Using the PATRIC Command-line Interface

PATRIC is an integration of different types of data and software tools that support research on bacterial pathogens. The typical biologist seeking access to the PATRIC data and tools will usually explore the web-based user interface. However, there are many instances in which programatic or command-line interfaces are more suitable. For users that wish command-line access to PATRIC, we provide the tools described in this document. We call these tools the P3-scripts. They are intended to run on your machine, going over the network to access the services provided by PATRIC.

Document Conventions

In this document, we observe the following conventions.

Text that you enter or type is shown in a white-background box.

This is input.

Output is shown in a yellow-background box. In general, you will only see the top portion of the output, since the whole thing could be quite large.

This is the top portion
of the output.

Output is usually tab-delimited, and you will see columns separated by multiple spaces that don’t always line up.

If it is necessary to show multiple excerpts of a single large output stream, the missing parts will be shown with a gray bar.

This is the top part.

This is somewhere in the middle.

NOTE: we add new genomes to the PATRIC database every week. Your
results from the examples in this tutorial may not match ours.

Installing the CLI Release

Since the CLI tools run on your computer, to use them you will need to download and install a software package in order to use them.

We currently have macOS and Debian/Ubuntu releases of the PATRIC Command Line Interface. A Windows version is in the works.

The releases are available at the PATRIC3 github site. Full installation installations are available in Installing the PATRIC Command Line Interface.

Command-Line Help

You can specify --help as a command-line option on any command to get a summary of the options and parameters, for example

p3-match --help

p3-match.pl [-bchiv] [long options...] match-value
        -i STR --input STR      name of the input file (if not the standard
                                input)
        -c STR --col STR        column number (1-based) or name
        -b INT --batchSize INT  input batch size
        --nohead                file has no headers
        -v --invert --reverse   output non-matching records
        --discards STR          name of file to contain discarded records
        -h --help               display usage information

The PATRIC Database

The main PATRIC database is organized as a series of large, heavily-indexed relational tables. From the perspective of the CLI, there are five main tables representing objects of interest, connected by four relationships.

The five entities are as follows.

Genome

A genome is a set of contigs and annotations representing our best estimate of the DNA sequence for an organism. Use p3-all-genomes to list all of the genomes or a subset. Given a list of genomes,

• Use p3-get-genome-data to retrieve data about the individual genomes.

• Use p3-get-genome-features to access the features of the genomes.

• Use p3-get-genome-contigs to access the genomes’ sequences.

• Use p3-get-genome-drugs to access drug resistance data about the genomes.

Fields from the Genome table appear in the output with a heading prefix of genome. Thus, the genome_name will be in a column named genome.genome_name.

Contig

Represents one of the DNA sequences that comprise a genome. A contig can be a chromosome, a plasmid, or a fragment thereof. Contig data can be accessed from genome IDs using p3-get-genome-contigs. Fields from the Contig table appear in the output with a heading prefix of contig. Thus, the length will be in a column named contig.length.

Drug

Represents an antimicrobial drug used for therapeutic treatment. This table is the anchor for all antimicrobial resistance data in PATRIC. Use p3-all-drugs to get a list of drugs. Use p3-get-drug-genomes to get resistance data relating to specific drugs from a list. Fields from the Drug table appear in the output with a heading prefix of drug. Thus, the molecular_formula will be in a column named drug.molecular_formula.

Feature

Represents a region of interest in a genome. This could be a CRISPR array, an RNA site, a protein encoding region, or a regulatory site, among others. A feature can be split across multiple regions, or even multiple contigs, but never multiple genomes. Given a list of genome IDs, use p3-get-genome-features to access the features in the genomes. Given a list of family IDs, use p3-get-family-features to access the features in the families. Given a list of feature IDs, use p3-get-feature-data to access data about those features. It is important to remember that the ID of the feature is called *patric_id*, not *feature_id*. The internal feature ID is a long string with a lot of data packed into it that may change if the genome is re-annotated (e.g. PATRIC.269798.23.NC_008255.CDS.22581.24344.fwd). The patric_id value is shorter and more consistent (fig|269798.23.peg.22). Fields from the Feature table appear in the output with a heading prefix of feature. Thus, the location will be in a column named feature.location.

Family

Represents a protein family, which is a set of features believed to be isofunctional homologs. Given a list of family IDs, use p3-get-family-features to get data about the features in the families or p3-get-family-data to get data about the families themselves. Given a list of feature IDs, use p3-get-feature-data to get the families to which the features belong. There are three types of protein families supported– local families which are confined to one genus, global families which cross the entire database, and figfams, which are computed using a different method. Fields from the Family table appear in the output with a heading prefix of family. Thus, the product will be in a column named family.product.

Files and Pipelines

The PATRIC CLI operates on tab-delimited files. That is, each record is divided into fields or columns separated by tab characters. The first record in each file contains the name of each column. Typically, a column name consists of a record name, a dot, and a field name. For example, the following file fragment contains a column from the genome table followed by two columns from the feature table.

genome.genome_id    feature.patric_id   feature.product
670.470 fig|670.470.repeat.1    repeat region
670.470 fig|670.470.repeat.2    repeat region
670.470 fig|670.470.repeat.3    repeat region
670.470 fig|670.470.rna.1   tRNA-Ala
670.470 fig|670.470.rna.2   tRNA-Ile
670.470 fig|670.470.repeat.4    repeat region
670.470 fig|670.470.rna.3   16S ribosomal RNA
670.470 fig|670.470.repeat.5    repeat region
670.470 fig|670.470.rna.4   tRNA-Val
670.470 fig|670.470.rna.5   tRNA-Ala
670.470 fig|670.470.repeat.6    repeat region

The scripts are designed so they can be chained together in pipelines where the output of one becomes input to the next. For example, the above file was generated by the pipeline

p3-all-genomes --eq genus,Methylobacillus | p3-get-genome-features --attr patric_id --attr product

In the first command of this pipeline, the --eq command-line option was used to filter a query, while the --attr option in the second command was used to specify the output columns and the order in which they appear. These options are available on all of the database scripts.

For get-type scripts (p3-get-genome-data, p3-get-feature-data, …), you must supply the id of the object of interest, e.g., the genome id, feature id, etc. By default, the last column in the input file is used as the key field for these get-type scripts. You can modify this behavior using the --col command-line option. The special value 0 denotes the last column, but you can also use a 1-based column number (1 for the first, 2 for the second) or a column name. If the field-name portion of the column name is unique, you can leave off the table-name portion. So, if you want to get location information from the features output by the pipeline above (identified in column feature.patric_id, which is the second one), you could use any of the three following commands

p3-get-feature-data --col=feature.patric_id --attr sequence_id --attr location <input.tbl

p3-get-feature-data --col=2 --attr sequence_id --attr location <input.tbl

p3-get-feature-data --col=patric_id --attr sequence_id --attr location <input.tbl

where input.tbl is the above output file.

The special script p3-extract allows you to select columns from a file and even change the order. Thus, the following pipeline removes the genome ID from our file and puts the feature ID at the end before asking p3-get-feature-data for the location information.

p3-extract feature.product feature.patric_id <input.tbl | p3-get-feature-data --attr sequence_id --attr location

The same flexibility provided for arguments of the --col option is available anywhere you specify column names, including the parameters of p3-extract. So, the following invocation is equivalent to the above.

p3-extract product 2 <input.tbl | p3-get-feature-data --attr sequence_id --attr location

Because of the presence of the headings, many standard file-manipulation commands won’t work the way you expect. For example, if you use a standard sort command, the headers will sort somewhere into the middle of the file. We provide p3 scripts for several of the most common needs.

