \ + --sequences usvi.fasta \ + --output-sequences sequences_usvi.fasta \ + --output-metadata no.tsv \ + --fields a b strain c d e f g h i j k l m n + +# Add sequence lengths to metadata +echo "accession|length" | tr '|' '\t' > lengths_usvi.tsv +smof stat --length --byseq sequences_usvi.fasta >> lengths_usvi.tsv + +tsv-join -H \ + --filter-file lengths_usvi.tsv\ + --key-fields accession \ + --append-fields length \ + raw_metadata_usvi.tsv \ + | tsv-select -H \ + --fields accession,strain,date,region,country,division,location,length,authors,institution,url \ + > metadata_usvi.tsv +``` + diff --git a/phylogenetic/data/metadata_usvi.tsv b/phylogenetic/data/metadata_usvi.tsv new file mode 100644 index 0000000..b790dae --- /dev/null +++ b/phylogenetic/data/metadata_usvi.tsv @@ -0,0 +1,26 @@ +accession strain date region country division location length authors institution url +VI44 USVI/44/2016 2016-10-17 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI20_12plex USVI/20/2016 2016-10-13 North America Usvi Saint Croix Saint Croix 10792 Black et al fh https://github.com/blab/zika-usvi/ +VI41 USVI/41/2016 2016-11-10 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI32_12plex USVI/32/2016 2016-08-11 North America Usvi Saint Croix Saint Croix 10792 Black et al fh https://github.com/blab/zika-usvi/ +VI12 USVI/12/2016 2016-11-04 North America Usvi Saint Croix Saint Croix 10636 Black et al fh https://github.com/blab/zika-usvi/ +VI46 USVI/46/2016 2016-07-15 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI23_12plex USVI/23/2016 2016-07-12 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI28_1d USVI/28/2016 2016-11-28 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI45 USVI/45/2016 2016-08-03 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI37 USVI/37/2016 2016-10-06 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI39_12plex USVI/39/2016 2016-11-09 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI36 USVI/36/2016 2016-09-13 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI34 USVI/34/2016 2016-08-01 North America Usvi Saint Thomas Saint Thomas 10792 Black et al fh https://github.com/blab/zika-usvi/ +VI11 USVI/11/2016 2016-03-22 North America Usvi Saint Thomas Saint Thomas 10636 Black et al fh https://github.com/blab/zika-usvi/ +VI6 USVI/6/2016 2016-10-19 North America Usvi Saint John Saint John 10636 Black et al fh https://github.com/blab/zika-usvi/ +VI3 USVI/3/2016 2016-09-26 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI27_1d USVI/27/2016 2016-08-19 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI13 USVI/13/2016 2016-08-13 North America Usvi Saint Thomas Saint Thomas 10636 Black et al fh https://github.com/blab/zika-usvi/ +VI7 USVI/7/2016 2016-10-27 North America Usvi Saint Thomas Saint Thomas 10636 Black et al fh https://github.com/blab/zika-usvi/ +VI38 USVI/38/2016 2016-10-25 North America Usvi Saint Thomas Saint Thomas 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI19_12plex USVI/19/2016 2016-11-21 North America Usvi Saint Croix Saint Croix 10792 Black et al fh https://github.com/blab/zika-usvi/ +VI1_1d USVI/1/2016 2016-09-28 North America Usvi Saint Croix Saint Croix 10792 Black et al fh https://github.com/blab/zika-usvi/ +VI42 USVI/42/2016 2016-10-26 