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Introduction

Staphopia is a web platform for the bioinformatic analysis of publicly available Staphylococcus aureus genomes. We process each genome through the same analysis pipeline, allowing comparable results between samples. These results are then stored in a centralized database.

Analyses Include:

The Staphopia API provides a simple way access the results these results.

Authentication

In order to use the Staphopia API, you must first register an account with Staphopia. Once you have registered an account you will receive an API Token. The API token provides read-only access to the API. You can not make any changes to your account or the database with the token.

Acquiring Your API Token

First you will want to navigate to Staphopia. Once you get there go ahead and login.

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Now that you’ve logged in you will see a button in the top right hand corner with your username.

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Click it and select Account Settings.

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From there you will want to select Personal API Token.

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The next page will display your API token used to access Staphopia’s API.

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With this API token you are all set to begin using the Staphopia API!

Samples

In Staphopia, a sample is a single sequenced genome. In the case of genomes publicly available from ENA/SRA, each exeriment accession is a sample. The sample is the central identifier in Staphopia. You will use sample IDs to gather associated analysis results.

In most cases you can use a simple GET request to get info on a single sample or POST requests to get info on multiple samples. In the cases where sequences (assembly, genes, etc…) are returned the requests will be limited to a single sample at a time.

Below are endpoints to access samples. Methods to access analysis results for a single sample and multiple samples will be described in following sections.

GET All Samples

Definition

GET https://staphopia.emory.edu/api/sample/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/

Example Response

{
    "count": 18521,
    "next": "https://staphopia.emory.edu/api/sample/?page=2",
    "previous": null,
    "results": [
        {
            "sample_id": 2425,
            "is_paired": true,
            "is_public": true,
            "is_published": true,
            "sample_tag": "ERX359411",
            "st_original": "188",
            "st_stripped": 188,
            "st_is_exact_match": true
        }
    ]
}

Returns a list of samples that either you own or have been made public. The resulting set can be filtered by sequence types.

Options

Option Type Description
st int Filter the samples based on a specific sequence type.

GET Public Samples

Definition

GET https://staphopia.emory.edu/api/sample/public/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/public/

Example Response

{
    "count": 18521,
    "next": "https://staphopia.emory.edu/api/sample/public/?page=2",
    "previous": null,
    "results": [
        {
            "sample_id": 94,
            "is_paired": true,
            "is_public": true,
            "is_published": true,
            "sample_tag": "ERX047891",
            "st_original": "2371",
            "st_stripped": 2371,
            "st_is_exact_match": true
        }
    ]
}

Returns a list of samples that have been made public.

GET Published Samples

Definition

GET https://staphopia.emory.edu/api/sample/published/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/published/

Example Response

{
    "count": 5947,
    "next": "https://staphopia.emory.edu/api/sample/published/?page=2",
    "previous": null,
    "results": [
        {
            "sample_id": 5666,
            "is_paired": true,
            "is_public": true,
            "is_published": true,
            "sample_tag": "ERX116914",
            "st_original": "8",
            "st_stripped": 8,
            "st_is_exact_match": true,
            "pmid": [
                26873713
            ]
        }
    ]
}

Returns a list of samples that have been associated with a publication.

GET MLST Distinct Sample Set

Definition

GET https://staphopia.emory.edu/api/sample/unique_st/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/unique_st/

Example Response

{
    "count": 417,
    "next": null,
    "previous": null,
    "results": [
        {
            "sample_id": 961,
            "st": 1,
            "is_paired": true,
            "is_public": true,
            "is_published": true,
            "sample_tag": "ERX147839",
            "rank": 3
        }
    ]
}

Returns a set up samples each having a different seqeunce type (MLST). The priority is to select published samples first, then quality of the sample.

GET Single Sample

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/

Example Response

{
    "count": 1,
    "next": null,
    "previous": null,
    "results": [
        {
            "sample_id": 500,
            "is_paired": true,
            "is_public": true,
            "is_published": true,
            "sample_tag": "ERX105420",
            "st_original": "239",
            "st_stripped": 239,
            "st_is_exact_match": true
        }
    ]
}

Returns a single sample which is public or that you own. An empty result will be returned if a request is made for a sample which is not public.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

GET Search Samples

Definition

GET https://staphopia.emory.edu/api/search/?q=<query_sting>

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/search/?q=PRJEB2756

Example Response

{
    "count": 318,
    "next": "https://staphopia.emory.edu/api/search/?page=2&q=PRJEB2756",
    "previous": null,
    "results": [
        {
            "sample_id": 262,
            "name": "ERX085322",
            "is_published": true,
            "st": 22,
            "rank": "Gold",
            "sample_accession": "SAMEA1317454",
            "strain": "BSAC516",
            "collection_date": "2003-01-01",
            "location": "United Kingdom: England",
            "isolation_source": "blood"
        },
        {
            "sample_id": 263,
            "name": "ERX085323",
            "is_published": true,
            "st": 22,
            "rank": "Gold",
            "sample_accession": "SAMEA1317339",
            "strain": "BSAC519",
            "collection_date": "2003-01-01",
            "location": "United Kingdom: England",
            "isolation_source": "blood"
        },
        {
            "TRUNCATED FOR DEMO PURPOSES": 0
        },
    ]
}

Searches a given query string against all metadata fields. Returns a set of samples that matched the query string.