P3 Script	Description	Unix Equivalent
p3-extract	Select and re-order specific columns.	cut
p3-sort	Sort by specified columns.	sort
p3-match	Select records that possess (or do not possess) a particular value in a specified column.	grep
p3-join	Horizontally join two files on a single key field.	join
p3-head	Display the first few lines of a file.	head
p3-echo	Create a small file.	echo

These commands do not work precisely like their unix equivalents. Most have fewer options: for example, p3-match searches for text in a single column rather than the entire file and does not support regular expressions.

p3-echo

The p3-echo command is your most important tool for creating small files that feed into pipes. The --title command-line option (abbreviated -t) allows you to specify the title for the column you are creating. Each positional parameter forms a single record with a single column.

p3-echo -t genome_id 1313.7001 1313.7002 1313.7016

genome_id
1313.7001
1313.7002
1313.7016

You can create a multi-column file by specifying multiple titles. There will be one output column for each title specified. In the example below, there are three titles, so the output table is three columns. Every triple of parameters produces a record.

p3-echo -t genome_id -t sequences -t gc_content 1313.7001  52  39.64  1313.7002  45  39.63  1313.7016  58  39.77

genome_id       sequences        gc_content
1313.7001       52      39.64
1313.7002       45      39.63
1313.7016       58      39.77

If a field contains special characters such as spaces or pipe symbols, use double quotes to ensure the characters are interpreted correctly.

p3-echo -t genome_id -t patric_id -t product 1313.7001 "fig|1313.7001.peg.1362" "hypothetical protein"

genome_id   patric_id   product
1313.7001   fig|1313.7001.peg.1362  hypothetical protein

If you leave off the title parameter, the default title id is used. This is a handy shortcut when you’re in a hurry.

p3-echo 1313.7001 1313.7016

id
1313.7001
1313.7016

Of course, you can only do that for a single-column output.

Database Script Examples

In this section we briefly discuss the main database scripts.

p3-all-genomes

This script lists all genomes with various characteristics. For example,

p3-all-genomes --eq genome_name,Streptomyces

genome.genome_id
284037.4
67257.17
68042.5
68042.6
1395572.3
68570.5
1160718.3
749414.3
66876.3
249567.6

would list all genomes in the genus Streptomyces. (That is, all genomes whose names start with that word.) The --eq parameter introduces an equality constraint. In PATRIC, string searches perform a word-based substring match, which allows us to easily do queries of this type. The various database commands all support the --eq option. In addition, you can specify output fields using the --attr option. Thus,

p3-all-genomes --eq genome_name,Streptomyces --attr genome_id --attr genome_name

would output both the ID and name of each genome found, as shown below.

genome.genome_id    genome.genome_name
284037.4    Streptomyces sporocinereus strain OsiSh-2
67257.17    Streptomyces albus subsp. albus strain NRRL F-4371
68042.5 Streptomyces hygroscopicus subsp. hygroscopicus strain NBRC 16556
68042.6 Streptomyces hygroscopicus subsp. hygroscopicus strain NBRC 13472
1395572.3   Streptomyces albulus PD-1
68570.5 Streptomyces albulus strain NK660
1160718.3   Streptomyces auratus AGR0001
749414.3    Streptomyces bingchenggensis BCW-1
66876.3 Streptomyces chattanoogensis strain NRRL ISP-5002
249567.6    Streptomyces decoyicus strain NRRL 2666

To get a complete list of the available fields, use the --fields option. This option is available for all the database scripts described in this section.

p3-all-genomes --fields

_version_
additional_metadata (multi)
altitude
antimicrobial_resistance (multi)
antimicrobial_resistance_evidence
assembly_accession
assembly_method
bioproject_accession
biosample_accession
biovar

The parenthetical (multi) indicates that a field has multiple values. The values returned will be separated by the current delimiter (which defaults to a double colon ::). There is also a parenthetical (derived) which indicates the value of the field is computed from other fields and can’t be used in filtering.

p3-get-genome-data

Given an input file of genome IDs, this script allows you to retrieve additional data and fields. For example, the following pipeline gets all Streptomyces genomes and then appends the genome name, number of contigs, and DNA length.

p3-all-genomes --eq genome_name,Streptomyces | p3-get-genome-data --attr genome_name --attr contigs --attr genome_length

genome.genome_id    genome.genome_name  genome.contigs  genome.genome_length
284037.4    Streptomyces sporocinereus strain OsiSh-2   125 10242506
67257.17    Streptomyces albus subsp. albus strain NRRL F-4371  307 9246299
68042.5 Streptomyces hygroscopicus subsp. hygroscopicus strain NBRC 16556   133 10141569
68042.6 Streptomyces hygroscopicus subsp. hygroscopicus strain NBRC 13472   680 9464604
1395572.3   Streptomyces albulus PD-1   425 9340057
68570.5 Streptomyces albulus strain NK660       9372401
1160718.3   Streptomyces auratus AGR0001    213 7825489
749414.3    Streptomyces bingchenggensis BCW-1  0   11936683
66876.3 Streptomyces chattanoogensis strain NRRL ISP-5002   217 9129105

In actual fact, the use of p3-get-genome-data in the above pipeline is redundant, since p3-all-genomes supports the same command-line options. In practice, you will use p3-get-genome-data to process genome ID files created on a separate occasion or via other scripts that don’t have the full power of p3-all-genomes. If you don’t specify any --attr values, you get the same output fields as found on the PATRIC genome list tab.

p3-all-genomes --eq genome_name,Streptomyces | p3-get-genome-data

genome.genome_id    genome.genome_name  genome.genome_id    genome.genome_status    genome.sequences    genome.patric_cds   genome.isolation_country    genome.host_name    genome.disease  genome.collection_year  genome.completion_date
284037.4    Streptomyces sporocinereus strain OsiSh-2   284037.4    WGS 125 9060    China   Rice        2012    2016-08-16T00:00:00Z
67257.17    Streptomyces albus subsp. albus strain NRRL F-4371  67257.17    WGS 307 8633                    2016-01-26T00:00:00Z
68042.5 Streptomyces hygroscopicus subsp. hygroscopicus strain NBRC 16556   68042.5 WGS 133 8955                    2016-02-05T00:00:00Z
68042.6 Streptomyces hygroscopicus subsp. hygroscopicus strain NBRC 13472   68042.6 WGS 680 8767                    2016-02-05T00:00:00Z
1395572.3   Streptomyces albulus PD-1   1395572.3   WGS 482 8332    China               2013-12-05T00:00:00Z
68570.5 Streptomyces albulus strain NK660   68570.5 Complete    2   8793    China               2014-06-18T00:00:00Z
1160718.3   Streptomyces auratus AGR0001    1160718.3   WGS 238 6866    China               2012-07-23T00:00:00Z
749414.3    Streptomyces bingchenggensis BCW-1  749414.3    Complete    1   10313   China               2010-05-28T00:00:00Z
66876.3 Streptomyces chattanoogensis strain NRRL ISP-5002   66876.3 WGS 217 8838    United States               2015-09-18T00:00:00Z
249567.6    Streptomyces decoyicus strain NRRL 2666 249567.6    WGS 304 8231    United States               2015-08-19T00:00:00Z
1907.4  Streptomyces glaucescens GLA.O  1907.4  Complete    2   6719    India               2014-10-01T00:00:00Z
1172567.3   Streptomyces globisporus C-1027 1172567.3   WGS 278 6980    China               2012-05-04T00:00:00Z

This is typical of the p3-get scripts: the default attributes match what you see on the web site as closely as possible.

p3-get-genome-features

Given a file of genome IDs, return data about the genome’s features. So, for example, the following pipeline would return the ID and function (product) of each feature in the Cytophaga genomes.

p3-all-genomes --eq genus,Cytophaga | p3-get-genome-features --attr patric_id --attr product

genome.genome_id    feature.patric_id   feature.product
269798.23   fig|269798.23.peg.1 hypothetical protein
269798.23   fig|269798.23.peg.2 Capsular polysaccharide synthesis enzyme Cap8C; Manganese-dependent protein-tyrosine phosphatase (EC 3.1.3.48)
269798.23   fig|269798.23.peg.3 Dihydroflavonol-4-reductase (EC 1.1.1.219)
269798.23   fig|269798.23.peg.4 TPR domain protein
269798.23   fig|269798.23.peg.5 Phosphosulfolactate synthase (EC 4.4.1.19)
269798.23   fig|269798.23.peg.6 DedA protein
269798.23   fig|269798.23.peg.7 Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)
269798.23   fig|269798.23.peg.8 hypothetical protein
269798.23   fig|269798.23.peg.9 Excinuclease ABC subunit B
269798.23   fig|269798.23.peg.10    DNA polymerase III epsilon subunit
269798.23   fig|269798.23.peg.11    hypothetical protein
269798.23   fig|269798.23.peg.12    putative fatty acid hydroxylase

