BioBB NetProp Command Line Help

Generic usage:

biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>

GDADisGenet

biobb_netprop Gene Disease Association DisGenet retrieval

Get help

Command:

gda_disgenet -h 

usage: gda_disgenet [-h] [--config CONFIG] --input_file_path INPUT_FILE_PATH --output_csv_path OUTPUT_CSV_PATH

Gene Disease Attributes retrieval from the DisGenet database.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        General path of working Dir.
  --output_csv_path OUTPUT_CSV_PATH
                        Results from the DisGenet database in CSV format. Accepted formats: csv.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): Path to the working dir.
output_csv_path (string): Path to the CSV file with the Gene Disease Attributes from the DisGenet database. File type: csv. Sample file. Accepted formats: CSV

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

retrieve_by (str) - Configuration params to pass for the retrieval of the association on the REST API (gene, uniprot_entry, disease, source, evidences_gene, evidences_disease).
gene_id (str) - Number identification for a gene or a list of genes separated by commas recognized by the database.
disease (str) - Disease id or a list of disease separated by commas.
disease_type (str) - Disease, phenotype, group.
source (str) - Source of the associations (CURATED, INFERRED, ANIMAL_MODELS, ALL, BEFREE, CGI, CLINGEN, CLINVAR, CTD_human, CTD_mouse, CTD_rat, GENOMICS_ENGLAND, GWASCAT, GWASDB, HPO, LHGDN, MGD, ORPHANET, PSYGENET, RGD, UNIPROT).
disease_vocabulary (str) - Disease vocabulary (icd9cm, icd10, mesh, omim, do, efo, nci, hpo, mondo, ordo).
disease_class * - MeSh disease classes.
min_score (str) - Min value of the gene-disease score range.
max_score (str) - Max value of the gene-disease score range.
min_ei (str) - Min value of evidence index score range.
max_ei (str) - Max value of evidence index score range.
max_dsi (str) - Max value of DSI range for the gene.
min_dsi (str) - Min value of DSI range for the gene.
max_pli (str) - Max value of pLI range for the gene.
min_pli (str) - Min value of pLI range for the gene.
format (str) - Format output file.
limit (str) - Number of GDAs to retrieve.
min_year (str) - The year of the earliest publications.
max_year (str) - The year of the latest publicatons.
offset (str) - Starting offset of the page.

YAML

Common config file 

properties:
    retrieve_by: 'disease'
    disease_id: C0002395
    min_score: 0.2
    max_score: 1.0

Command line

gda_disgenet --config config.yml --input_file_path /path/to/working/dir --output_csv_path gda_results.csv

JSON

Common config file 

{
  "properties": {
	"retrieve_by": "disease",
        "disease_id": C0002395,
        "min_score": 0.2,
        "max_score": 1.0,
  }
}

Command line

gda_disgenet --config config.json --input_file_path /path/to/working/dir --output_csv_path gda_results.csv

VDADisGenet

biobb_netprop Variant Disease Association DisGenet retrieval

Get help

Command:

vda_disgenet -h

usage: vda_disgenet [-h] [--config CONFIG] --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Variant Disease Attributes retrieval from the DisGenet database.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        General path of working Dir.
  --output_file_path OUTPUT_FILE_PATH
                        Results from the DisGenet database in CSV format. Accepted formats: csv, json, tsv and xml.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): Path to the working dir.
output_file_path (string): Path to the CSV file with the Variant Disease Attributes from the DisGenet database. File type: csv. Sample file. Accepted formats: CSV