Arguments

Property Type Required Description
q str true Query string to search.

Working With A Single Sample

GET Tags

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/tags/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/tags/

Example Response

{
    "count": 1,
    "results": [
        {
            "sample_id": 500,
            "tag_id": 10,
            "tag": "unique-st-set",
            "comment": "A set of ENA samples, each of which have a different ST. Priority is published over unpublished samples, and Gold rank samples over other. Samples with > 90k variants were excluded. Set was last generated on 5/30/17 (407 samples)"
        }
    ]
}

Returns a list of tags associated with a given sample_id.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

GET Metadata

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/metadata/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/metadata/

Example Response

{
    "count": 1,
    "results": [
        {
            "sample_id": 500,
            "contains_ena_metadata": true,
            "study_accession": "PRJEB2655",
            "study_title": "Diversity_of_MRSA",
            "study_alias": "Diversity_of_MRSA-sc-2011-08-22T15:47:08Z-1943",
            "secondary_study_accession": "ERP000871",
            "sample_accession": "SAMEA2298736",
            "secondary_sample_accession": "ERS391194",
            "submission_accession": "ERA312487",
            "experiment_accession": "ERX470731",
            "experiment_title": "Illumina HiSeq 2000 paired end sequencing",
            "experiment_alias": "SC_EXP_12291_8#37",
            "tax_id": 1280,
            "scientific_name": "Staphylococcus aureus",
            "instrument_platform": "ILLUMINA",
            "instrument_model": "Illumina HiSeq 2000",
            "library_layout": "PAIRED",
            "library_strategy": "WGS",
            "library_selection": "RANDOM",
            "center_name": "Sanger Institute",
            "center_link": "http://www.sanger.ac.uk/",
            "first_public": "2014-05-19",
            "cell_line": "",
            "collected_by": "",
            "collection_date": "2012-01-01",
            "country": "Tanzania",
            "description": "12291_8#37",
            "environmental_sample": "false",
            "biosample_first_public": "2014-04-28",
            "germline": "false",
            "isolate": "",
            "isolation_source": "Wound",
            "location": "",
            "serotype": "",
            "serovar": "",
            "sex": "",
            "submitted_sex": "",
            "strain": "MRSA08T",
            "sub_species": "",
            "tissue_type": "",
            "biosample_tax_id": "1280",
            "biosample_scientific_name": "Staphylococcus aureus",
            "sample_alias": "MRSA08T-sc-1810333",
            "checklist": "ERC000011",
            "biosample_center_name": "The Wellcome Trust Sanger Institute",
            "environment_biome": "",
            "environment_feature": "",
            "environment_material": "",
            "project_name": "",
            "host": "Human",
            "host_tax_id": "9606",
            "host_status": "Diseased",
            "host_sex": "",
            "submitted_host_sex": "",
            "host_body_site": "",
            "investigation_type": "",
            "sequencing_method": "",
            "broker_name": ""
        }
    ]
}

Returns metadata associated with a given sample_id.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

GET Sequencing Metrics

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/qc/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/qc/

Example Response

{
    "count": 1,
    "results": [
        {
            "sample_id": 500,
            "is_original": false,
            "rank": 3,
            "total_bp": 281481600,
            "coverage": 100.0,
            "read_total": 2814816,
            "read_min": 100,
            "read_mean": 100.0,
            "read_std": 0.0,
            "read_median": 100,
            "read_max": 100,
            "read_25th": 100,
            "read_75th": 100,
            "qual_mean": 37.3733,
            "qual_std": 1.7408,
            "qual_median": 38,
            "qual_25th": 37,
            "qual_75th": 38
        }
    ]
}

Returns sequencing quality metrics associated with a given sample_id. By default the error corrected and quality filtered results are returned.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

Options

Option Type Description
original bool Return sequencing quality of the original input FASTQ file.