You can use the --fields option to list all the fields available in a feature record. In addition, you have access to the usual filtering parameters– --eq as well as --lt, --gt, --le, --ge, and --ne. So, for example, the following command would restrict the features to CDS features of at least 500 base pairs.

p3-all-genomes --eq genus,Cytophaga | p3-get-genome-features --eq feature_type,CDS --ge na_length,500 --attr patric_id --attr product

genome.genome_id    feature.patric_id   feature.product
269798.23   fig|269798.23.peg.2 Capsular polysaccharide synthesis enzyme Cap8C; Manganese-dependent protein-tyrosine phosphatase (EC 3.1.3.48)
269798.23   fig|269798.23.peg.3 Dihydroflavonol-4-reductase (EC 1.1.1.219)
269798.23   fig|269798.23.peg.4 TPR domain protein
269798.23   fig|269798.23.peg.5 Phosphosulfolactate synthase (EC 4.4.1.19)
269798.23   fig|269798.23.peg.6 DedA protein
269798.23   fig|269798.23.peg.7 Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)
269798.23   fig|269798.23.peg.8 hypothetical protein
269798.23   fig|269798.23.peg.9 Excinuclease ABC subunit B
269798.23   fig|269798.23.peg.10    DNA polymerase III epsilon subunit
269798.23   fig|269798.23.peg.12    putative fatty acid hydroxylase
269798.23   fig|269798.23.peg.13    Glycosyl transferase

p3-get-genome-contigs

Given a file of genome IDs, returns the contigs. The following pipeline returns all the contigs in genome 28903.66.

p3-echo -t genome_id 28903.66 | p3-get-genome-contigs --attr sequence_id --attr sequence

The output will have three columns, including the genome ID, the ID of the contig, and the actual DNA sequence (which can be quite long). Again, use the --fields option to see which fields are available for output and filtering in the contig records.

p3-get-genome-drugs

Given a file of genome IDs, output the drug resistance information we have on those genomes. For many genomes, no such data is yet available, so it is not hard to get an empty file output from this command. The following pipeline outputs the default resistance data information for all the Acinetobacter pittii genomes.

p3-all-genomes --eq "genome_name,Acinetobacter pittii" | p3-get-genome-drugs

genome.genome_id    genome_drug.genome_id   genome_drug.antibiotic  genome_drug.resistant_phenotype
48296.102   48296.102   meropenem   Resistant
48296.102   48296.102   imipenem    Resistant
48296.102   48296.102   ciprofloxacin   Susceptible
48296.102   48296.102   gentamicin  Susceptible
48296.102   48296.102   amikacin    Susceptible
48296.102   48296.102   tigecycline
48296.104   48296.104   imipenem    Resistant
48296.104   48296.104   ciprofloxacin   Susceptible
48296.104   48296.104   gentamicin  Susceptible

p3-all-drugs

This script lists anti-microbial drugs from the database. Use the --fields option to see a list of all the fields you can select. The default is to simply list the antibiotic name, as shown below.

p3-all-drugs

drug.antibiotic_name
amikacin
amoxicillin
amoxicillin/clavulanic acid
ampicillin
ampicillin/sulbactam
azithromycin
aztreonam
bacitracin
capreomycin
cefaclor
cefazolin

p3-get-drug-genomes

Given a file of antibiotic names, display all the resistance data for those antibiotics. The following pipeline lists all the genomes resistant to at least one drug.

p3-all-drugs | p3-get-drug-genomes --attr genome_id --attr genome_name --resistant

drug.antibiotic_name    genome_drug.genome_id   genome_drug.genome_name
amikacin    1304920.3   Klebsiella pneumoniae 361_1301
amikacin    1427177.3   Mycobacterium tuberculosis XTB13-081
amikacin    1427178.3   Mycobacterium tuberculosis XTB13-082
amikacin    1427180.3   Mycobacterium tuberculosis XTB13-084
amikacin    1427185.3   Mycobacterium tuberculosis XTB13-091
amikacin    1427191.3   Mycobacterium tuberculosis XTB13-097
amikacin    1427192.3   Mycobacterium tuberculosis XTB13-098
amikacin    1427193.3   Mycobacterium tuberculosis XTB13-100
amikacin    1427199.3   Mycobacterium tuberculosis XTB13-107
amikacin    1427200.3   Mycobacterium tuberculosis XTB13-108
amikacin    1427202.3   Mycobacterium tuberculosis XTB13-110
amikacin    1427204.3   Mycobacterium tuberculosis XTB13-112
amikacin    1427207.3   Mycobacterium tuberculosis XTB13-115

Rather than typing --eq resistant_phenotype,resistant, the p3-get-drug-genomes script provides the special command-line options --resistant and --susceptible to filter for the appropriate resistance phenotypes automatically.

p3-get-family-features

Given a list of protein family IDs, get all the features in the families. PATRIC supports three types of protein families– local, global, and figfam. The --ftype parameter specifies the type of family desired. So, for example, the following pipeline finds the global family for the feature fig|1105121.3.peg.460 and then lists the ID and product of each family member.

p3-echo -t feature_id "fig|1105121.3.peg.460" | p3-get-feature-data --attr pgfam_id | p3-get-family-features --ftype=global --attr patric_id --attr product

Note that the features found are listed in the column feature.patric_id, while the original feature is maintained in the first column feature_id.

feature_id  feature.pgfam_id    feature.patric_id   feature.product
fig|1105121.3.peg.460   PGF_00112374    fig|1313.8637.peg.2087  hypothetical protein
fig|1105121.3.peg.460   PGF_00112374    fig|1313.8636.peg.1563  hypothetical protein
fig|1105121.3.peg.460   PGF_00112374    fig|1313.8645.peg.110   hypothetical protein
fig|1105121.3.peg.460   PGF_00112374    fig|1313.12423.peg.2037 hypothetical protein
fig|1105121.3.peg.460   PGF_00112374    fig|1330044.3.peg.533   hypothetical protein
fig|1105121.3.peg.460   PGF_00112374    fig|1313.5699.peg.1778  hypothetical protein
fig|1105121.3.peg.460   PGF_00112374    fig|1313.5750.peg.307   hypothetical protein
fig|1105121.3.peg.460   PGF_00112374    fig|1313.5754.peg.739   hypothetical protein
fig|1105121.3.peg.460   PGF_00112374    fig|1313.5758.peg.1823  hypothetical protein
fig|1105121.3.peg.460   PGF_00112374    fig|1313.5781.peg.1819  hypothetical protein
fig|1105121.3.peg.460   PGF_00112374    fig|1313.5778.peg.686   hypothetical protein
fig|1105121.3.peg.460   PGF_00112374    fig|1313.5729.peg.1554  hypothetical protein

p3-get-feature-data

Given a file of feature IDs, return data from those features. Again, use the --fields option to list the fields you can use for filtering and display. The following pipeline lists the function (product) and protein sequence of each peg of less than 300 base pairs in the genome 1105121.3.