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

retrieve_by (str) - Configuration params to pass for the retrieval of the association on the REST API (gene, variant, disease, source, evidences_gene, evidences_disease).
variant_id (str) - Number identification for a gene or a list of genes separated by commas recognized by the database.
disease_id (str) - Disease id or a list of disease separated by commas.
disease_type (str) - Disease, phenotype, group.
type (str) - Disease, phenotype, group.
source (str) - Source of the associations (CURATED, INFERRED, ANIMAL_MODELS, ALL, BEFREE, CGI, CLINGEN, CLINVAR, CTD_human, CTD_mouse, CTD_rat, GENOMICS_ENGLAND, GWASCAT, GWASDB, HPO, LHGDN, MGD, ORPHANET, PSYGENET, RGD, UNIPROT).
disease_vocabulary (str) - Disease vocabulary (icd9cm, icd10, mesh, omim, do, efo, nci, hpo, mondo, ordo).
disease_class * - MeSh disease classes.
min_score (str) - Min value of the gene-disease score range.
max_score (str) - Max value of the gene-disease score range.
min_ei (str) - Min value of evidence index score range.
max_ei (str) - Max value of evidence index score range.
max_dsi (str) - Max value of DSI range for the gene.
min_dsi (str) - Min value of DSI range for the gene.
max_pli (str) - Max value of pLI range for the gene.
min_pli (str) - Min value of pLI range for the gene.
format (str) - Format output file.
limit (str) - Number of GDAs to retrieve.
min_year (str) - The year of the earliest publications.
max_year (str) - The year of the latest publicatons.
offset (str) - Starting offset of the page.

YAML

Common config file 

properties:
    retrieve_by: 'disease'
    disease_id: C0002395
    min_score: 0.2
    max_score: 1.0

Command line

vda_disgenet --config config.yml --input_file_path /path/to/working/dir --output_file_path vda_results.csv

JSON

Common config file 

{
  "properties": {
        "retrieve_by": "disease",
        "disease_id": C0002395,
        "min_score": 0.2,
        "max_score": 1.0,
  }
}

Command line

vda_disgenet --config config.json --input_file_path /path/to/working/dir --output_file_path vda_results.csv

DDADisGenet

biobb_netprop Disease Disease Association DisGenet retrieval

Get help

Command:

dda_disgenet -h

usage: dda_disgenet [-h] [--config CONFIG] --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Disease Disease Attributes retrieval from the DisGenet database.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        General path of working Dir.
  --output_file_path OUTPUT_FILE_PATH
                        Results from the DisGenet database in CSV format. Accepted formats: csv, json, tsv and xml.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): Path to the working dir.
output_file_path (string): Path to the CSV file with the Disease Disease Attributes from the DisGenet database. File type: csv. Sample file. Accepted formats: CSV

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

retrieve_by (str) - Configuration params to pass for the retrieval of the association on the REST API (genes or variants).
disease_id (str) - Disease id or a list of disease separated by commas.
source (str) - Source of the associations (CURATED, INFERRED, ANIMAL_MODELS, ALL, BEFREE, CGI, CLINGEN, CLINVAR, CTD_human, CTD_mouse, CTD_rat, GENOMICS_ENGLAND, GWASCAT, GWASDB, HPO, LHGDN, MGD, ORPHANET, PSYGENET, RGD, UNIPROT).
disease_vocabulary (str) - Disease vocabulary (icd9cm, icd10, mesh, omim, do, efo, nci, hpo, mondo, ordo).
pvalue (str) - Pvalue of the disease-disease score range.
format (str) - Format output file.
limit (str) - Number of disease to retrieve.
remove_tmp (bool) - (True) [WF property] Remove temporal files.
restart (bool) - (False) [WF property] Do not execute if output files exist.

YAML

Common config file 

properties:
    retrieve_by: 'genes'
    disease_id: C0002395
    pvalue: 0.7
    limit: 10

Command line

dda_disgenet --config config.yml --input_file_path /path/to/working/dir --output_file_path dda_results.csv

JSON

Common config file 

{
  "properties": {
        "retrieve_by": "disease",
        "disease_id": C0002395,
        "pvalue": 0.7,
        "limit": 10,
  }
}

Command line

dda_disgenet --config config.json --input_file_path /path/to/working/dir --output_file_path dda_results.csv

GADisGenet

biobb_netprop Gene Attribute DisGenet retrieval

Get help

Command:

ga_disgenet -h

usage: ga_disgenet [-h] [--config CONFIG] --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Gene Attributes retrieval from the DisGenet database.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_file_path INPUT_FILE_PATH
                        General path of working Dir.
  --output_file_path OUTPUT_FILE_PATH
                        Results from the DisGenet database in CSV format. Accepted formats: csv, json, tsv and xml.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_file_path (string): Path to the working dir.
output_file_path (string): Path to the CSV file with the Gene Attributes from the DisGenet database. File type: csv. Sample file. Accepted formats: CSV, TSV, JSON and XML.