GET Assembly Metrics

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/assembly/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/assembly/

Example Response

{
    "count": 1,
    "results": [
        {
            "sample_id": 500,
            "is_scaffolds": false,
            "is_plasmids": false,
            "total_contig": 91,
            "total_contig_length": 2801206,
            "min_contig_length": 56,
            "median_contig_length": 380,
            "mean_contig_length": 30782.0,
            "max_contig_length": 378840,
            "n50_contig_length": 168699,
            "l50_contig_count": 6,
            "ng50_contig_length": 168699,
            "lg50_contig_count": 6,
            "contigs_greater_1k": 33,
            "contigs_greater_10k": 24,
            "contigs_greater_100k": 10,
            "contigs_greater_1m": 0,
            "percent_contigs_greater_1k": 36.3,
            "percent_contigs_greater_10k": 26.4,
            "percent_contigs_greater_100k": 11.0,
            "percent_contigs_greater_1m": 0.0,
            "contig_percent_a": 33.7,
            "contig_percent_t": 33.54,
            "contig_percent_g": 16.66,
            "contig_percent_c": 16.1,
            "contig_percent_n": 0.0,
            "contig_non_acgtn": 0.0,
            "num_contig_non_acgtn": 0
        }
    ]
}

Returns assembly related metrics associated with a given sample_id. By default metrics for the assembled contigs is returned.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

Options

Option Type Description
scaffolds bool Return assembly metrics for the generated scaffolds.
plasmids bool Return assembly metrics for the assembled plasmids.

GET Assembled Contigs

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/contigs/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/contigs/

Example Response

{
    "count": 85,
    "results": [
        {
            "sample_id": 500,
            "name": "NODE_16_length_34020_cov_43.5996",
            "length": 34020,
            "is_plasmids": false,
            "sequence": "AGCCTTGTCCTACATATT...TRUNCATED FOR DEMO PURPOSES...AAAACGTTCGTTCAAACTGA"
        }
    ]
}

Returns assembled contig sequences associated with a given sample_id. By default the assembled contigs are returned.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

Options

Option Type Description
plasmids bool Return assembled plasmid contigs.

GET MLST

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/st/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/st/

Example Response

{
    "message": "success",
    "took": "4.90 ms",
    "count": 1,
    "results": [
        {
            "sample_id": 500,
            "st": 239,
            "ariba": 239,
            "mentalist": 239,
            "blast": 239
        }
    ]
}

Retrieve MLST results based on Ariba, Mentalist and BLAST for a given sample_id.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

GET cgMLST

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/cgmlst/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/cgmlst/

Example Response

{
    "message": "success",
    "took": "20.58 ms",
    "count": 1,
    "results": [
        {
            "sample_id": 500,
            "SACOL0001": 2,
            "SACOL0002": 2,
            "SACOL0003": 1,
            "SACOL0004": 2,
            "SACOL0005": 2,
            "SACOL0006": 9,
            "SACOL0007": 2,
            "SACOL0009": 2,
            "SACOL0010": 2,
            "SACOL0011": 2,
            "SACOL0012": 13,
            "SACOL0013": 2,
            "SACOL0014": 2,
            "SACOL0015": 2,
            "SACOL0016": 13,
            "SACOL0018": 2,
            "SACOL0019": 2,
            "SACOL0020": 16,
            "TRUNCATED FOR DEMO PURPOSES": 0
        }
    ]
}

Returns the cgMLST as determined by MentaLiST for a given sample_id.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

GET Genes

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/genes/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/genes/

Example Response

{
    "count": 2883,
    "next": "https://merlin.genetics.emory.edu/api/sample/500/genes/?page=2",
    "previous": null,
    "results": [
        {
            "sample_id": 500,
            "annotation_id": 1282,
            "start": 34945,
            "end": 35139,
            "is_positive": false,
            "is_tRNA": false,
            "is_rRNA": false,
            "phase": 0,
            "prokka_id": "ERX470731_00998",
            "dna": "ATGAATTTACAGTCATACATAGGCAAATTAGTCAAATTAACGCTTACTAATAATAAAATATTAATTGGAAAAGTGATAGACTTTGATGATAAAGTTGATAATTTTGATGGTTATAATTCGATAGAAATTGATACAGGTAGAATTACATATGATATATCAGAAAATAAAATTAAAACTATTGTTTTACAAAAATAG",
            "aa": "MNLQSYIGKLVKLTLTNNKILIGKVIDFDDKVDNFDGYNSIEIDTGRITYDISENKIKTIVLQK",
            "cluster_id": 2201,
            "cluster_name": "UniRef50_C4WAM4",
            "contig_id": 720100,
            "inference_id": 1,
            "note_id": 2,
            "product_id": 10,
            "product": "putative protein"
        }
    ]
}

Returns the predicted/annotated genes associated with a given sample_id.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

Options

Option Type Description
cluster_id int Filter the samples based on a cluster id.
product_id int Filter the samples based on a product id.