p3-echo -t genome_id 1105121.3 | p3-get-genome-features --lt na_length,300 --eq feature_type,CDS --attr patric_id | p3-get-feature-data --attr product --attr aa_sequence

genome_id   feature.patric_id   feature.product feature.aa_sequence
1105121.3   fig|1105121.3.peg.1487  BOX elements    MKIKEQTRKLAASCSKHCFEVVDKTDEVSYIYNPRRR
1105121.3   fig|1105121.3.peg.1508  hypothetical protein    MISTTYRNHRKRFGLRMNLIAEKVSKTLDKTFDKDVREIPTSQFYQKFVDEMGRTYSGNLILQELITVNGAYKATYIGELSSN
1105121.3   fig|1105121.3.peg.1557  hypothetical protein    MKREVISNGNDGPSQEILIFTKQIRHWILSDQVISGKRKLFFREDTPKEILDLYENIKSKLDFAYQEVYSNNGLKKYEK
1105121.3   fig|1105121.3.peg.1598  BOX elements    MKIKEQTRKLAAGCSKHCFEVVDRTDEVSNLHTARRR
1105121.3   fig|1105121.3.peg.1776  hypothetical protein    MVASASASSTSTQAQEQVDKSELRALSQELDQRLKALATVSDPKIDATKAVLLDAQKAPEDSALTE
1105121.3   fig|1105121.3.peg.10    hypothetical protein    MENLLDVIEQFLGLSDEKLEELADKNQLLRLQEEKERKNA
1105121.3   fig|1105121.3.peg.94    BOX elements    MKIKEQTRKLAAGCSKHCFEVVDKTDEVSYIYLRQGEADAV
1105121.3   fig|1105121.3.peg.220   Ribonucleotide reductase of class III (anaerobic), large subunit (EC 1.17.4.2)  MVKRTCGYLGNPQARPMVNGRHKEIAARVKHMNGSTIKIAGHQVTN
1105121.3   fig|1105121.3.peg.228   LSU ribosomal protein L23p (L23Ae)  MNLYDVIKKPVITESSMAQLEAGKYVFEVDTRAHKLLIKQAVEAAFEGVKVANVNTINVKPKAKRVGRYTGFTNKTKKAIITLTADSKAIELFAAEAE
1105121.3   fig|1105121.3.peg.230   SSU ribosomal protein S19p (S15e)   MGRSLKKGPFVDEHLMKKVEAQANDEKKKVIKTWSRRSTIFPSFIGYTIAVYDGRKHVPVYIQEDMVGHKLGEFAPTRTYKGHAADDKKTRRK

The use of p3-get-feature-data here is redundant, since you could get the same result by placing the attribute requests directly on p3-get-genome-features.

p3-echo -t genome_id 1105121.3 | p3-get-genome-features --lt na_length,300 --eq feature_type,CDS --attr patric_id --attr product --attr aa_sequence

p3-get-feature-data is provided for the situation where you are piping in the feature list from something external or precomputed.

What Is a PATRIC Workspace?

Users of PATRIC have access to a wealth of public data that support interpretation of prokaryotic genomes. The PATRIC team actively integrates newly-sequenced genomes, data relating to antimicrobial resistance, expression data, pathway data and subsystem data into an integrated framework that can be queried using either the PATRIC UI or the CLI.

In the PATRIC UI, your workspace looks a lot like a standard file system, divided into folders full of data. In addition to files you upload, such as FASTA and FASTQ files, there will also be typed objects such as genomes, feature groups, and genome groups. The CLI allows you to move these typed objects between your workspace and your file system so you can manipulate them at will.

Logging In

To access your workspace, you need a PATRIC account. If you do not have one already, go to https://user.patricbrc.org/register and register now.

Now that you have a working user name and password, you can use the p3-login script to tell the CLI who you are. For example, if your name is rastuser25, you would type

p3-login rastuser25

The script asks you for your password and places a special file on your hard drive that can be used to get authorized access to your workspace data. To log out again, simply use

p3-login --logout

At any time, you can verify your login status using

p3-login --status

If you are logged out, it will respond

You are currently logged out of PATRIC.

If you are logged in, you will get something like

You are logged in as rastuser25@patricbrc.org.

Working with Genome Groups

Your workspace looks like a full-blown file system, but there are three special folders.

• Genome Groups contains named lists of genomes.

• Feature Groups contains named lists of features.

• QuickData contains folders full of genomes you submitted through the CLI annotation interface.

To create a genome group, you use p3-put-genome-group. Say, for example, you want to examine Streptococcus penumoniae genomes that are resistant to penicillin. The following query command will return this list of genomes (we will discuss all query commands in more details later).

p3-echo -t antibiotic penicillin | p3-get-drug-genomes --eq "genome_name,Streptococcus pneumoniae"  --resistant --attr genome_id --attr genome_name >resist.tbl

This particular command asks for data from the anti-microbial resistance table. Each record in this table posits a relationship between a genome and an antibiotic drug. We are accessing the table from the direction of taking a drug and finding resistant genomes. To do this, we need a file with a drug name in it. The p3-echo command creates this file: the -t antibiotic parameter tells it we want a one-column file with a column header of antibiotic. We put the single record penicillin in that column.

The antibiotic file is then piped into p3-get-drug-genomes. Its parameters do the following.

--eq "genome_name,Streptococcus pneumoniae"

Only include records for Streptococcus pneumoniae genomes. Because this is a string field, it does a substring match. A genome name including follow-on strain information (e.g. Streptococcus pneumoniae strain LMG2888) will still match.

--resistant

Only include records that state the genome is resistant. This is a special parameter for the p3-get-drug-genomes and p3-get-genome-drugs commands that is provided for convenience.

--attr genome_id

Output the genome ID.

--attr genome_name

Output the genome name.

When the command completes, the file resist.tbl will contain around 114 lines beginning with the following.

antibiotic   genome_drug.genome_id   genome_drug.genome_name
penicillin   1313.7006   Streptococcus pneumoniae P310010-154
penicillin   1313.7016   Streptococcus pneumoniae P310937-212
penicillin   1313.7018   Streptococcus pneumoniae P311313-217
penicillin   760749.3    Streptococcus pneumoniae GA05248
penicillin   760763.3    Streptococcus pneumoniae GA11304
penicillin   760765.3    Streptococcus pneumoniae GA11663
penicillin   760766.3    Streptococcus pneumoniae GA11856
penicillin   760769.3    Streptococcus pneumoniae GA13338
penicillin   760771.3    Streptococcus pneumoniae GA13455
penicillin   760776.3    Streptococcus pneumoniae GA14373
penicillin   760777.3    Streptococcus pneumoniae GA14688

Now we want to create a group for these genomes called resist_strep. We use the following command.

p3-put-genome-group --col=2 resist_strep <resist.tbl

The --col=2 tells the command that the genome IDs are in the second column. The genome group is simply a set of genome IDs, so the other columns will be ignored by the command. You can read the group back at any time using p3-get-genome-group.

p3-get-genome-group resist_strep

Will output

resist_strep.genome_id
1313.7006
1313.7016
1313.7018
760749.3
760763.3
760765.3
760766.3
760769.3
760771.3

and so on. Note that if you want to see the names as well, you can use the p3-get-genome-data command to add them

p3-get-genome-group resist_strep | p3-get-genome-data --attr genome_name

resist_strep.genome_id  genome.genome_name
1313.7006   Streptococcus pneumoniae P310010-154
1313.7016   Streptococcus pneumoniae P310937-212
1313.7018   Streptococcus pneumoniae P311313-217
760749.3    Streptococcus pneumoniae GA05248
760763.3    Streptococcus pneumoniae GA11304
760765.3    Streptococcus pneumoniae GA11663
760766.3    Streptococcus pneumoniae GA11856
760769.3    Streptococcus pneumoniae GA13338
760771.3    Streptococcus pneumoniae GA13455
760776.3    Streptococcus pneumoniae GA14373
760777.3    Streptococcus pneumoniae GA14688

Next we will ask for the genomes that are susceptible to penicillin. We use the same command as before except we put susceptible in place of resistant. We’re going to pipe the results directly into p3-put-genome-group to store them in our workspace.

p3-echo -t antibiotic penicillin | p3-get-drug-genomes --eq "genome_name,Streptococcus pneumoniae"  --susceptible --attr genome_id --attr genome_name | p3-put-genome-group --col=2 weak_strep

Now when you ask for the group back, you would get something like the following.

p3-get-genome-group weak_strep

weak_strep.genome_id
1313.6939
1313.6941
1313.6942
1313.6944
1313.6947
1313.7001
1313.7002
1313.7007
1313.7009

Working with Feature Groups

We want to look at features in the resistant Streptococcus pneumoniae genomes that distinguish them from the susceptible ones. Then we will gather those features into a feature group and store them in our workspace so we can work with them later. We have the genomes we want stored in the genome groups weak_strep and resist_strep. The command that processes them is called p3-signature-families.

p3-signature-families compares two genome groups– group 1 contains genomes that are interesting for some reason, group 2 contains genomes that are not. We can pipe one of the two groups directly into the command, but the other needs to be in a file. We will start by creating a file called weak.tbl that contains the weak_strep genomes.

p3-get-genome-group weak_strep >weak.tbl

Now we pipe in resist_strep (the interesting set) and specify weak.tbl as the source of group 2.

p3-get-genome-group resist_strep | p3-signature-families --gs2=weak.tbl >families.tbl

The output contains protein families that are common in the interesting set (resistant to penicillin) but not in the other set. If a set file is not specified, it is taken from the standard input. In this case, that would be the interesting set, since there is no –gs1 parameter.

