bwalsh / mafreader

command line utility to read MAF files and create CIViC links

MAFReader Quickstart

MAFReader is a simple command line tool that reads a MAF file, calls CIViC for each line therein.

MAFReader outputs a table in markdown format for easy inclusion into downstream reports

MAFReader requires Python 3.*. To check your python version, run:

    $ python -V
    Python 3.4.2

Usage:

    $ python mafeader.py -h
    usage: mafreader [-h] [-i INPUT_FILE] [-o OUTPUT_FILE] [-c HOST]
                 [-col ENTREZ_ID_COLUMN]

    optional arguments:
      -h, --help            show this help message and exit
      -i INPUT_FILE, --input_file INPUT_FILE
                            input file (assumed to be tab separated MAF format);
                            defaults to stdin
      -o OUTPUT_FILE, --output_file OUTPUT_FILE
                            output file; defaults to stdout
      -c HOST, --host HOST  url of reference civic host (default:
                            civic.genome.wustl.edu)
      -col ENTREZ_ID_COLUMN, --entrez_id_column ENTREZ_ID_COLUMN
                            column in the input file that contains the entrez id.
                            Defaults to 1 (0 based)

Process

On entry MAFReader reads all variants from CIViC for a particular gene, using entrez_id as the gene identifier.

• If there is no data returned from CIViC, MAFReader displays gene not found in civic and moves on.
• If there is data returned from CIViC, MAFReader searches the CIViC EvidenceItems returned and matches on {Chromosome}:{Start_position}-{End_position} ({Reference_Allele}->{Tumor_Seq_Allele1})
  • If there is a match MAFReader displays [civic variant] with a link to the specific variant in CIViC
  • Otherwise MAFReader displays [civic gene] with a link to the gene in CIViC

Output

$ python mafreader.py  -i resources/simple.maf

hugo_symbol	entrez_gene_id	CIViC variant name	drugs	link
391	207	E17K	MK-2206	civic variant
11998	7157	R175H	N/A	civic variant
1316	238	EML4-ALK		civic gene
CAPZA1	829			gene not found in civic

Customization

For local CIViC deployments use the -c option "-c locahost:3000"

Issues

• MAFReader calls CIViC for each variant in the MAF file. An optimization would be to modify CIViC to accept a batch of entrez_ids to match on.

• MAFReader does not cache any reponses from CIViC. An optimization would be for MAFReader to cache responses and leverage the ETag header CIViC provides.

• MAFReader does not populate CIViC with any information if it encounters a "no find".