bapi

bapi

bapi is an open source and cross-platform command line tool to query the APIs of bioinformatics related websites and conduct the text-mining of PubMed abstract.

Now, it can be used to query the APIs of dataset2tools, GDC Portal, and NCBI.

In the future, we will include more useful APIs of bioinformatics, such as BioMart, Fairsharing, EGA-Archive, and your request.

In addition, you can use the bapi to conduct the simple text-mining of PubMed abstract at the sentence level.

• support calculate correlations between any keywords at the sentence level (PubMed)
• support extract URLs from Pubmed abstract
• support convert PubMed abstract from XML => JSON
• support to prettify JSON stream
• support convert key-value JSON to slice JSON

Installation

# Binary
Linux: https://github.com/Miachol/bapi/releases/download/v0.1.0/bapi_linux64
Mac: https://github.com/Miachol/bapi/releases/download/v0.1.0/bapi_osx
Win: https://github.com/Miachol/bapi/releases/download/v0.1.0/bapi.exe

# For windows user, we recommend to run bapi at git bash mode (support awk and other GNU tools)
# See more: https://git-scm.com/

# Golang developer
go get -u github.com/Miachol/bapi

Usage

You can direct to type bapi to see all subcommands and global flags of bapi. Now, this project is unstable, the name or flags may changed in the future.

Query bioinformatics website APIs. More see here https://github.com/Miachol/bapi.

Usage:
  bapi [flags]
  bapi [command]

Available Commands:
  dta         Query dataset2tools website APIs: datasets (d), tools (t), and canned analysis (a).
  fmt         A set of file format (fmt) command of bapi.
  gdc         Query GDC portal website APIs.
  help        Help about any command
  ncbi        Query ncbi website APIs.

Flags:
  -e, --email string             Email specifies the email address to be sent to the server (NCBI website is required). (default "your_email@domain.com")
      --format string            Rettype specifies the format of the returned data (CSV, TSV, JSON for gdc; XML/TEXT for ncbi).
      --from int                 Parameters of API control the start item of retrived data. (default -1)
  -h, --help                     help for bapi
  -q, --query string             Query specifies the search query for record retrieval (required).
      --quiet                    No log output.
  -r, --retries int              Retry specifies the number of attempts to retrieve the data. (default 5)
      --retries-sleep-time int   Sleep time after one retry. (default 5)
      --size int                 Parameters of API control the lenth of retrived data. Default is auto determined. (default -1)
      --timeout int              Set the timeout of per request. (default 35)
      --version                  version for bapi

Use "bapi [command] --help" for more information about a command.

GDC query:

Query GDC portal APIs. More see here https://github.com/Miachol/bapi.

Usage:
  bapi gdc [flags]

Examples:
  # Query projects in GDC portal
  bapi gdc -p
  # Query projects in GDC portal in pretty JSON
  bapi gdc -p --json-pretty
  # Query TARGET-NBL project in GDC portal in pretty JSON
  bapi gdc -p -q TARGET-NBL --json-pretty
  # Query projects in TSV format
  bapi gdc -p --format TSV > tcga_projects.tsv
  # Query projects in CSV format
  bapi gdc -p --format CSV > tcga_projects.csv
  # Query projects via control the start item and total item
  bapi gdc -p --from 1 --szie 2
  # See status of GDC portal
  bapi gdc -s
  # Retrive cases info from GDC portal
  bapi gdc -c
  # Retrive files info from GDC portal
  bapi gdc -f
  # Retrive annotations info from GDC portal. 
  bapi gdc -a

  // Download manifest for gdc-client
  bapi gdc -m -q "5b2974ad-f932-499b-90a3-93577a9f0573,556e5e3f-0ab9-4b6c-aa62-c42f6a6cf20c" -o my_manifest.txt
  bapi gdc -m -q "5b2974ad-f932-499b-90a3-93577a9f0573,556e5e3f-0ab9-4b6c-aa62-c42f6a6cf20c" > my_manifest.txt
  bapi gdc -m -q "5b2974ad-f932-499b-90a3-93577a9f0573,556e5e3f-0ab9-4b6c-aa62-c42f6a6cf20c" -n

  // Download data
  bapi gdc -d -q "5b2974ad-f932-499b-90a3-93577a9f0573" -n

Query NCBI:

Query ncbi website APIs. More see here https://github.com/Miachol/bapi.

Usage:
  bapi ncbi [flags]

Examples:
  # Search Pubmed database with "B-ALL" query and returns XML format file
  bapi ncbi -d pubmed -q B-ALL --format XML -e your_email@domain.com
  # Split returns XML files
  bapi ncbi -q "RNA-seq and bioinformatics[journal]" -e "your_email@domain.com" -m 100 | awk '/<[?]xml version="1.0" [?]>/{close(f); f="abstract.http.XML.tmp" ++c;next} {print>f;}'

  # Calculate the words corelations at sentence level
  k="algorithm, tool, model, pipleline, method, database, workflow, dataset, bioinformatics, sequencing, http, github.com, gitlab.com, bitbucket.org, RNA-Seq, DNA, profile, landscape"
  bapi ncbi --xml2json pubmed abstract.http.XML.tmp* -k "${k}" --call-cor | sed 's;}{;,;g' > final.json

  # Support to input the pipe stream with '-' flag
  bapi ncbi -q "Galectins control MTOR and AMPK in response to lysosomal damage to induce autophagy OR MTOR-independent autophagy induced by interrupted endoplasmic reticulum-mitochondrial Ca2+ communication: a dead end in cancer cells. OR The PARK10 gene USP24 is a negative regulator of autophagy and ULK1 protein stability OR Coordinate regulation of autophagy and the ubiquitin proteasome system by MTOR." | bapi ncbi --xml2json pubmed -k "MAPK, MTOR, autophagy" --call-cor - | sed 's;}{;,;g' | bapi fmt --json-to-slice - > final.json

  # json2csv install from https://github.com/zemirco/json2csv#readme
  json2csv -i final.json -o final.csv  

Query dataset2tools:

Query dataset2tools APIs. More see here https://github.com/Miachol/bapi.

Usage:
  bapi dta [flags]

Examples:
  # retrive canned_analysis
  bapi dta -a DCA00000060
  # retrive dataset in pretty JSON format
  bapi dta -s GSE31106 | bapi fmt --json-pretty -
  # pretty JSON format with indent control
  bapi dta --type dataset | bapi fmt --json-pretty --indent 2 -
  # retrive geneset
  bapi dta -g upregulated | json2csv -o out.csv

Maintainer

• @Jianfeng

License

Academic Free License version 3.0