Our signature families analysis script has no output, because we redirected it to families.tbl. We can peek at the results using the --all option of p3-extract.

p3-extract --all <families.tbl

counts_in_set1  counts_in_set2  family.family_id    family.product
92  10  PGF_00112374    hypothetical protein
92  10  PGF_00303700    hypothetical protein
92  10  PGF_03497231    hypothetical protein
91  10  PGF_03497236    hypothetical protein

We found four protein families. The next step is to convert the families into feature IDs. The p3-get-family-features script performs that function. We will use the following command.

p3-get-family-features --gFile=resist.tbl --gCol=2 --ftype=global --col=family.family_id <families.tbl

The parameters work as follows.

–gFile=resist.tbl

Only features from the genomes listed in the file resist.tbl should be included in the output.

–gCol=2

The genome IDs in resist.tbl are in the second column.

--ftype=global

The family IDs in the input file are global families. (Local families and FIGfams are also supported, but the p3-signature-families script uses global families.)

–col=family.family_id

The protein family IDs in the input file are in a column named family.family_id.

The output looks something like this.

counts_in_set1  counts_in_set2  family.family_id    family.product  feature.patric_id   feature.refseq_locus_tag    feature.gene_id feature.plfam_id    feature.pgfam_id    feature.product
92  10  PGF_00112374    hypothetical protein    fig|1105121.3.peg.460   SPAR163_0451    0   PLF_1301_00002060   PGF_00112374    hypothetical protein
92  10  PGF_00112374    hypothetical protein    fig|1069626.3.peg.432   SPAR154_0430    0   PLF_1301_00002060   PGF_00112374    hypothetical protein
92  10  PGF_00112374    hypothetical protein    fig|1313.6771.peg.1961  ERS013947_01920     PLF_1301_00002060   PGF_00112374    hypothetical protein
92  10  PGF_00112374    hypothetical protein    fig|1313.5503.peg.1279  ERS013945_01218     PLF_1301_00002060   PGF_00112374    hypothetical protein
92  10  PGF_00112374    hypothetical protein    fig|1313.5634.peg.1224  ERS013952_01170     PLF_1301_00002060   PGF_00112374    hypothetical protein
92  10  PGF_00112374    hypothetical protein    fig|1069624.3.peg.437   SPAR151_0439    0   PLF_1301_00002060   PGF_00112374    hypothetical protein
92  10  PGF_00112374    hypothetical protein    fig|1069628.3.peg.451   SPAR156_0440    0   PLF_1301_00002060   PGF_00112374    hypothetical protein
92  10  PGF_00112374    hypothetical protein    fig|1313.5669.peg.1163  ERS013960_01123     PLF_1301_00002060   PGF_00112374    hypothetical protein
92  10  PGF_00112374    hypothetical protein    fig|1313.6725.peg.2115  ERS013931_02059     PLF_1301_00002060   PGF_00112374    hypothetical protein
92  10  PGF_00112374    hypothetical protein    fig|1313.5465.peg.1094  ERS013930_01056     PLF_1301_00002060   PGF_00112374    hypothetical protein
92  10  PGF_00112374    hypothetical protein    fig|1313.5418.peg.2058  ERS013923_02003     PLF_1301_00002060   PGF_00112374    hypothetical protein
92  10  PGF_00112374    hypothetical protein    fig|1313.5645.peg.1124  ERS013964_01084     PLF_1301_00002060   PGF_00112374    hypothetical protein

We didn’t tell p3-get-family-features what attributes of the features to display, so it defaulted to the columns normally found on the PATRIC web page Features tab. We don’t have time to examine these features in detail now, but we can put them in a feature group by piping them into p3-put-feature-group as follows.

p3-get-family-features --gFile=resist.tbl --gCol=2 --ftype=global --col=family.family_id <families.tbl | p3-put-feature-group --col=feature.patric_id resist_fids

In the p3-put-feature-group command, the --col=feature.patric_id parameter tells the command that the feature IDs are in the column with that heading, and resist_fids is the group name. When you decide to examine the features in greater detail, you can pull back the feature IDs using p3-get-feature-group.

p3-get-feature-group resist_fids

The output will look something like this.

resist_fids.patric_id
fig|1105121.3.peg.460
fig|1069626.3.peg.432
fig|1313.6771.peg.1961
fig|1313.5503.peg.1279
fig|1313.5634.peg.1224
fig|1069624.3.peg.437
fig|1069628.3.peg.451
fig|1313.5669.peg.1163
fig|1313.6725.peg.2115

At any time, you can get a complete list of the groups in your workspace using the p3-list-genome-groups command or the p3-list-feature-groups command. So, if you have been following along the above examples and your workspace was empty before you began, you would see the following.

p3-list-genome-groups

resist_strep
weak_strep

p3-list-feature-groups

resist_fids

Extracting and Mining Genome Typed Objects (GTOs)

Sometimes you want to store a genome on your local hard drive. PATRIC provides a special format for encapsulating all the data from a genome called the genome typed object or GTO. The p3-gto script allows you to download one or more PATRIC genomes in GTO format. The following command downloads two strep genomes – 1313.7001 and 1313.7016– in GTO format and stores them in the current directory.

p3-gto 1313.7001 1313.7016

The GTO files have the same name as the genome ID with a suffix of .gto. So, the above command creates 1313.7001.gto and 1313.7016 in the current directory. If you execute this command and look at 1313.7001.gto, you will see something like the following (with large portions in the middle removed).

