PrecisionMedicine

Description

TPM 파일에 유전자 타입을 추가해주는 코드입니다.

Usage

java -jar TPMGeneTypeAdder.jar -gtf [gtf_file path] -tpm [tpm_folder or file path]

[gtf_file path]: GTF파일의 경로를 입력
[tpm_folder or file path]: TPM파일 또는 TPM파일을 포함하고 있는 폴더 경로를 입력
Warning: TPM파일의 이름은 반드시 tpm.txt 로 끝나야합니다.
TPM을 계산하는 데 사용한 GTF파일과 인풋 GTF파일의 버전이 다를 경우, gene type이 추가되지 않고 NA로 표기될 수 있습니다.
이 경우, 에러 메시지가 출력되니, 확인하면 됩니다.

TPM file format (tab-delimiter)

"gene_id" "gene_id_from_count" "gene_name" "tpm"
"ENSG00000000003" "ENSG00000000003.15" "TSPAN6" 6.50783847486202
"ENSG00000000005" "ENSG00000000005.6" "TNMD" 0.05883036057964
"ENSG00000000419" "ENSG00000000419.12" "DPM1" 1.76355733912858
"ENSG00000000457" "ENSG00000000457.14" "SCYL3" 6.19024457999974
"ENSG00000000460" "ENSG00000000460.17" "C1orf112" 0.496825479436153
"ENSG00000000938" "ENSG00000000938.13" "FGR" 3.4868137118047
"ENSG00000000971" "ENSG00000000971.15" "CFH" 6.25725597320327
"ENSG00000001036" "ENSG00000001036.14" "FUCA2" 6.10303959458075
"ENSG00000001084" "ENSG00000001084.13" "GCLC" 1.17386149970417
"ENSG00000001167" "ENSG00000001167.14" "NFYA" 14.8093151043689
"ENSG00000001460" "ENSG00000001460.18" "STPG1" 1.55057563256919
"ENSG00000001461" "ENSG00000001461.17" "NIPAL3" 10.5475007905505
"ENSG00000001497" "ENSG00000001497.16" "LAS1L" 6.53869478056353

Output file format (tab-delimiter)

"gene_id" "gene_id_from_count" "gene_name" "tpm" "gene_type"
"ENSG00000000003" "ENSG00000000003.15" "TSPAN6" 6.50783847486202 "protein_coding"
"ENSG00000000005" "ENSG00000000005.6" "TNMD" 0.05883036057964 "protein_coding"
"ENSG00000000419" "ENSG00000000419.12" "DPM1" 1.76355733912858 "protein_coding"
"ENSG00000000457" "ENSG00000000457.14" "SCYL3" 6.19024457999974 "protein_coding"
"ENSG00000000460" "ENSG00000000460.17" "C1orf112" 0.496825479436153 "protein_coding"
"ENSG00000000938" "ENSG00000000938.13" "FGR" 3.4868137118047 "protein_coding"
"ENSG00000000971" "ENSG00000000971.15" "CFH" 6.25725597320327 "protein_coding"
"ENSG00000001036" "ENSG00000001036.14" "FUCA2" 6.10303959458075 "protein_coding"
"ENSG00000001084" "ENSG00000001084.13" "GCLC" 1.17386149970417 "protein_coding"
"ENSG00000001167" "ENSG00000001167.14" "NFYA" 14.8093151043689 "protein_coding"
"ENSG00000001460" "ENSG00000001460.18" "STPG1" 1.55057563256919 "protein_coding"
"ENSG00000001461" "ENSG00000001461.17" "NIPAL3" 10.5475007905505 "protein_coding"
"ENSG00000001497" "ENSG00000001497.16" "LAS1L" 6.53869478056353 "protein_coding"