0

I have a text file with following information:

Hugo_Symbol Tumor_Sample_Barcode    Entrez_Gene_Id  Center  NCBI_Build
MTHFR   TCGA-BD-A2L6-01A-11D-A20W-10    4524    BCM GRCh38
SLC30A1 TCGA-BD-A2L6-01A-11D-A20W-10    7779    BCM GRCh38
USH2A   TCGA-BD-A2L6-01A-11D-A20W-10    7399    BCM GRCh38
SOS1    TCGA-BD-A2L6-01A-11D-A20W-10    6654    BCM GRCh38
TMEM51  TCGA-O8-A75V-01A-11D-A32G-10    55092   BCM GRCh38
FLG TCGA-O8-A75V-01A-11D-A32G-10    2312    BCM GRCh38
FLG TCGA-O8-A75V-01A-11D-A32G-10    2312    BCM GRCh38
PRDM16  TCGA-G3-A7M5-01A-11D-A33Q-10    63976   BCM GRCh38
DNAJC11 TCGA-G3-A7M5-01A-11D-A33Q-10    55735   BCM GRCh38
HNRNPCL2    TCGA-G3-A7M5-01A-11D-A33Q-10    440563  BCM GRCh38
C1orf94 TCGA-G3-A7M5-01A-11D-A33Q-10    84970   BCM GRCh38
NFYC    TCGA-G3-A7M5-01A-11D-A33Q-10    4802    BCM GRCh38
IPP TCGA-G3-A7M5-01A-11D-A33Q-10    3652    BCM GRCh38

As you see there are multiple samples I want to split the file into multiple files based on the column "Tumor_Sample_Barcode". The output files need to be named with samplename.txt.

First output - TCGA-BD-A2L6-01A-11D-A20W-10.txt

Hugo_Symbol Tumor_Sample_Barcode    Entrez_Gene_Id  Center  NCBI_Build
MTHFR   TCGA-BD-A2L6-01A-11D-A20W-10    4524    BCM GRCh38
SLC30A1 TCGA-BD-A2L6-01A-11D-A20W-10    7779    BCM GRCh38
USH2A   TCGA-BD-A2L6-01A-11D-A20W-10    7399    BCM GRCh38
SOS1    TCGA-BD-A2L6-01A-11D-A20W-10    6654    BCM GRCh38

Second output - TCGA-O8-A75V-01A-11D-A32G-10.txt

Hugo_Symbol Tumor_Sample_Barcode    Entrez_Gene_Id  Center  NCBI_Build
TMEM51  TCGA-O8-A75V-01A-11D-A32G-10    55092   BCM GRCh38
FLG TCGA-O8-A75V-01A-11D-A32G-10    2312    BCM GRCh38
FLG TCGA-O8-A75V-01A-11D-A32G-10    2312    BCM GRCh38

Third output - TCGA-G3-A7M5-01A-11D-A33Q-10.txt

Hugo_Symbol Tumor_Sample_Barcode    Entrez_Gene_Id  Center  NCBI_Build
PRDM16  TCGA-G3-A7M5-01A-11D-A33Q-10    63976   BCM GRCh38
DNAJC11 TCGA-G3-A7M5-01A-11D-A33Q-10    55735   BCM GRCh38
HNRNPCL2    TCGA-G3-A7M5-01A-11D-A33Q-10    440563  BCM GRCh38
C1orf94 TCGA-G3-A7M5-01A-11D-A33Q-10    84970   BCM GRCh38
NFYC    TCGA-G3-A7M5-01A-11D-A33Q-10    4802    BCM GRCh38
IPP TCGA-G3-A7M5-01A-11D-A33Q-10    3652    BCM GRCh38

How to do this linux?

