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Top Forums Shell Programming and Scripting split file by delimiter with csplit Post 302679743 by Chirel on Tuesday 31st of July 2012 02:30:48 PM
Old 07-31-2012
Hi

Try this
Code:
csplit -s -f part INFILE.fasta  '/^>/' {*}

This should create lot's of partxx files.
 

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csplit(1)						      General Commands Manual							 csplit(1)

Name
       csplit - context split

Syntax
       csplit [ -s ] [ -k ] [ -f prefix ] file arg1 [ ...argn ]

Description
       The command reads file and separates it into n+1 sections, as defined by the arguments arg1...argn.  By default, the sections are placed in
       xx00...xxn (n may not be greater than 99).  The named file is sectioned in the following way:

       00:   From the start of file up to (but not including) the line referenced by arg1.

       01:   From the line referenced by arg1 up to the line referenced by arg2.
	     .
	     .
	     .

       n:    From the line referenced by argn to the end of file.

       If the file argument is a minus (-) then standard input is used. A minus is an ASCII octal 055.

Options
       -s		   Suppresses the printing of all character counts.  If the -s option is omitted, the command prints the character  counts
			   for each file created.

       -k		   Leaves  previously  created files intact.  If the -k option is omitted, automatically removes created files if an error
			   occurs.

       -fprefix 	   Names the created files prefix00...prefixn.	The default is xx00...xxn.

       The arguments (arg1...argn) to can be a combination of the following:

	     /rexp/[offset]	 A file is created for the section from the current line up to (but not including) the line containing the regular
				 expression  rexp.   The  current line becomes the line containing rexp.  The optional offset is plus (+) or minus
				 (-) the number of lines.  For example, /Page/-5.

	     %rexp%[offset]	 This argument is the same as /rexp/[offset], except that no file is created for the section.

	     lnno		 A file is created from the current line up to (but not including) lnno.  The current line becomes lnno.

	     {num}		 Repeat argument.  This argument may follow any of the above arguments.  If it follows a rexp argument, that argu-
				 ment  is  applied  num  more times.  If it follows lnno, the file will be split every lnno lines (num times) from
				 that point.

       Enclose all rexp type arguments that contain blanks or other characters meaningful to the Shell in the appropriate quotes.  Regular expres-
       sions should not contain embedded new-lines.  The command does not affect the original file; it is the user's responsibility to remove it.

Examples
       csplit -f cobol file /procedure division/ /par5./ /par16./
       This example creates four files, cobol00...cobol03.  After editing the files that created, they can be recombined as follows:
       cat cobol0[0-3] > file
       Note that this example overwrites the original file.

       csplit -k file  100  {99}
       This  example splits the file every 100 lines, up to 10,000 lines.  The -k option causes the created files to be retained if there are less
       than 10,000 lines; however, an error message would still be printed.

       csplit -k prog.c  '%main(%'  '/^}/+1'  {20}
       Assuming that follows the normal C coding convention of ending routines with a right brace (}) at the beginning of the line,  this  example
       creates a file containing each separate C routine (up to 21) in

Diagnostics
       The diagnostics are self explanatory except for the following:
       arg - out of range
       This message means that the given argument did not reference a line between the current position and the end of the file.

See Also
       ed(1), sh(1)

																	 csplit(1)
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