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

retrieve_by (str) - Configuration params to pass for the retrieval of the association on the REST API (gene, uniprot, source).
gene_id (str) - Number identification for a gene or a list of genes separated by commas recognized by the database.
uniprot_id (str) - Uniprot id or a list of disease separated by commas.
source (str) - Source of the associations (CURATED, INFERRED, ANIMAL_MODELS, ALL, BEFREE, CGI, CLINGEN, CLINVAR, CTD_human, CTD_mouse, CTD_rat, GENOMICS_ENGLAND, GWASCAT, GWASDB, HPO, LHGDN, MGD, ORPHANET, PSYGENET, RGD, UNIPROT).
max_dsi (str) - Max value of DSI range for the gene.
min_dsi (str) - Min value of DSI range for the gene.
max_pli (str) - Max value of pLI range for the gene.
min_pli (str) - Min value of pLI range for the gene.
format (str) - Format output file.
limit (str) - Number of GAs to retrieve.

Common config file 

properties:
    retrieve_by: 'gene'
    gene_id: 'AD3L'
    max_dsi: 0.7

Command line

ga_disgenet --config config.yml --input_file_path /path/to/working/dir --output_file_path ga_results.json

JSON

Common config file 

{
  "properties": {
        "retrieve_by": "gene",
        "gene_id": AD3L,
        "max_dsi": 0.7,
  }
}

Command line

ga_disgenet --config config.json --input_file_path /path/to/working/dir --output_file_path ga_results.csv

VADisGenet

biobb_netprop Variant Attribute DisGenet retrieval

Get help

Command:

va_disgenet -h

usage: va_disgenet [-h] [--config CONFIG] --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Variant Attributes retrieval from the DisGenet database.

optional arguments:
  -h, --help            show this help message and exit
  --config config       configuration file

required arguments:
  --input_file_path input_file_path
                        general path of working dir.
  --output_file_path output_file_path
                        results from the disgenet database in csv format. accepted formats: csv, json, tsv and xml.

i / o arguments

syntax: input_argument (datatype) : definition

config input / output arguments for this building block:

input_file_path (string): path to the working dir.
output_file_path (string): path to the CSV file with the Variant Attributes from the DisGenet database. file type: csv, json, tsv, xml. sample file. accepted formats: csv, tsv, json and xml.

config

syntax: input_parameter (datatype) - (default_value) definition

config parameters for this building block:

retrieve_by (str) - configuration params to pass for the retrieval of the association on the rest api (gene, variant, source).
gene_id (str) - number identification for a gene or a list of genes separated by commas recognized by the database.
variant_id (str) - List of variants (dbSNP Identifiers) separated by “,” up to 100.
source (str) - source of the associations (curated, inferred, animal_models, all, befree, cgi, clingen, clinvar, ctd_human, ctd_mouse, ctd_rat, genomics_england, gwascat, gwasdb, hpo, lhgdn, mgd, orphanet, psygenet, rgd, uniprot).
max_dsi (str) - max value of dsi range for the gene.
min_dsi (str) - min value of dsi range for the gene.
max_pli (str) - max value of pli range for the gene.
min_pli (str) - min value of pli range for the gene.
format (str) - format output file.
limit (str) - number of gas to retrieve.

common config file 

properties:
    retrieve_by: 'variant'
    variant_id: 'ad3l'
    max_dsi: 0.7

command line

va_disgenet: --config config.yml --input_file_path /path/to/working/dir --output_file_path va_results.json

JSON

Common config file 

{
  "properties": {
        "retrieve_by": "variant",
        "variant_id": AD3L,
        "max_dsi": 0.7,
  }
}

Command line

va_disgenet --config config.json --input_file_path /path/to/working/dir --output_file_path va_results.csv

DADisGenet

biobb_netprop Disease Attribute DisGenet retrieval

Get help

Command:

da_disgenet -h

usage: da_disgenet [-h] [--config CONFIG] --input_file_path INPUT_FILE_PATH --output_file_path OUTPUT_FILE_PATH

Disease Attributes retrieval from the DisGenet database.

optional arguments:
  -h, --help            show this help message and exit
  --config config       configuration file

required arguments:
  --input_file_path input_file_path
                        general path of working dir.
  --output_file_path output_file_path
                        results from the disgenet database in csv format. accepted formats: csv, json, tsv and xml.

