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Full Discussion: Common records after matching on different columns
Top Forums Shell Programming and Scripting Common records after matching on different columns Post 302597444 by Shell_Life on Friday 10th of February 2012 10:28:02 AM
Old 02-10-2012
Quote:
Originally Posted by jacobs.smith
The shell script produces the following output.

opfromshell.txt
Code:
chr1 300 400 1.txt
chr1 350 467 1.txt

But, I was looking for

Originaloutput.txt
Code:
chr1 300 400 1.txt
chr1 350 467 1.txt
chr1 201 299 2.txt
chr2 800 1000 2.txt
chr2 100 200 2.txt
chr3 500 600 2.txt

Please, no offense. Since the earlier replies in that post worked, I didn't want to bother Shell_life.
If you had noticed, I made the two file names as variables for the shell.

This way, to have your desired output, you just run it twice:
1)
Code:
mF1='1.txt'
mF2='2.txt'

2)
Code:
mF1='2.txt'
mF2='1.txt'

Here is the same solution again:

Code:
#!/bin/ksh
typeset -i mFromA mToA mFromB mToB
mF1='1.txt'      ### <======= Change file name here (I)
mF2='2.txt'      ### <======= Change file name here (II)
mPrevTag=''
#### sort is used to reduce the number of "grep"
sort ${mF1} | while read mTagA mFromA mToA; do
  if [[ "${mTagA}" != "${mPrevTag}" ]]; then
    grep "${mTagA}" ${mF2} > ${mF2}.tmp
  fi
  mFound="N"
  while read mTagB mFromB mToB; do
    if [[ ${mToA} -ge ${mFromB} && ${mFromA} -le ${mToB} ]]; then
      mFound="Y"
      break
    fi
  done < ${mF2}.tmp
  if [[ "${mFound}" = "N" ]]; then
    echo ${mTagA} ${mFromA} ${mToA} ${mF1}
  fi
  mPrevTag=${mTagA}
done

 

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LEARN ABOUT DEBIAN

h5jam

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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