  • Thank you for the reply. But I don't see any headers in the output files. How to get the columns names also in the outputs? – user3351523 Jan 31 '18 at 12:51
  • 1
    @user3351523, "headers" should be the next moment. The first moment should be your posting a testable input (as a text, not as image) – RomanPerekhrest Jan 31 '18 at 12:53
  • Yes, sorry for that. I posted test table input as text now. How to get the headers in output files? – user3351523 Jan 31 '18 at 12:57
3

Awk solution:

awk 'NR==1{ h=$0 }NR>1{ print (!a[$2]++? h ORS $0 : $0) > $2".txt" }' file
  • NR==1{ h=$0 } - capture the 1st line/record as header line (NR points to a record number, $0 - contains the current line)
  • NR > 1 - for all records except the first one:
    • <cond>? <operand_1> : <operand_2> - classical ternary operator
    • !a[$2]++? - check for the 1st occurrence of barcode value $2 used as a key of associative array a
    • h ORS $0 - common header line concatenated with ORS(output record separator, defaults to \n) and current record $0
    • print ... > $2".txt" - print custom content or the current line(if nothing was specified) into file <barcode_value>.txt

Or a more self-explanatory version:

awk 'NR==1 {header = $0; next}
     !header_printed[$2]++ {print header > $2".txt"}
     {print > $2".txt"}' < file

Viewing results:

$ head TCGA*.txt
==> TCGA-BD-A2L6-01A-11D-A20W-10.txt <==
Hugo_Symbol Tumor_Sample_Barcode    Entrez_Gene_Id  Center  NCBI_Build
MTHFR   TCGA-BD-A2L6-01A-11D-A20W-10    4524    BCM GRCh38
SLC30A1 TCGA-BD-A2L6-01A-11D-A20W-10    7779    BCM GRCh38
USH2A   TCGA-BD-A2L6-01A-11D-A20W-10    7399    BCM GRCh38
SOS1    TCGA-BD-A2L6-01A-11D-A20W-10    6654    BCM GRCh38

==> TCGA-G3-A7M5-01A-11D-A33Q-10.txt <==
Hugo_Symbol Tumor_Sample_Barcode    Entrez_Gene_Id  Center  NCBI_Build
PRDM16  TCGA-G3-A7M5-01A-11D-A33Q-10    63976   BCM GRCh38
DNAJC11 TCGA-G3-A7M5-01A-11D-A33Q-10    55735   BCM GRCh38
HNRNPCL2    TCGA-G3-A7M5-01A-11D-A33Q-10    440563  BCM GRCh38
C1orf94 TCGA-G3-A7M5-01A-11D-A33Q-10    84970   BCM GRCh38
NFYC    TCGA-G3-A7M5-01A-11D-A33Q-10    4802    BCM GRCh38
IPP TCGA-G3-A7M5-01A-11D-A33Q-10    3652    BCM GRCh38

==> TCGA-O8-A75V-01A-11D-A32G-10.txt <==
Hugo_Symbol Tumor_Sample_Barcode    Entrez_Gene_Id  Center  NCBI_Build
TMEM51  TCGA-O8-A75V-01A-11D-A32G-10    55092   BCM GRCh38
FLG TCGA-O8-A75V-01A-11D-A32G-10    2312    BCM GRCh38
FLG TCGA-O8-A75V-01A-11D-A32G-10    2312    BCM GRCh38

To adjust a filename based on 15-char sequence of barcode value:

awk 'NR==1{ h=$0 }NR>1{ print (!a[$2]++? h ORS $0 : $0) > substr($2, 1, 15)".txt" }' file 
  • Thank you very much !! Could you please explain the command? – user3351523 Jan 31 '18 at 13:13
  • Please explain the command and could you also tell me how to get the output files with only 0-15 substring in the sample names like TCGA-BD-A2L6-01.txt, TCGA-G3-A7M5-01.txt and TCGA-O8-A75V-01.txt – user3351523 Jan 31 '18 at 13:31
  • 1
    @user3351523, yes, see my explanation – RomanPerekhrest Jan 31 '18 at 13:47

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.