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI30_1d USVI/30/2016 2016-08-07 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/ +VI2 USVI/2/2016 2016-09-28 North America Usvi Saint Croix Saint Croix 10807 Black et al fh https://github.com/blab/zika-usvi/ diff --git a/phylogenetic/data/sequences_usvi.fasta b/phylogenetic/data/sequences_usvi.fasta new file mode 100644 index 0000000..4af1564 --- /dev/null +++ b/phylogenetic/data/sequences_usvi.fasta @@ -0,0 +1,4530 @@ +>VI44 +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnna +agaaagatctggctgccatgctgagaataatcaatgctaggaaggagaagaagagacgag +gcgcagatactagtgtcggaattgttggcctcctgctgaccacagctatggcagcggagg +tcactagacgtgggagtgcatactatatgtacttggacagaaacgatgctggggaggcca +tatcttttccaaccacattggggatgaataagtgttatatacagatcatggatcttggac +acatgtgtgatgccaccatgagctatgaatgccctatgctggatgagggggtggaaccag +atgacgtcgactgttggtgcaacacgacgtcaacttgggttgtgtacggaacctgccatc +acaaaaaaggtgaagcacggagatctagaagagctgtgacgctcccctcccattccacca 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+gcccatacaccagcactatgatggaaaccctggagcgactgcagcgtaggtatgggggag +gactggtcagagtgccactctcccgcaactctacacatgagatgtactgggtctctggag +cgaaaagcaacaccataaaaagtgtgtccaccacgagccagctcctcttggggcgcatgg +acgggcctaggaggccagtgaaatatgaggaggatgtgaatctcggctctggcacgcggg +ctgtggtaagctgcgctgaagctcccaacatgaagatcattggtaaccgcattgaaagga +tccgcagtgagcacgcggaaacgtggttctttgacgagaaccacccatataggacatggg +cttaccatggaagctatgaggcccccacacaagggtcagcgtcctctctaataaacgggg +ttgtcaggctcctgtcaaaaccctgggatgtggtgactggagtcacaggaatagccatga +ccgacaccacaccgtatggtcagcaaagagttttcaaggaaaaagtggacactagggtgc +cagacccccaagaaggcactcgtcaggttatgagcatggtctcttcctggttgtggaaag +agctaggcaaacacaaacggccacgagtctgcaccaaagaagagttcatcaacaaggttc +gtagcaatgcagcattaggggcaatatttgaagaggaaaaagagtggaagactgcagtgg +aagctgtgaacgatccaaggttctgggctctagtggacaaggaaagagagcaccacctga +gaggagagtgccagagctgtgtgtacaacatgatgggaaaaagagaaaagaaacaagggg +aatttggaaaggccaagggcagccgcgccatctggtatatgtggctaggggctagatttc +tagagttcgaagcccttggattcttgaacgaggatcactggatggggagagagaactcag +gaggtggtgttgaagggctgggattacaannacncggatannnnnnngaagagatgagtc +gnatancangaggaangatgtatgcagatgacacnnctggctnggacanccgcattagca +ngnttgatctngagaatgannctcnaatnnncaaccaaatggagaaagggcacagggcct +tggcattggccataatcaagtacacataccaaaacaaagtggtaaaggtccttagaccag +ctgaaaaanggaaaacagttatggacattatttcgagacaagaccaaanggggagcggac +aagttgtcacttacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncaaacgaatggcagtcagtggag +atgattgcgttgtnnagccnatnnatgatangtttnnncatgncctcaggtnnttgaann +ntatnnnnnnannnnngaaggnnacannanagtggaaancctcaactggatnggacannn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnatttccacagaagggacctccgactgatggccaatgccatttgttcatctg +tgccagttgactgggttccaactgggagaactacctggtcaatccatggaaagggagaat +ggatgaccactgaagacatgcttgtggtgtggaacagagtgtggattgaggagaacgacc +acatggaagacaagaccccagttacgaaatggacagacattccctatttgggaaaaaggg +aagacttgtggtgtggatctctcatagggcacagaccgcgcaccacctgggctgagaaca +ttaaaaacacagtcaacatggtgcgcaggatcataggtgatgaagaaaagtacatggact +acctatccacccaagttcgctacttgggtgaagaagggtctacacctggagtgctgtaag +caccaatcttantgttgtcaggcctgctagtcannnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn +nnnnnnn diff --git a/phylogenetic/profiles/ci/copy_example_data.smk b/phylogenetic/profiles/ci/copy_example_data.smk index 495d778..c4637a0 100644 --- a/phylogenetic/profiles/ci/copy_example_data.smk +++ b/phylogenetic/profiles/ci/copy_example_data.smk @@ -17,5 +17,4 @@ rule copy_example_data: cp -f {input.usvi_metadata} {output.usvi_metadata} """ -ruleorder: copy_example_data > decompress -ruleorder: copy_example_data > decompress_usvi \ No newline at end of file +ruleorder: copy_example_data > decompress \ No newline at end of file diff --git a/phylogenetic/rules/merge_sequences_usvi.smk b/phylogenetic/rules/merge_sequences_usvi.smk index 5ae8b3d..13e97af 100644 --- a/phylogenetic/rules/merge_sequences_usvi.smk +++ b/phylogenetic/rules/merge_sequences_usvi.smk @@ -1,30 +1,25 @@ -rule download_usvi: - """Downloading sequences and metadata from data.nextstrain.org""" - output: - sequences = "data/sequences_usvi.fasta.zst", - metadata = "data/metadata_usvi.tsv.zst" - params: - sequences_url = "https://data.nextstrain.org/files/zika/sequences_usvi.fasta.zst", - metadata_url = "https://data.nextstrain.org/files/zika/metadata_usvi.tsv.zst" - shell: - """ - curl -fsSL --compressed {params.sequences_url:q} --output {output.sequences} - curl -fsSL --compressed {params.metadata_url:q} --output {output.metadata} - """ +""" +This part of the workflow appends USVI data to the main dataset. -rule decompress_usvi: - """Decompressing sequences and metadata""" - input: - sequences = "data/sequences_usvi.fasta.zst", - metadata = "data/metadata_usvi.tsv.zst" - output: - sequences = "data/sequences_usvi.fasta", - metadata = "data/metadata_usvi.tsv" - shell: - """ - zstd -d -c {input.sequences} > {output.sequences} - zstd -d -c {input.metadata} > {output.metadata} - """ +REQUIRED INPUTS: + + usvi_sequences = data/sequences_usvi.fasta + usvi_metadata = data/metadata_usvi.tsv + main_sequences = data/sequences.fasta + main_metadata = data/metadata.tsv + +OUTPUTS: + + merged_sequences = data/sequences_all.fasta + merged_metadata = data/metadata_all.tsv + + +This part of the workflow usually includes the following steps: + + - Any transformation to match the columns of the tsv files + - Concatenation of the tsv and the sequences files + +""" rule append_usvi: """Appending USVI sequences""" From f66a276cefda35262ebefd7e8ae1a78d526c403e Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Thu, 1 Feb 2024 14:55:11 -0800 Subject: [PATCH 7/7] Update the phylogenetic data url to match ingest data url The phylogenetic data url was updated to match the ingest data url from https://github.com/nextstrain/zika/blob/c0b9a6d38af405324c968aed9922cc2b3d136db2/ingest/config/optional.yaml#L7 --- phylogenetic/rules/prepare_sequences.smk | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk index 2a11420..2ef99b7 100644 --- a/phylogenetic/rules/prepare_sequences.smk +++ b/phylogenetic/rules/prepare_sequences.smk @@ -27,8 +27,8 @@ rule download: sequences = "data/sequences.fasta.zst", metadata = "data/metadata.tsv.zst" params: - sequences_url = "https://data.nextstrain.org/files/zika/sequences.fasta.zst", - metadata_url = "https://data.nextstrain.org/files/zika/metadata.tsv.zst" + sequences_url = "https://data.nextstrain.org/files/workflows/zika/sequences.fasta.zst", + metadata_url = "https://data.nextstrain.org/files/workflows/zika/metadata.tsv.zst" shell: """ curl -fsSL --compressed {params.sequences_url:q} --output {output.sequences}