GET SCCmec Primer Hits

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/sccmec_primers/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/sccmec_primers/

Example Response

{
    "count": 27,
    "results": [
        {
            "sample_id": 500,
            "title": "ccrA1",
            "length": 24,
            "bitscore": 25,
            "evalue": 0.61,
            "identity": 13,
            "mismatch": 0,
            "gaps": 0,
            "hamming_distance": 11,
            "query_from": 6,
            "query_to": 18,
            "hit_from": 109052,
            "hit_to": 109040,
            "align_len": 13,
            "qseq": "ATATCATCAATCA",
            "hseq": "ATATCATCAATCA",
            "midline": "|||||||||||||",
            "contig_id": 720102,
            "program_id": 7
        }
    ]
}

Example Response (‘predict’ option active)

{
    "count": 1,
    "results": [
        {
            "sample_id": "500",
            "I": false,
            "II": false,
            "III": false,
            "IV": false,
            "V": false,
            "VI": false,
            "VII": false,
            "VIII": false,
            "IX": false,
            "X": false,
            "XI": false
        }
    ]
}

Returns the BLAST results of hits against SCCmec Primer sequences associated with a given sample_id.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

Options

Option Type Description
exact_hits bool Return on those hits that were exact matches.
predict bool Predict SCCmec type based on presence of exact matches.

GET SCCmec Subtype Hits

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/sccmec_subtypes/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/sccmec_subtypes/

Example Response

{
    "count": 20,
    "results": [
        {
            "sample_id": 500,
            "title": "ivh-r",
            "length": 20,
            "bitscore": 23,
            "evalue": 1.19,
            "identity": 12,
            "mismatch": 0,
            "gaps": 0,
            "hamming_distance": 8,
            "query_from": 2,
            "query_to": 13,
            "hit_from": 33879,
            "hit_to": 33890,
            "align_len": 12,
            "qseq": "AAACACTGATAT",
            "hseq": "AAACACTGATAT",
            "midline": "||||||||||||",
            "contig_id": 104718,
            "program_id": 7
        }
    ]
}

Example Response (‘predict’ option active)

{
    "count": 1,
    "results": [
        {
            "sample_id": 500,
            "Ia": false,
            "IIa": false,
            "IIb": false,
            "IIIa": true,
            "IVa": false,
            "IVb": false,
            "IVc": false,
            "IVd": false,
            "IVg": false,
            "IVh": false
        }
    ]
}

Returns the BLAST results of hits against SCCmec Subtype Primer sequences associated with a given sample_id.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

Options

Option Type Description
exact_hits bool Return on those hits that were exact matches.
predict bool Predict SCCmec subtype based on presence of exact matches.

GET SCCmec Protein Hits

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/sccmec_proteins/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/sccmec_proteins/