{
   "analysis_events" : [],
   "scientific_name" : "Streptococcus pneumoniae P210774-233",
   "source" : "PATRIC",
   "source_id" : "1313.7001",
   "id" : "1313.7001",
   "taxonomy" : [
      "cellular organisms",
      "Bacteria",
      "Terrabacteria group",
      "Firmicutes",
      "Bacilli",
      "Lactobacillales",
      "Streptococcaceae",
      "Streptococcus",
      "Streptococcus pneumoniae"
   ],
   "contigs" : [
      {
         "genetic_code" : "11",
         "dna" : "gaaaggacaaaatttgtcctttctcaagcttagctgacttcaacccactacagttgacaaagagcctgttttctcaataggattgtactcaggtgagtagggaggaagaggtaaaagtttatgcccaaactcttcacacaagagttctagcttacccattctatggaatcttgcattatccataataataaccgatggtgtggttaatgttggtaagagaaatttctgaaaccatacttcaaaaaagtcgctcgtcatcgtctcttcgtaagtcattggagcgattaattcaccatttgttagacctgcaaccaaagaaatcctctgatatcttcttccagatactttgcctcttcttaactgaccttttaatgagcgaccatattctcgataaaaataagtatcgaatcctgtttcgtcaatctaaacaggtgctaggtgctttaaactattaaaattcttaagaaataaggctacttatcgccctgaatatcaaaaaagaaaggacaaaatttgtcctttctcaagcttagctgacttcaacccactacagttgacaaagagcctgttttctcaataggattgtactcaggtgagtagggaggaagaggtaaaagtttatgcccaaactcttcacacaagagttctagcttacccattctatggaatcttgcattatccataataataaccgatggtgtggttaatgttggtaagagaaatttctgaaaccatacttcaaaaaagtcgctcgtcatcgtctcttcgtaagtcattggagcgattaattcaccatttgttagacctgcaaccaaagaaatcctctgatatcttcttccagatactttgcctcttcttaactgaccttttaatgagcgaccatattctcgataaaaataagtatcgaatcctgtttcgtcaatctaaacaggtgctaggtgctttaaactattaaaattcttaagaaataaggctactttttctgggtcttgttcatagtaggtgtggttctttttttcgagtgtagcccatagctttgagcgcatagtggatggtagttggatgacagccaaattcagaagctatttcagtcaaataagcgtct",
         "id" : "1313.7001.con.0001"
      },
      {
         "id" : "1313.7001.con.0002",
         "genetic_code" : "11",
         "dna" : "aaagaagctgttcgaaaagtaggcgatggttatgtctttgaggagaatggagtttctcgttatatcccagccaaggatctttcagcagaaacagcagcaggcattgatagcaaactggccaagcaggaaagtttatctcataagctaggagctaagaaaactgacctcccatctagtgatcgagaattttacaataaggcttatgacttactagcaagaattcaccaagatttacttgataataaaggtcgacaagttgattttgaggctttggataacctgttggaacgactcaaggatgtctcaagtgataaagtcaagttagtggatgatattcttgccttcttagctccgattcgtcatccagaacgtttaggaaaaccaaattcgcaaattacctacactgatgatgagattcaagtagccaagttggcaggcaagtacacaacagaagacggttatatctttgatcctcgtgatataaccagtgatgagggggatgcctatgtaactccacatatgacccatagccactggattaaaaaagatagtttgtctgaagctgagagagcggcagcccaggcttatgctaaagagaaaggtttgacccctccttcgacagaccatcaggatgcaggaaatactgaggcaaaaggagcagaagctatctacaaccgcgtgaaagcagctaagaaggtgccacttgatcgtatgccttacaatcttcaatatactgtagaagtcaaaaacggtagtttaatcatacctcattatgaccattaccataacatcaaatttgagtggtttgacgaaggcctttatgaggcacctaaggggtatactcttgaggatcttttggcgactgtcaagtactatgtcgaacatccaaacgaacgtccgcattcagataatggttttggtaacgctagcgaccatgttcaaagaaacaaaaatggtcaagctgataccaatcaaacggagaaacctcagacagaaaaacctgaggaagataaggaacatgatgaagtaagtgagccaactca"
      },

   ],
   "ncbi_taxonomy_id" : "1313",
   "close_genomes" : [],
   "domain" : "Bacteria",
   "genetic_code" : "11",
   "features" : [
      {
         "type" : "repeat_region",
         "family_assignments" : [],
         "annotations" : [
            [
               "Add feature from PATRIC",
               "PATRIC",
               1500218027.10933,
               ""
            ],
            [
               "Set function to repeat region",
               "PATRIC",
               1500218027.10933,
               ""
            ]
         ],
         "aliases" : [],
         "id" : "fig|1313.7001.repeat.1",
         "function" : "repeat region",
         "location" : [
            [
               "1313.7001.con.0001",
               "67",
               "+",
               413
            ]
         ]
      },
      {
         "location" : [
            [
               "1313.7001.con.0001",
               "567",
               "+",
               539
            ]
         ],
         "function" : "repeat region",
         "id" : "fig|1313.7001.repeat.2",
         "aliases" : [],
         "annotations" : [
            [
               "Add feature from PATRIC",
               "PATRIC",
               1500218027.10944,
               ""
            ],
            [
               "Set function to repeat region",
               "PATRIC",
               1500218027.10944,
               ""
            ]
         ],
         "family_assignments" : [],
         "type" : "repeat_region"
      },

   ]
}

This is a JSON-format string, which is to say, it displays an object with fields, some of which are other objects (denoted by curly braces) or lists (denoted by square brackets). JSON is a standard portable data format, described in detail here and supported by most programming languages. Without even fully understanding the notation, you can still see in the above listing that various bits of key metadata (scientific name, taxonomy, ID) are present in the file, along with the ID and sequence of each contig and various pertinent data about each feature.

You can use a minus sign (-) in the parameter list to specify that the genome list come from the standard input. The following creates GTOs for every genome in the genome group weak_strep.

p3-get-genome-group weak_strep | p3-gto -

This capability can be mixed with explicit genome IDs. So the following script creates a GTO for 594.8, all of the genomes in group weak_strep, and then genome 149539.441.

p3-get-genome-group weak_strep | p3-gto 594.8 - 149539.441

You can also use the --outDir option to specify that the output be put in a different directory. The following creates a new subdirectory PathogenGTO in the current directory and puts all the GTOs in it.

p3-get-genome-group weak_strep | p3-gto --outDir=PathogenGTO 594.8 - 149539.441

You are not required to write code to manipulate GTOs. Instead, we’ve included some useful scripts in the PATRIC CLI. First and foremost is p3-gto-scan. For example, if you run

p3-gto-scan 1313.7001.gto

you would see the following analysis

Processing contigs of 1313.7001.gto.
Processing features of 1313.7001.gto.
All done.
contigs                52
dna               2101113
features             3382
functionAnalyzed     1418
functionRead         3382
functionReused       1964
roleMatch            1492
roleProcessed        3478

This rather arcane output tells you several things. First, that there are 52 contigs and 2,101,113 base pairs in the genome. It has 3382 features containing 1418 distinct assigned functions (functionAnalyzed). 3382 features had assigned functions (functionRead). This means every feature had a valid functional assignment, which is usually the case. 1964 of the features had redundant functions, that is, functions also found earlier in the genome (functionReused). 3478 roles were found (roleProcessed) of which 1492 were distinct (roleMatch).

If you want to see the actual roles, specify the command-line option --verbose.

p3-gto-scan --verbose 1313.7001.gto

Role name   1313.7001.gto
(2E,6E)-farnesyl diphosphate synthase (EC 2.5.1.10) 1
1,2-diacylglycerol 3-glucosyltransferase (EC 2.4.1.337) 1
1,4-alpha-glucan (glycogen) branching enzyme, GH-13-type (EC 2.4.1.18)  1
1-phosphofructokinase (EC 2.7.1.56) 1
16S rRNA (cytidine(1402)-2'-O)-methyltransferase (EC 2.1.1.198) 1
16S rRNA (cytosine(1402)-N(4))-methyltransferase EC 2.1.1.199)  1
16S rRNA (cytosine(967)-C(5))-methyltransferase (EC 2.1.1.176)  1
16S rRNA (guanine(1207)-N(2))-methyltransferase (EC 2.1.1.172)  1
16S rRNA (guanine(527)-N(7))-methyltransferase (EC 2.1.1.170)   1
16S rRNA (guanine(966)-N(2))-methyltransferase (EC 2.1.1.171)   1
16S rRNA (uracil(1498)-N(3))-methyltransferase (EC 2.1.1.193)   1

In this table, each role name is shown along with the number of times it occurs in the genome. You can see the features as well by adding the --features command line.

p3-gto-scan --verbose --features 1313.7001.gto

Role name   1313.7001.gto   Features containing role
(2E,6E)-farnesyl diphosphate synthase (EC 2.5.1.10) 1   fig|1313.7001.peg.1606
1,2-diacylglycerol 3-glucosyltransferase (EC 2.4.1.337) 1   fig|1313.7001.peg.679
1,4-alpha-glucan (glycogen) branching enzyme, GH-13-type (EC 2.4.1.18)  1   fig|1313.7001.peg.595
1-phosphofructokinase (EC 2.7.1.56) 1   fig|1313.7001.peg.227
16S rRNA (cytidine(1402)-2'-O)-methyltransferase (EC 2.1.1.198) 1   fig|1313.7001.peg.1813
16S rRNA (cytosine(1402)-N(4))-methyltransferase EC 2.1.1.199)  1   fig|1313.7001.peg.503
16S rRNA (cytosine(967)-C(5))-methyltransferase (EC 2.1.1.176)  1   fig|1313.7001.peg.1301
16S rRNA (guanine(1207)-N(2))-methyltransferase (EC 2.1.1.172)  1   fig|1313.7001.peg.83
16S rRNA (guanine(527)-N(7))-methyltransferase (EC 2.1.1.170)   1   fig|1313.7001.peg.1682
16S rRNA (guanine(966)-N(2))-methyltransferase (EC 2.1.1.171)   1   fig|1313.7001.peg.145
16S rRNA (uracil(1498)-N(3))-methyltransferase (EC 2.1.1.193)   1   fig|1313.7001.peg.728

Later on in this file you can see an example of a role that occurs in multiple features. You will note that a double colon (::) is used to separate the individual feature IDs.