i / o arguments

syntax: input_argument (datatype) : definition

config input / output arguments for this building block:

input_file_path (string): path to the working dir.
output_file_path (string): path to the csv file with the Disease Attributes from the DisGenet database. file type: csv, json, tsv, xml. sample file. accepted formats: csv, tsv, json and xml.

config

syntax: input_parameter (datatype) - (default_value) definition

config parameters for this building block:

retrieve_by (str) - configuration params to pass for the retrieval of the association on the rest api (disease, diseaseName, source, mappings, similarity).
diseaseName (str) - Disease name recognized by the database.
disease_id (str) - number identification for a gene or a list of genes separated by commas recognized by the database.
variant_id (str) - List of variants (dbSNP Identifiers) separated by “,” up to 100.
source (str) - source of the associations (curated, inferred, animal_models, all, befree, cgi, clingen, clinvar, ctd_human, ctd_mouse, ctd_rat, genomics_england, gwascat, gwasdb, hpo, lhgdn, mgd, orphanet, psygenet, rgd, uniprot).
max_dsi (str) - max value of dsi range for the gene.
min_dsi (str) - min value of dsi range for the gene.
max_pli (str) - max value of pli range for the gene.
min_pli (str) - min value of pli range for the gene.
format (str) - format output file.
limit (str) - number of gas to retrieve.

common config file 

properties:
    retrieve_by: 'disease'
    disease_id: 'C00002352'
    max_dsi: 0.7

command line

da_disgenet: --config config.yml --input_file_path /path/to/working/dir --output_file_path da_results.json

JSON

Common config file 

{
  "properties": {
        "retrieve_by": "disease",
        "disease_id": 'C00002352',
        "max_dsi": 0.7,
  }
}

Command line

da_disgenet --config config.json --input_file_path /path/to/working/dir --output_file_path da_results.csv

Parse HIPPIE

biobb_netprop Parse HIPPIE database wrapper.

Get help

Command:

parsehippie -h

usage: parsehippie [-h] [--config CONFIG] --input_file_path1 INPUT_FILE_PATH1 --input_file_path2 INPUT_FILE_PATH2 --output_sif_path OUTPUT_SIF_PATH

Parsing the HIPPIE database using the Human genome as reference.

optional arguments:
  -h, --help            show this help message and exit
  --config config       configuration file

required arguments:
  --input_file_path1 input_file_path
                        Path for the HIPPIE database downloaded in a specific dir, **mandatory to download on its own**.
  --input_file_path2 input_file_path
                        Path for the HIPPIE genes to be parsed, **mandatory to download on its own**.
  --output_sif_path output_sif_path
                        Path for the resulting panda dataframe from the HIPPIE PPi parsing, in sif format. accepted formats: sif.

i / o arguments

syntax: input_argument (datatype) : definition

config input / output arguments for this building block:

input_file_path1 (string): Path for the HIPPIE database downloaded locally.
input_file_path2 (string): Path for the HIPPIE genes to be parsed in the HIPPIE PPi database.
output_sif_path (string): Path for the resulting panda dataframe from the HIPPIE PPi parsing. File type: csv, json, tsv, xml. sample file. Accepted formats: sif.

config

syntax: input_parameter (datatype) - (default_value) definition

config parameters for this building block:

hippie_score (str) - HIPPIE score used as filter, based on the number of studies, experimental techniques and their quality to measure the interaction detected.
disgenet_score (str) - DisGenet score used as a filter, gene-disease/variant-disease/disease-disease range scores to consider as minimal value of quality from the DisGenet retrieval.

common config file 

properties:
	hippie_score: 0.2 
	disgenet_score: 0.8

command line

parsehippie --config config.yml --input_file_path1 /path/to/hippieDatabase.txt --input_file_path2 /path/to/hippieHumanGenes.txt --output_file_path interactome.sif

Making Nodes

biobb_netprop Making Nodes using NetworkX wrapper.