Example Response

{
    "count": 16,
    "results": [
        {
            "sample_id": 500,
            "title": "ccrA1|UniRef90_Q9S0L6 Cassette chromosome recombinase A1 n=14 Tax=Staphylococcus RepID=Q9S0L6_STAAU",
            "length": 449,
            "bitscore": 722,
            "evalue": 0.0,
            "identity": 351,
            "mismatch": 98,
            "gaps": 1,
            "hamming_distance": 98,
            "query_from": 1,
            "query_to": 449,
            "hit_from": 65753,
            "hit_to": 67096,
            "align_len": 449,
            "qseq": "MKQAIGYLRQSTTKQQSLAAQKQTIEALAKKHNIQYITFYSDKQSGRTDKRNGYQQITELIQQGQCDVLCCYRLNRLHRNLKNALKLMKLCQKYHVHILSVHDGYFDMDKAFDRLKLNIFISLAELESDNIGEQVKNGIKEKAKQGKMITTHAPFGYHYHNGTFTIDTVKAPTVKAVFNYYLQGYGYKKIAQYLEADDKFINRKPYQVRNIILNPNYCGRVINQYGQYENMFPAIVSTTIYEEAQVTRTQKPVKRKPSENQLKQKIKCPYCDSTLTNMTIRKKHHTLRYYVCPQNMNASRFVCEFKGINAQELETSVLATCQDFFQNQQLYSKINHTIQQRLKRQRDIETKTTLNHEQLIEKLAQDKIDAETFREQTQSLRQQSKPISSISTYQIRKAFQNIIQQRFTLNMLYPYIDEINISKNKSLAGIYFKNEPLNIVKQTMELSIV",
            "hseq": "MKRAIGYLRQSTTKQQSLPAQKQAIELLAPKHNIQNIQYISDKQSGRTDNRTGYQQVTERIQQRQCDVLCCYRLNRLHRNLKNALKLMKLCQKYHVHILSVHDGYFDMDKAFDRLKLNIFMSLAELESDNIGEQVKNGLREKAKQGKLITTHAPFGYHYQNGTFIINNDESPTVKAVFNYYLQGYGYKKIAQYLEDDNKLITRKPYQVRNIIMNPNYCGRVINQYGQYNNMVPPIVSATKYEHAQAIRNKKQLHCIPSENQLKQKIKCPCCDSTLTNMTIRKK-HTLRYYICPKNMNESRFVCSFKGINAQKLEVQVLATCQNFFQNQQLYSKINNAIHQRLKKQRVIEAKSTLTQEQLIDKLAKGMIDAESFRKQTHLMNQKHKTISSISDNQLQTSLQKVIQKSFTLNMLHPYIDEIRITKNKALVGIYFKNEPLNIVNQTSQSSIA",
            "midline": "MK+AIGYLRQSTTKQQSL AQKQ IE LA KHNIQ I + SDKQSGRTD R GYQQ+TE IQQ QCDVLCCYRLNRLHRNLKNALKLMKLCQKYHVHILSVHDGYFDMDKAFDRLKLNIF+SLAELESDNIGEQVKNG++EKAKQGK+ITTHAPFGYHY NGTF I+  ++PTVKAVFNYYLQGYGYKKIAQYLE D+K I RKPYQVRNII+NPNYCGRVINQYGQY NM P IVS T YE AQ  R +K +   PSENQLKQKIKCP CDSTLTNMTIRKK HTLRYY+CP+NMN SRFVC FKGINAQ+LE  VLATCQ+FFQNQQLYSKIN+ I QRLK+QR IE K+TL  EQLI+KLA+  IDAE+FR+QT  + Q+ K ISSIS  Q++ + Q +IQ+ FTLNML+PYIDEI I+KNK+L GIYFKNEPLNIV QT + SI ",
            "contig_id": 104734,
            "program_id": 8
        }
    ]
}

Returns the BLAST results of hits against SCCmec Protein sequences associated with a given sample_id.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

GET SCCmec Cassette Coverage

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/sccmec_coverages/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/sccmec_coverages/

Example Response

{
    "count": 22,
    "results": [
        {
            "sample_id": 500,
            "name": "III",
            "total": 0.95,
            "minimum": 0,
            "mean": 58.64,
            "median": 45,
            "maximum": 196,
            "meca_total": 0.98,
            "meca_minimum": 0,
            "meca_mean": 7.99,
            "meca_median": 4,
            "meca_maximum": 79,
            "cassette_id": 21
        }
    ]
}

Returns the alignment coverage across each full length SCCmec cassette associated with a given sample_id.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

GET SNPs

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/snps/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/snps/

Example Response

{
    "count": 26098,
    "results": [
        {
            "sample_id": 500,
            "snp_id": 184,
            "annotation_id": 1,
            "reference_position": 62,
            "reference_base": "G",
            "alternate_base": "A",
            "reference_codon": ".",
            "alternate_codon": ".",
            "reference_amino_acid": ".",
            "alternate_amino_acid": ".",
            "amino_acid_change": ".",
            "is_synonymous": 9,
            "is_transition": 1,
            "is_genic": 0,
            "AC": "[1]",
            "GT": "1",
            "AD": "[0, 74]",
            "GQ": "99",
            "AF": "1.0",
            "MQ": "60.0",
            "PL": "[3305, 0]",
            "DP": "74",
            "QD": "35.89",
            "quality": "3275",
            "feature_id": 1,
            "reference_id": 1,
            "filters_id": 9
        }
    ]
}

Returns the SNPs associated with a given sample_id.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

Options

Option Type Description
paginate bool Paginate the response.

GET InDels

Definition

GET https://staphopia.emory.edu/api/sample/<sample_id>/indels/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" https://staphopia.emory.edu/api/sample/500/indels/

Example Response

{
    "count": 1581,
    "results": [
        {
            "sample_id": 500,
            "indel_id": 1784,
            "annotation_id": 1,
            "reference_position": 14111,
            "reference_base": "AT",
            "alternate_base": "A",
            "is_deletion": true,
            "feature_id": 1,
            "reference_id": 1,
            "AC": "[1]",
            "GT": "1",
            "AD": "[0, 89]",
            "GQ": "99",
            "AF": "1.0",
            "MQ": "60.12",
            "PL": "[3841, 0]",
            "DP": "93",
            "QD": "26.9",
            "quality": "3801.97",
            "filters_id": 9
        }
    ]
}

Returns the InDels associated with a given sample_id.