6-phospho-beta-galactosidase (EC 3.2.1.85)  1   fig|1313.7001.peg.607
6-phospho-beta-glucosidase (EC 3.2.1.86)    4   fig|1313.7001.peg.1031::fig|1313.7001.peg.1517::fig|1313.7001.peg.443::fig|1313.7001.peg.896
6-phosphofructokinase (EC 2.7.1.11) 1   fig|1313.7001.peg.1372
6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) 1   fig|1313.7001.peg.542

This is a common convention in the PATRIC CLI– when a single column contains multiple values, we use a double colon to separate them. You can use the --delim option to change this default. Supported alternate delimiters include space, tab, and comma. For example, the following would show if you coded --delim=space.

6-phospho-beta-galactosidase (EC 3.2.1.85)  1   fig|1313.7001.peg.607
6-phospho-beta-glucosidase (EC 3.2.1.86)    4   fig|1313.7001.peg.1031 fig|1313.7001.peg.1517 fig|1313.7001.peg.443 fig|1313.7001.peg.896
6-phosphofructokinase (EC 2.7.1.11) 1   fig|1313.7001.peg.1372
6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) 1   fig|1313.7001.peg.542

The true power in p3-gto-scan comes when you use it to compare multiple GTO files. The following command displays a summary of the differences between 1313.7001.gto and 1313.7016.gto.

p3-gto-scan 1313.7001.gto 1313.7016.gto

Processing contigs of 1313.7001.gto.
Processing features of 1313.7001.gto.
Processing contigs of 1313.7016.gto.
Processing features of 1313.7016.gto.
Role name   1313.7001.gto   1313.7016.gto
2,3-butanediol dehydrogenase, R-alcohol forming, (R)- and (S)-acetoin-specific (EC 1.1.1.4) 0   1
2-isopropylmalate synthase (EC 2.3.3.13)    1   2
23S rRNA (adenine(2058)-N(6))-dimethyltransferase (EC 2.1.1.184) => Erm(B)  0   1
4-hydroxybenzoate polyprenyltransferase and related prenyltransferases  0   1
5S rRNA 2   3
6-phospho-beta-galactosidase (EC 3.2.1.85)  1   2
AAA superfamily ATPase  0   1
ABC transporter amino acid-binding protein  0   1
ABC transporter, ATP-binding protein    13  11
ABC transporter, ATP-binding protein (cluster 3, basic aa/glutamine/opines) 3   4
ABC transporter, permease protein (cluster 3, basic aa/glutamine/opines)    5   6
ABC transporter, substrate-binding protein PebA (cluster 3, basic aa/glutamine/opines)  2   1

weak similarity to aminoglycoside phosphotransferase    1   0
* Features  3382    3304
* DNA   2101113 2052306
All done.
contigs               110
dna               4153419
features             6686
functionAnalyzed     1457
functionRead         6686
functionReused       5229
roleMatch            1356
roleMismatch          175
roleProcessed        6877

Only roles that differ between the two genomes are shown (175, the number in roleMismatch). For each, the role name is shown followed by the number of occurrences in 1313.7001.gto and then the number of occurrences in 1313.7016.gto. So, we can see that 2-isopropylmalate synthase occurs once in 1313.7001 but twice in 1313.7016. At the end of the role listing, feature and DNA counts are shown. We see that 1313.7016 has 78 fewer features and around 50,000 fewer base pairs (48,807 to be exact). 1356 roles occurred the same number of times in both genomes (roleMatch).

You can specify as many GTO file names as you wish in the parameter list for p3-gto-scan. As with the single-genome case, --features causes the features to be listed in the last column. The --verbose option causes even the matching roles to be listed, so you can get counts for everything.

The status and statistical messages are sent to the standard error output, and the role table to the standard output. Thus, if you redirect these to separate files, the direct output from p3-gto-scan can be used to get a convenient list of roles from the script. The file thus created is tab-delimited with headers, just like a normal CLI output file.

The script p3-gto-fasta creates FASTA files from a single GTO. Three command-line options (all mutually exclusive) are supported.

--contig

Output a DNA fasta for the genome’s contigs. This is the default.

--protein

Output a protein fasta for the genome’s features. Obviously, only protein-encoding features will be included.

--feature

Output a DNA fasta for the genome’s features. All features are included.

You specify the name of the GTO file as the first parameter of p3-gto-fasta.

p3-gto-fasta 1313.7001.gto >1313.7001.fna

After this script, 1313.7001.fna will look something like this.

>1313.7001.con.0001
gaaaggacaaaatttgtcctttctcaagcttagctgacttcaacccactacagttgacaa
agagcctgttttctcaataggattgtactcaggtgagtagggaggaagaggtaaaagttt
atgcccaaactcttcacacaagagttctagcttacccattctatggaatcttgcattatc
cataataataaccgatggtgtggttaatgttggtaagagaaatttctgaaaccatacttc
aaaaaagtcgctcgtcatcgtctcttcgtaagtcattggagcgattaattcaccatttgt
tagacctgcaaccaaagaaatcctctgatatcttcttccagatactttgcctcttcttaa
ctgaccttttaatgagcgaccatattctcgataaaaataagtatcgaatcctgtttcgtc
aatctaaacaggtgctaggtgctttaaactattaaaattcttaagaaataaggctactta
tcgccctgaatatcaaaaaagaaaggacaaaatttgtcctttctcaagcttagctgactt
caacccactacagttgacaaagagcctgttttctcaataggattgtactcaggtgagtag
ggaggaagaggtaaaagtttatgcccaaactcttcacacaagagttctagcttacccatt

In the feature-based fasta files, the functional assignment is included as a comment, as shown below.

p3-gto-fasta --protein 1313.7001.gto

>fig|1313.7001.peg.1182 beta-glycosyl hydrolase
MKHEKQQRFSIRKYAVGAASVLIGFAFQAQTVAADGVTTTTENQPTIHTVSDSPQSSENR
TEETPKAELQPETPATDKVASLPKTEEKPQEEVSSTPSDKAEVVTPTSAEKETANKKAEE
ASPKKEEAKEVDSKESNTDKTDKDKPAKKDEAKAEADKPETEAGKERAATVNEKLAKKKI
VSIDAGRKYFSPEQLKEIIDKAKHYGYTDLHLLVGNDGLRFMLDDMSITANGKTYASDDV
KRAIEKGTNDYYNDPNGNHLTESQMTDLINYAKDKGIGLIPTVNSPGHMDAILNAMKELG
IQNPNFSYFGKESARTVNLDNEQAVAFTKALIDKYAAYFAKKTEIFNIGLDEYANDATDA
KGWSVLQADKYYPNEGYPVKGYEKFIAYANDLARIVKSHGLKPMAFNDGIYYNSDTSFGS
FDKDIIVSMWTGGWGGYDVASSKLLAEKGHQILNTNDAWYYVLGRNADGQGWYNLDQGLN
GIKNTPITSVPKTEGADIPIIGGMVAAWADTPSARYSPSRLFKLMRHFANANAEYFAADY
ESAEQALNEVPKDLNRYTAESVAAVKEAEKAIRSLDSNLSRAQQDTIDQAIAKLQETVNN
LTLTPEAQKEEEAKREVEKLAKNKVISIDAGRKYFTLNQLKRIVDKASELGYSDVHLLLG
NDGLRFLLDDMTITANGKTYASDDVKKAIIEGTKAYYDDPNGTTLTQAEVTELIEYAKSK
DIGLIPAINSPGHMDAMLVAMEKLGIKNPQAHFDKVSKTTMDLKNEEAMNFVKALIGKYM

