fbget

python>  import firebrowse
python>  print  firebrowse.Samples().mRNASeq(gene="egfr", cohort="ucs")
{
  "mRNASeq": [
    {
      "cohort": "UCS",
      "expression_log2": 7.06162500904694,
      "gene": "EGFR",
      "geneID": 1956,
      "protocol": "RSEM",
      "sample_type": "TP",
      "tcga_participant_barcode": "TCGA-QN-A5NN",
      "z-score": -0.598993525060403

    },
    ...

python>  import fbget
python>  print fbget.mrnaseq("egfr", cohort="ucs")
tcga_participant_barcode	gene	expression_log2	z-score	cohort	sample_type	protocol	geneID
TCGA-QN-A5NN	EGFR	7.06162500905	-0.59899352506	UCS	TP	RSEM	1956
TCGA-QM-A5NM	EGFR	8.16734387649	-0.298443593752	UCS	TP	RSEM	1956
TCGA-NG-A4VW	EGFR	8.93092623547	0.0932667888031	UCS	TP	RSEM	1956

    # Every line of these examples can be cut and directly pasted to your
    # UNIX-like command line.  Comments will be ignored, while everything
    # not beginning with the # comment character will be executed, as long
    # as fbget is in your $PATH

    # Get the RNASeq expression level of the POLE gene, for all TCGA samples
    # (both tumors and normals, in RSEM form, saved to file)
    fbget --outfile=fbget-test-pole.tsv mrnaseq pole

    # Similar query, but constrained to just the DLBC disease cohort
    fbget mrnaseq pole cohort=dlbc

    # Now constrained to single patient, and showing case insensitivity
    fbget mrnaseq pOlE baRcOdE=TCGA-RQ-A6JB

    # What is the DLBC cohort, anyway?
    fbget cohort dlbc
    # DLBC    Lymphoid Neoplasm Diffuse Large B-cell Lymphoma

    # List all the disease cohorts offered by FireBrowse (note that aggregate
    # cohorts like COADREAD,KIPAN,GBMLGG,STES are not available at the TCGA DCC)
    fbget cohorts

    # Display help (docstring) for the function which retrieves clinical data
    fbget help clinical

    # Calling functions with no arguments also displays help (docstring)
    fbget clinical

    # Now get some actual clinical data, but only for thyroid (THCA) cohort
    fbget clinical tHcA

    # Display the complete list of clinical data element names (CDEs)
    fbget clinical_names

    # List the functions may be called through fbget (-l does the same thing)
    fbget --list

    # Get the 10 most significantly mutated ovarian cancer genes (per MutSig2CV)
    fbget smg OV rank=10

    # Union of the names of parameters admitted by any FireBrowse function
    fbget param_names

    # Show the kinds of values that may be supplied via the cohort parameter
    # (applies to any function which admits the cohort parameter)
    fbget param_values cohort

    # Ditto, for the barcode and clinical data element (CDE) names
    fbget param_values barcode
    fbget param_values fh_cde
 
    # The documentation for param_values is helpful in its own right, too
    fbget help param_values

    # Levels of copy number alteration in TERT gene for 3 disease cohorts,
    # as computed by GISTIC2, redirected to file
    fbget cn_levels tert cohort=acc,KICH,LaMl,UCS > fbget-test-tert-cn.tsv

    # Which genes had significant copy number deletion (per GISTIC2 q values)
    # in BRCA & UCEC cohorts? (alternate method of saving to file, CLI option)
    fbget --outfile=fbget-test-cn-del.tsv cn_genes_del cohort=BRCA,ucec

    # Retrieve mature strand microRNASeq from UVM, as comma-separated values
    fbget mirseq hsa-let-7b-5p cohort=uvm format=csv

    # Repeat the same call to show that bogus parameters induce failure
    fbget mirseq has-let-7b-5p cohort=uvm format=Dum_De_Dum_Dumb

     barcode2type
     centers
     clinical
     clinical_fh
     clinical_names
     clinical_names_fh
     cn_genes_all
     cn_genes_amp
     cn_genes_del
     cn_genes_focal
     cn_levels
     cohort
     cohorts
     counts
     dates
     featuretable
     heartbeat
     help
     maf
     mirseq
     mrnaseq
     mrnaseq_quartiles
     param_names
     param_values
     patients
     platforms
     reports
     samplecode2type
     sampletype2code
     sampletypes
     smg
     stddata
     tssites

Help on function smg in fbget:
fbget.smg = smg(*args, **kwargs)

    High level wrapper for the FireBrowse Analyses.MutationSMG method.
    By default it returns ALL pages of data, in TSV format.

    This service provides a list of significantly mutated genes,
    as scored by MutSig.  It may be filtered by cohort, rank,
    gene, tool and/or Q-value threshold, but at least one cohort
    must be supplied.

    For more details consult the interactive documentation at
        http://firebrowse.org/api-docs/#!/Analyses
    OR use help(param_values) to see the range of values accepted
    for each parameter, the defaults for each (if any), and the
    degrees of optionality/requiredness offered by the API.

    Parameters: 
        format  (str)  Format of result.
        cohort  (str)  Narrow search to one or more TCGA disease cohorts.
        tool  (str)  Narrow search to include only data/results produced by the selected Firehose tool.
        rank  (int)  Number of significant genes to return.
        gene  (str)  Comma separated list of gene name(s).
        q  (float)  Only return results with Q-value <= given threshold.
        page  (int)  Which page (slice) of entire results set should be returned. 
        page_size  (int)  Number of records per page of results.  Maximum is 2000.
        sort_by  (str)  Which column in the results should be used for sorting paginated results?

usage: fbget.py [-h] [-d] [-e] [-l] [-o OUTFILE] [-s SERVER] [-V] [-v] function [arg [arg ...]]

Python & UNIX CLI wrappers for the FireBrowse RESTful API

fbget simplifies use and extends the power of FireBrowse, by
providing: low- and high-level Python wrappers to its RESTful
API; an interface through which the high level functions may be
called directly from the UNIX command line, without writing any
Python code; and enabling the results of such to be immediately
streamed to UNIX tools for further processing or analysis.  In
addition, both the fbget CLI tool and the high level wrappers
will by default retrieve all pages of data returned by the
FireBrowse RESTful API, in TSV form that is most commonly used
for bioinformatics analysis.

For more information visit http://firebrowse.org

positional arguments:
  function              name of the function to be called
  arg                   arguments to pass to function

optional arguments:
  -h, --help            show this help message and exit
  -d, --docs            emit documentation for entire api
  -e, --examples        show usage examples
  -l, --list            list all callable functions
  -o OUTFILE, --outfile OUTFILE
                        Specify output file (will be overwritten if already exists) [sys.stdout]
  -s SERVER, --server SERVER
                        the server hosting the FireBrowse instance                  [firebrowse.org]
  -V, --verbose         Verbose: emit to stderr RESTful calls made, etc             [False]
  -v, --version         show program's version number and exit
  -x, --debug           debugging: trace RESTful calls as they are issued