Get help

Command:

maknodes -h

usage: maknodes [-h] [--config CONFIG] --input_file_path1 INPUT_FILE_PATH1 --input_file_path2 INPUT_FILE_PATH2 --input_file_dataset INPUT_FILE_DATASET --output_sif_path OUTPUT_SIF_PATH

Parsing the HIPPIE database using the Human genome as reference.

optional arguments:
  -h, --help            show this help message and exit
  --config config       configuration file

required arguments:
  --input_file_path1 input_file_path
                        Path for the panda dataframe, coming out of the **Parse Hippie** wrapped function.
  --input_file_path2 input_file_path
                        Path for the GDA/VDA retrieval attributes and genes, coming out of the DisGenet wrapped functions.
  --input_file_dataset input_file_dataset
                        Path for the DisGenet database, curated or not, **downloaded locally on its own**.
  --output_sif_path output_sif_path
                        Path for the resulting panda dataframe from the HIPPIE PPi and DisGenet genes coupling, in sif format. Accepted formats: sif.

i / o arguments

syntax: input_argument (datatype) : definition

config input / output arguments for this building block:

input_file_path1 (string): Path for the panda dataframe, coming out of the Parse Hippie wrapped function.
input_file_path2 (string): Path for the GDA/VDA retrieval attributes and genes, coming out of the DisGenet wrapped functions.
input_file_dataset (string): Path for the DisGenet database, curated or not, downloaded locally on its own.
output_sif_path (string): Path for the resulting panda dataframe from the HIPPIE PPi and DisGenet geens coupling. File type: sif. sample file. Accepted formats: sif.

config

syntax: input_parameter (datatype) - (default_value) definition

config parameters for this building block:

curated (bool) - (True) Choosing the curated or not database version
disease_id (str) - (”sample”) Disease ID used in DisGenet retrieval.
disgenet_score (str) - (0.0) Score that was used in the DiGenet retrieval.
scoring_mode (str) - (”sample”) Defining the Scoring system to be used to rate the PPI Network, can be dis (considering the DisGenet Score), norm_dis (considering the normalized DisGenet Score), binary.

common config file 

properties:
        curated: True
	disease_id: C0002352
        disgenet_score: 0.8
	scoring_mode: dis

command line

maknodes --config config.yml --input_file_path1 /path/to/interactome.sif --input_file_path2 /path/to/GDAVDAGenes.txt --input_file_dataset /path/to/disgenetDatabase --output_sif_path interactome.sif

Call NetProp

biobb_netprop GUILD wrappper, for network-based prioritization framework to unveil genes associated with a disease phenotype (disease-genes).

Get help

Command:

call_netprop -h

usage: call_netprop [-h] [--config CONFIG] --input_file_path1 INPUT_FILE_PATH1 --input_file_path2 INPUT_FILE_PATH2 --input_netprop_dir INPUT_NETPROP_DIR --output_file_path OUTPUT_FILE_PATH

Parsing the HIPPIE database using the Human genome as reference.

optional arguments:
  -h, --help            show this help message and exit
  --config config       configuration file

required arguments:
  --input_file_path1 input_file_path
                        Path for the HIPPIE PPi and DisGenet genes parsed, coming out of the NetworkX wrapper function.
  --input_file_path2 input_file_path
                        Path for the HIPPIE PPi dataframe, coming out of the **maknodes** wrapped function.
  --input_netprop_dir input_netprop_dir
                        Path for the GUILD dir.
  --output_file_path output_file_path
                        Path for the resulting TXT column file the GUILD PPi algorithm. Accepted formats: txt.

i / o arguments

syntax: input_argument (datatype) : definition

config input / output arguments for this building block:

input_file_path1 (string): Path for HIPPIE PPi and DisGenet genes parsed, coming out of the NetworkX wrapper function.
input_file_path2 (string): Path for the HIPPIE PPi dataframe, coming out of the maknodes wrapped function.
input_netprop_dir (string): Path for the GUILD dir, dowloaded locally.
output_file_path (string): Path for the resulting panda dataframe from the HIPPIE PPi and DisGenet geens coupling. File type: sif. sample file. Accepted formats: sif.

config

syntax: input_parameter (datatype) - (default_value) definition

config parameters for this building block:

algorithm (string) - Choosing the reference algorithm for GUILD to be used, can be s for NetScore, or z for NetZScore.

common config file 

properties:
        algorithm: 's'

command line

call_netprop --config config.yml --input_file_path1 /path/to/interactome.sif --input_file_path2 /path/to/GDAVDAGenes.txt --input_file_dataset /path/to/disgenetDatabase --output_sif_path interactome.sif