Arguments

Property Type Required Description
sample_id int true Unique number associated with a sample.

Options

Option Type Description
paginate bool Paginate the response.

Working With Multiple Samples

POST Metadata

Definition

POST https://staphopia.emory.edu/api/metadata/bulk_by_sample/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" \
     -H "Content-Type: application/json" \
     https://staphopia.emory.edu/api/metadata/bulk_by_sample/ \
     -d '{"ids" : [500,501]}'

Example Response

{
    "count": 2,
    "results": [
        {
            "sample_id": 500,
            "contains_ena_metadata": true,
            "study_accession": "PRJEB2756",
            "study_title": "Staphylococcus aureus (BSAC) study",
            "study_alias": "Staphylococcus_aureus__BSAC__study-sc-2011-11-15T19:00:43Z-2036",
            "secondary_study_accession": "ERP001012",
            "sample_accession": "SAMEA1464583",
            "secondary_sample_accession": "ERS072738",
            "submission_accession": "ERA131752",
            "experiment_accession": "ERX105420",
            "experiment_title": "Illumina HiSeq 2000 paired end sequencing",
            "experiment_alias": "SC_EXP_7712_8#27",
            "tax_id": 1280,
            "scientific_name": "Staphylococcus aureus",
            "instrument_platform": "ILLUMINA",
            "instrument_model": "Illumina HiSeq 2000",
            "library_layout": "PAIRED",
            "library_strategy": "WGS",
            "library_selection": "RANDOM",
            "center_name": "Sanger Institute",
            "center_link": "http://www.sanger.ac.uk/",
            "first_public": "2012-05-28",
            "cell_line": "",
            "collected_by": "",
            "collection_date": "2003-01-01",
            "country": "United Kingdom: England",
            "description": "7712_8#27",
            "environmental_sample": "false",
            "biosample_first_public": "2012-05-28",
            "germline": "false",
            "isolate": "",
            "isolation_source": "blood",
            "location": "",
            "serotype": "Not known",
            "serovar": "Not known",
            "sex": "",
            "submitted_sex": "",
            "strain": "st697",
            "sub_species": "",
            "tissue_type": "",
            "biosample_tax_id": "1280",
            "biosample_scientific_name": "Staphylococcus aureus",
            "sample_alias": "BSAC697-sc-1304334",
            "checklist": "ERC000011",
            "biosample_center_name": "The Wellcome Trust Sanger Institute",
            "environment_biome": "",
            "environment_feature": "",
            "environment_material": "",
            "project_name": "",
            "host": "Homo sapien",
            "host_tax_id": "",
            "host_status": "Carriage",
            "host_sex": "",
            "submitted_host_sex": "",
            "host_body_site": "",
            "investigation_type": "",
            "sequencing_method": "",
            "broker_name": ""
        }
    ]
}

Returns metadata associated with a given set of Sample IDs.

Arguments

Property Type Required Description
ids int array true An array of sample IDs as integers.

POST Sequencing Metrics

Definition

POST https://staphopia.emory.edu/api/sequence-quality/bulk_by_sample/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" \
     -H "Content-Type: application/json" \
     https://staphopia.emory.edu/api/sequence-quality/bulk_by_sample/ \
     -d '{"ids" : [500,501]}'

Example Response

{
    "count": 2,
    "results": [
        {
            "sample_id": 500,
            "is_original": true,
            "rank": 3,
            "total_bp": 418786000,
            "coverage": 148.78,
            "read_total": 4187860,
            "read_min": 100,
            "read_mean": 100.0,
            "read_std": 0.0,
            "read_median": 100,
            "read_max": 100,
            "read_25th": 100,
            "read_75th": 100,
            "qual_mean": 34.5463,
            "qual_std": 2.7428,
            "qual_median": 36,
            "qual_25th": 34,
            "qual_75th": 36
        }
    ]
}

Returns sequencing quality metrics associated with a given set of Sample IDs. By default the error corrected and quality filtered results are returned.

Arguments

Property Type Required Description
ids int array true An array of sample IDs as integers.

Options

Option Type Description
original bool Return sequencing quality of the original input FASTQ file.