Only protein-encoding genes are output with the --protein option; however, you see all the features when you use the --feature option.

p3-gto-fasta --feature 1313.7001.gto

>fig|1313.7001.repeat.1 repeat region
tgttttctcaataggattgtactcaggtgagtagggaggaagaggtaaaagtttatgccc
aaactcttcacacaagagttctagcttacccattctatggaatcttgcattatccataat
aataaccgatggtgtggttaatgttggtaagagaaatttctgaaaccatacttcaaaaaa
gtcgctcgtcatcgtctcttcgtaagtcattggagcgattaattcaccatttgttagacc
tgcaaccaaagaaatcctctgatatcttcttccagatactttgcctcttcttaactgacc
ttttaatgagcgaccatattctcgataaaaataagtatcgaatcctgtttcgtcaatcta
aacaggtgctaggtgctttaaactattaaaattcttaagaaataaggctactt
>fig|1313.7001.repeat.2 repeat region
tgttttctcaataggattgtactcaggtgagtagggaggaagaggtaaaagtttatgccc
aaactcttcacacaagagttctagcttacccattctatggaatcttgcattatccataat

Using RAST to Create New Genomes

If you have a DNA fasta file and you know the taxonomic ID with a certain degree of confidence, you can use the script p3-rast to annotate the DNA and produce a new genome. The standard output of the script is a GTO. In almost every case, you will want to redirect this to a file. In addition, the new genome is stored in your workspace. It will appear in listings from p3-all-genomes, and you can find its files via the web interface in your QuickData folders.

To invoke p3-rast, you specify a taxonomic ID or the ID of a genome with the same taxonomic ID plus the name to give to the new genome. The contigs should be in the form of a FASTA file via the standard input. All this data is submitted to the PATRIC annotation service. When the service completes, it stores the new genome in your workspace and sends back a GTO. The example below shows a submission of sequences taken from a metagenomic sample named SRS576036 chosen because they have a high similarity to sequences from Catenibacterium mitsuokai (taxon ID 100886).

p3-rast 100886 "Catenibacterium from sample SRS576036" <sample.fna >test.gto 2>test.log

Now test.gto contains a GTO of the resulting genome and test.log contains information about the RAST job. If we use the --private option of p3-all-genomes, we will see the new genome in the list.

p3-all-genomes --private --attr genome_name

genome.genome_id       genome.genome_name
100886.26       Catenibacterium from sample SRS576036

The genome was assigned the ID 100886.26. We can see this in the GTO file as well.

{
   "genetic_code" : "11",

         ],
         "family_assignments" : [],
         "type" : "CDS",
         "id" : "fig|100886.26.peg.1540"
      },
      {
         "protein_translation" : "MLQIENASIAYGNDILFSGFNLQLERGEIASISGPSGCGKSSLLNAILGFTPLKEGRIVLNGILLDKGNVDVVRKQTAWIPQELALPLEWVKDMVQLPFGLKANRGTPFSETRLFACFEDLGLEQELYYKRVNEISGGQRQRMMIAVASMIGKPLTIVDEPTSALDSGSAEKVLSFFRRQTENGSAILTVSHDKRFANGCDRHIIMK",
         "aliases" : [],
         "location" : [
            [
               "100886.26.con.0010",
               "23684",
               "-",
               624
            ]

         "type" : "CDS"
      }
   ],
   "id" : "100886.26",
   "contigs" : [
      {
         "id" : "100886.26.con.0001",

}

The genome ID appears as a part of every feature ID, as an ID in its own right, and as the first part of every contig ID.

As long as you are signed in, the genomes you create using p3-rast will participate in all queries.

p3-all-genomes --eq taxon_id,100886 --attr genome_name

genome.genome_id        genome.genome_name
100886.3        Catenibacterium mitsuokai
100886.26       Catenibacterium from sample SRS576036

However, just as you can restrict p3-all-genomes to your own private genomes using the --private option, you can restrict it to public genomes only using the --public option.

p3-all-genomes --public --eq taxon_id,100886 --attr genome_name

genome.genome_id        genome.genome_name
100886.3        Catenibacterium mitsuokai

The GTO produced by p3-rast has extra information in it describing the annotation process, but it is functionally equivalent to the output were you to re-fetch the genome using the standard script.

p3-gto 100886.26

A p3-gto-scan for test.gto would return the same role profile as for 100886.26.gto.

Customizing Your Toolkit

The set of commands that we support via the p3-scripts offers a fairly broad set of capabilities. For example, say you want the name of a specific genome from the ID. You can do this easily using

p3-echo -t genome_id 670.470 | p3-get-genome-data --attr genome_name

genome_id       genome.genome_name
670.470 Vibrio parahaemolyticus strain S176-10

If you do this a lot, you may find the extra typing tedious. It is worth, therefore, a brief discussion of how to create shortcut scripts.

Custom Scripts in the BASH Environment

In BASH (the most popular Unix shell) you can add functions to your .bashrc file, using $-notation to indicate the incoming command-line variables. So, to create the command

gn 670.470

You would use the function definition

function gn {
    p3-all-genomes --eq=genome_id,$1 --attr genome_name
}

You must reload the shell to activate your changes to the .bashrc file. Use

exec bash

to replace your current shell with a new instance.

In the function, the $1 is replaced by the first parameter on the command, which in our example is 670.470. If you type

gn 1313.7001

the $1 is replaced by 1313.7001, so the output would be

genome_id       genome.genome_name
1313.7001       Streptococcus pneumoniae P210774-233

You can have more than one parameter. The second is called $2, the third $3, and so on. The following function creates a genome group of everything resistant to a particular drug. The drug is the first parameter, the group name the second.

function rg {
    p3-echo -t antibiotic $1 | p3-get-drug-genomes --resistant --attr genome_id | p3-put-genome-group $2
}

Once the above definition is in place, the following command will put all the methicillin-resistant genomes into the group meth_resist.

rg methicillin meth_resist

Custom Scripts for the Windows CMD Shell

In Windows, you create a file with the extension .cmd that has your script in it, and put the file somewhere in your path. The incoming command-line variables use %-notation. The special command @echo off is normally put at the beginning of the file to prevent the file internals from displaying.

So, to create the command

gn 670.470

You would create the file

@echo off
p3-all-genomes --eq=genome_id,%1 --attr genome_name

and save it as gn.cmd in your script directory (which should be some directory you have defined and placed on your path).

In the function, the %1 is replaced by the first parameter on the command, which in our example is 670.470. If you type

gn 1313.7001

the %1 is replaced by 1313.7001, so the output would be

genome_id       genome.genome_name
1313.7001       Streptococcus pneumoniae P210774-233

You can have more than one parameter. The second is called %2, the third %3, and so on. The following function creates a genome group of everything resistant to a particular drug. The drug is the first parameter, the group name the second.

@echo off
p3-echo -t antibiotic %1 | p3-get-drug-genomes --resistant --attr genome_id | p3-put-genome-group %2

Once the above is saved as rg.cmd, the following command will put all the methicillin-resistant genomes into the roup meth_resist.

rg methicillin meth_resist

More Applications

The following documents describe more applications for the PATRIC CLI.

1. Looking for Hypothetical Proteins in Clusters of Related Features

2. Computing Signature Clusters: an Application of the Command-Line Tools

3. Common Tasks With P3 Scripts

4. What Distinguishes One Set of Genomes from Another? (coming soon)

5. Uploading Genomes and Assembling Reads (coming soon)