ad115 / icgc-data-parser Goto Github PK

I'm wondering if it would be appropriate to add functionality of reading files such as simple_somatic_mutation.open.BRCA-US.tsv.gz.

Reading this data is the initial step of a project I will be starting soon. I would be more than willing to implement the parser.

For reference, the file has these columns:

1. icgc_mutation_id
2. icgc_donor_id
3. project_code
4. icgc_specimen_id
5. icgc_sample_id
6. matched_icgc_sample_id
7. submitted_sample_id
8. submitted_matched_sample_id
9. chromosome
10. chromosome_start
11. chromosome_end
12. chromosome_strand
13. assembly_version
14. mutation_type
15. reference_genome_allele
16. mutated_from_allele
17. mutated_to_allele
18. quality_score
19. probability
20. total_read_count
21. mutant_allele_read_count
22. verification_status
23. verification_platform
24. biological_validation_status
25. biological_validation_platform
26. consequence_type
27. aa_mutation
28. cds_mutation
29. gene_affected
30. transcript_affected
31. gene_build_version
32. platform
33. experimental_protocol
34. sequencing_strategy
35. base_calling_algorithm
36. alignment_algorithm
37. variation_calling_algorithm
38. other_analysis_algorithm
39. seq_coverage
40. raw_data_repository
41. raw_data_accession
42. initial_data_release_date