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Full Discussion: Name grouping
Top Forums Shell Programming and Scripting Name grouping Post 302925280 by cmccabe on Saturday 15th of November 2014 12:50:28 PM
Old 11-15-2014
Name grouping

Code:
 awk 'FNR==NR {a[$1]; next} $NF in a' genes.txt refseq_exons.txt > output.txt

I can not figure out how to group the same name in $4 together.

Basically, all the SKI together in separate rows and all the TGFB2. Thank you Smilie.

Code:
chr1	2160133	2161174	SKI
chr1	218518675	218520389	TGFB2
chr1	218536675	218536759	TGFB2
chr1	218578510	218578674	TGFB2
chr1	218607423	218607556	TGFB2
chr1	218607679	218607790	TGFB2
chr1	218609311	218609489	TGFB2
chr1	218610684	218610838	TGFB2
chr1	218614545	218617961	TGFB2
chr1	2234416	2234542	SKI
chr1	2234723	2234839	SKI
chr1	2235278	2235541	SKI
chr1	2235731	2236024	SKI
chr1	2237458	2237689	SKI
chr1	2238015	2241652	SKI

 

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h5jam(1)						      General Commands Manual							  h5jam(1)

NAME
h5jam - Add a user block to a HDF5 file SYNOPSIS
h5jam -u user_block -i in_file.h5 [-o out_file.h5] [--clobber] DESCRIPTION
h5jam concatenates a user_block file and an HDF5 file to create an HDF5 file with a user block. The user block can be either binary or text. The output file is padded so that the HDF5 header begins on byte 512, 1024, etc.. (See the HDF5 File Format.) If out_file.h5 is given, a new file is created with the user_block followed by the contents of in_file.h5. In this case, infile.h5 is unchanged. If out_file.h5 is not specified, the user_block is added to in_file.h5. If in_file.h5 already has a user block, the contents of user_block will be added to the end of the existing user block, and the file shifted to the next boundary. If --clobber is set, any existing user block will be overwritten. EXAMPLE USAGE
Create new file, newfile.h5, with the text in file mytext.txt as the user block for the HDF5 file file.h5. h5jam -u mytext.txt -i file.h5 -o newfile.h5 Add text in file mytext.txt to front of HDF5 dataset, file.h5. h5jam -u mytext.txt -i file.h5 Overwrite the user block (if any) in file.h5 with the contents of mytext.txt. h5jam -u mytext.txt -i file.h5 --clobber RETURN VALUE
h5jam returns the size of the output file, or -1 if an error occurs. CAVEATS
This tool copies all the data (sequentially) in the file(s) to new offsets. For a large file, this copy will take a long time. The most efficient way to create a user block is to create the file with a user block (see H5Pset_user_block), and write the user block data into that space from a program. The user block is completely opaque to the HDF5 library and to the h5jam and h5unjam tools. The user block is simply read or written as a string of bytes, which could be text or any kind of binary data. It is up to the user to know what the contents of the user block means and how to process it. When the user block is extracted, all the data is written to the output, including any padding or unwritten data. This tool moves the HDF5 file through byte copies, i.e., it does not read or interpret the HDF5 objects. SEE ALSO
h5dump(1), h5ls(1), h5diff(1), h5import(1), gif2h5(1), h52gif(1), h5perf(1), h5unjam(1). h5jam(1)
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