POST Assembly Metrics

Definition

POST https://staphopia.emory.edu/api/assembly/stat/bulk_by_sample/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" \
     -H "Content-Type: application/json" \
     https://staphopia.emory.edu/api/assembly/stat/bulk_by_sample/ \
     -d '{"ids" : [500,501]}'

Example Response

{
    "count": 2,
    "results": [
        {
            "sample_id": 500,
            "is_scaffolds": false,
            "is_plasmids": false,
            "total_contig": 165,
            "total_contig_length": 3032220,
            "min_contig_length": 56,
            "median_contig_length": 534,
            "mean_contig_length": 18377.0,
            "max_contig_length": 254900,
            "n50_contig_length": 130552,
            "l50_contig_count": 9,
            "ng50_contig_length": 130552,
            "lg50_contig_count": 9,
            "contigs_greater_1k": 71,
            "contigs_greater_10k": 41,
            "contigs_greater_100k": 9,
            "contigs_greater_1m": 0,
            "percent_contigs_greater_1k": 43.0,
            "percent_contigs_greater_10k": 24.8,
            "percent_contigs_greater_100k": 5.5,
            "percent_contigs_greater_1m": 0.0,
            "contig_percent_a": 33.56,
            "contig_percent_t": 33.77,
            "contig_percent_g": 16.01,
            "contig_percent_c": 16.65,
            "contig_percent_n": 0.0,
            "contig_non_acgtn": 0.0,
            "num_contig_non_acgtn": 0
        }
    ]
}

Returns assembly related metrics associated with a given set of Sample IDs. By default metrics for the assembled contigs is returned.

Arguments

Property Type Required Description
ids int array true An array of sample IDs as integers.

Options

Option Type Description
scaffolds bool Return assembly metrics for the generated scaffolds.
plasmids bool Return assembly metrics for the assembled plasmids.

POST MLST

Definition

POST https://staphopia.emory.edu/api/mlst/bulk_by_sample/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" \
     -H "Content-Type: application/json" \
     https://staphopia.emory.edu/api/mlst/bulk_by_sample/ \
     -d '{"ids" : [500,501]}'

Example Response

{
    "message": "success",
    "took": "3.39 ms",
    "count": 2,
    "results": [
        {
            "sample_id": 500,
            "st": 239,
            "ariba": 239,
            "mentalist": 239,
            "blast": 239
        },
        {
            "sample_id": 501,
            "st": 30,
            "ariba": 30,
            "mentalist": 30,
            "blast": 30
        }
    ]
}

Returns the MLST results associated with a given set of Sample IDs.

Arguments

Property Type Required Description
ids int array true An array of sample IDs as integers.

POST cgMLST

Definition

POST https://staphopia.emory.edu/api/cgmlst/bulk_by_sample/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" \
     -H "Content-Type: application/json" \
     https://staphopia.emory.edu/api/cgmlst/bulk_by_sample/ \
     -d '{"ids" : [500,501]}'

Example Response

{
    "message": "success",
    "took": "35.44 ms",
    "count": 2,
    "results": [
        {
            "sample_id": 500,
            "SACOL0001": 2,
            "SACOL0002": 2,
            "SACOL0003": 1,
            "SACOL0004": 2,
            "SACOL0005": 2,
            "SACOL0006": 9,
            "SACOL0007": 2,
            "SACOL0009": 2,
            "SACOL0010": 2,
            "TRUNCATED FOR DEMO PURPOSES": 0
        },
        {
            "sample_id": 501,
            "SACOL0001": 2,
            "SACOL0002": 2,
            "SACOL0003": 1,
            "SACOL0004": 2,
            "SACOL0005": 2,
            "SACOL0006": 2,
            "SACOL0007": 2,
            "SACOL0009": 2,
            "SACOL0010": 2,
            "TRUNCATED FOR DEMO PURPOSES": 0
        }
    ]
}

Returns the cgMLST results associated with a given set of Sample IDs.

Arguments

Property Type Required Description
ids int array true An array of sample IDs as integers.

POST SCCmec Primer Hits

Definition

POST https://staphopia.emory.edu/api/sccmec/primer/bulk_by_sample/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" \
     -H "Content-Type: application/json" \
     https://staphopia.emory.edu/api/sccmec/primer/bulk_by_sample/ \
     -d '{"ids" : [500,501]}'

Example Response

{
    "count": 54,
    "results": [
        {
            "sample_id": 500,
            "title": "ccrA1",
            "length": 24,
            "bitscore": 30,
            "evalue": 0.01,
            "identity": 16,
            "mismatch": 0,
            "gaps": 0,
            "hamming_distance": 8,
            "query_from": 7,
            "query_to": 22,
            "hit_from": 79024,
            "hit_to": 79009,
            "align_len": 16,
            "qseq": "TATCATCAATCAGTAC",
            "hseq": "TATCATCAATCAGTAC",
            "midline": "||||||||||||||||",
            "contig_id": 104617,
            "program_id": 7
        }
    ]
}

Example Response (‘predict’ option active)

{
    "count": 2,
    "results": [
        {
            "sample_id": 500,
            "I": false,
            "II": false,
            "III": true,
            "IV": false,
            "V": false,
            "VI": false,
            "VII": false,
            "VIII": false,
            "IX": false,
            "X": false,
            "XI": false
        }
    ]
}

Returns the BLAST results of hits against SCCmec Primer sequences associated with a given set of Sample IDs.

