☰

Mesclar arquivos usando uma coluna comum (awk)

tag-icon • tag-icon awk text
Mesclar arquivos usando uma coluna comum (awk)

Eu tenho dois arquivos de texto:

arquivo 1:

#CHROM  POS ID  REF ALT
1   61442   rs2531261   A   G
1   924629  rs28622096  A   G,T
1   974662  rs2465135   G   T
1   995481  rs9442393   T   G

arquivo 2

#CHROM  POS ID  REF ALT FORMAT
1   61442   rs2531261   A   G   GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1   924629  rs28622096  A   G,T GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1   974662  rs2465135   G   T   GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1   987909  rs34235844  G   GTG GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1   995481  rs9442393   T   G   GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD

Gostaria de combinar os arquivos com base na coluna 3 (ID). Meu arquivo de saída deve ser assim:

saída:

#CHROM  POS ID  REF ALT FORMAT
1   61442   rs2531261   A   G   GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1   924629  rs28622096  A   G,T GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1   974662  rs2465135   G   T   GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1   995481  rs9442393   T   G   GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD

Eu quero usar awk.

Responder1

Parece que você querfiltrofile2 com base nos IDs do arquivo 1 (em vez demesclaros arquivos):

$ awk 'NR==FNR {a[$3] = 1; next} $3 in a' file1 file2
#CHROM  POS ID  REF ALT FORMAT
1   61442   rs2531261   A   G   GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1   924629  rs28622096  A   G,T GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1   974662  rs2465135   G   T   GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD
1   995481  rs9442393   T   G   GT:GL:GQ:DP:CGA_RDP:EHQ:HQ:CGA_CEGL:PS:CGA_CEHQ:AD

informação relacionada