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Full Discussion: Check ID in a file matches to the name of the file
Top Forums UNIX for Beginners Questions & Answers Check ID in a file matches to the name of the file Post 302998779 by nans on Wednesday 7th of June 2017 07:05:17 AM
Old 06-07-2017
Check ID in a file matches to the name of the file
I have a number of text tab files in my directory named 1.vcf 2.vcf etc. Each file file has headers of 120-130 rows starting with "#", it looks like this

Code:
...
##contig=<ID=GL000194.1,length=191469,assembly=hg19>
##contig=<ID=GL000225.1,length=211173,assembly=hg19>
##contig=<ID=GL000192.1,length=547496,assembly=hg19>
##contig=<ID=vcontig,length=337,assembly=hg19>
##reference=human_hg19.fasta
##source=SelectVariants
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  1
1       12012010        rs1000002       A       C       14325.14        .       AC=1;AF=0.500;AN=2;BaseQRankSum=-13...

As these files are created with an automated pipeline, I wish to introduce an id check, to see if each file name (1.vcf,2.vcf..) corresponds to the correct ID within the content file.
The ID is always present is the last line of the header after 'FORMAT'.
The files are always named according to ID.
I have been doing this manually so far, is there a way to script it ?
Last edited by nans; 06-07-2017 at 02:06 PM..
 

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LEARN ABOUT CENTOS

set_color

set_color(1)							       fish							      set_color(1)

NAME

       set_color - set_color - set the terminal color

set_color - set the terminal color
   Synopsis
       set_color [-v --version] [-h --help] [-b --background COLOR] [COLOR]

   Description
       Change the foreground and/or background color of the terminal. COLOR is one of black, red, green, brown, yellow, blue, magenta, purple,
       cyan, white and normal.

       o -b, --background Set the background color

       o -c, --print-colors Prints a list of all valid color names

       o -h, --help Display help message and exit

       o -o, --bold Set bold or extra bright mode

       o -u, --underline Set underlined mode

       o -v, --version Display version and exit

       Calling set_color normal will set the terminal color to whatever is the default color of the terminal.

       Some terminals use the --bold escape sequence to switch to a brighter color set. On such terminals, set_color white will result in a grey
       font color, while set_color --bold white will result in a white font color.

       Not all terminal emulators support all these features. This is not a bug in set_color but a missing feature in the terminal emulator.

       set_color uses the terminfo database to look up how to change terminal colors on whatever terminal is in use. Some systems have old and
       incomplete terminfo databases, and may lack color information for terminals that support it. Download and install the latest version of
       ncurses and recompile fish against it in order to fix this issue.

Version 1.23.1							  Sun Jan 8 2012						      set_color(1)
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