Arguments

Property Type Required Description
ids int array true An array of sample IDs as integers.

Options

Option Type Description
exact_hits bool Return on those hits that were exact matches.
predict bool Predict SCCmec type based on presence of exact matches.

POST SCCmec Subtype Hits

Definition

POST https://staphopia.emory.edu/api/sccmec/subtype/bulk_by_sample/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" \
     -H "Content-Type: application/json" \
     https://staphopia.emory.edu/api/sccmec/subtype/bulk_by_sample/ \
     -d '{"ids" : [500,501]}'

Example Response

{
    "count": 40,
    "results": [
        {
            "sample_id": 500,
            "title": "ivh-r",
            "length": 20,
            "bitscore": 23,
            "evalue": 1.19,
            "identity": 12,
            "mismatch": 0,
            "gaps": 0,
            "hamming_distance": 8,
            "query_from": 2,
            "query_to": 13,
            "hit_from": 33879,
            "hit_to": 33890,
            "align_len": 12,
            "qseq": "AAACACTGATAT",
            "hseq": "AAACACTGATAT",
            "midline": "||||||||||||",
            "contig_id": 104718,
            "program_id": 7
        }
    ]
}

Example Response (‘predict’ option active)

{
    "count": 2,
    "results": [
        {
            "sample_id": 500,
            "Ia": false,
            "IIa": false,
            "IIb": false,
            "IIIa": true,
            "IVa": false,
            "IVb": false,
            "IVc": false,
            "IVd": false,
            "IVg": false,
            "IVh": false
        }
    ]
}

Returns the BLAST results of hits against SCCmec Subtype Primer sequences associated with a given set of Sample IDs.

Arguments

Property Type Required Description
ids int array true An array of sample IDs as integers.

Options

Option Type Description
exact_hits bool Return on those hits that were exact matches.
predict bool Predict SCCmec subtype based on presence of exact matches.

POST SNPs

Definition

POST https://staphopia.emory.edu/api/variant/snp/bulk_by_sample/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" \
     -H "Content-Type: application/json" \
     https://staphopia.emory.edu/api/variant/snp/bulk_by_sample/ \
     -d '{"ids" : [500,501]}'

Example Response

{
    "count": 74966,
    "results": [
        {
            "sample_id": 500,
            "snp_id": 184,
            "annotation_id": 1,
            "reference_position": 62,
            "reference_base": "G",
            "alternate_base": "A",
            "reference_codon": ".",
            "alternate_codon": ".",
            "reference_amino_acid": ".",
            "alternate_amino_acid": ".",
            "amino_acid_change": ".",
            "is_synonymous": 9,
            "is_transition": 1,
            "is_genic": 0,
            "AC": "[1]",
            "GT": "1",
            "AD": "[0, 74]",
            "GQ": "99",
            "AF": "1.0",
            "MQ": "60.0",
            "PL": "[3305, 0]",
            "DP": "74",
            "QD": "35.89",
            "quality": "3275",
            "feature_id": 1,
            "reference_id": 1,
            "filters_id": 9
        }
    ]
}

Returns the SNPs associated with a given set of Sample IDs.

Arguments

Property Type Required Description
ids int array true An array of sample IDs as integers.

POST InDels

Definition

POST https://staphopia.emory.edu/api/variant/indel/bulk_by_sample/

Example Request

curl -H "Authorization: Token YOUR_API_TOKEN_HERE" \
     -H "Content-Type: application/json" \
     https://staphopia.emory.edu/api/variant/indel/bulk_by_sample/ \
     -d '{"ids" : [500,501]}'

Example Response

{
    "count": 4605,
    "results": [
        {
            "sample_id": 500,
            "indel_id": 1784,
            "annotation_id": 1,
            "reference_position": 14111,
            "reference_base": "AT",
            "alternate_base": "A",
            "is_deletion": true,
            "feature_id": 1,
            "reference_id": 1,
            "AC": "[1]",
            "GT": "1",
            "AD": "[0, 89]",
            "GQ": "99",
            "AF": "1.0",
            "MQ": "60.12",
            "PL": "[3841, 0]",
            "DP": "93",
            "QD": "26.9",
            "quality": "3801.97",
            "filters_id": 9
        }
    ]
}

Returns the InDels associated with a given set of Sample IDs.

Arguments

Property Type Required Description
ids int array true An array of sample IDs as integers.
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