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Top Forums Shell Programming and Scripting Parsing a fasta sequence with start and end coordinates Post 302514160 by empyrean on Friday 15th of April 2011 01:56:13 AM
Old 04-15-2011
cut command is not working properly.. its splicing whole file in to 10 frament length lines
 

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cut(1)							      General Commands Manual							    cut(1)

Name
       cut - cut out selected fields of each line of a file

Syntax
       cut -clist [file1 file2...]
       cut -flist [-dchar] [-s] [file1 file2...]

Description
       Use  the  command to cut out columns from a table or fields from each line of a file.  The fields as specified by list can be fixed length,
       that is, character positions as on a punched card (-c option), or the length can vary from line to line and be marked with a  field  delim-
       iter character like tab (-f option).  The command can be used as a filter.  If no files are given, the standard input is used.

       Use to make horizontal ``cuts'' (by context) through a file, or to put files together in columns.  To reorder columns in a table, use and

Options
       list	   Specifies  ranges  that must be a comma-separated list of integer field numbers in increasing order.  With optional - indicates
		   ranges as in the -o option of nroff/troff for page ranges; for example, 1,4,7; 1-3,8; -5,10 (short for 1-5,10);  or	3-  (short
		   for third through last field).

       -clist	   Specifies character positions to be cut out.  For example, -c1-72 would pass the first 72 characters of each line.

       -flist	   Specifies  the  fields  to be cut out.  For example, -f1,7 copies the first and seventh field only.	Lines with no field delim-
		   iters are passed through intact (useful for table subheadings), unless -s is specified.

       -dchar	   Uses the specified character as the field delimiter.  Default is tab.  Space or other characters with special  meaning  to  the
		   shell must be quoted.  The -d option is used only in combination with the -f option, according to XPG3 and SVID2/SVID3.

       -s	   Suppresses  lines  with  no	delimiter  characters.	 Unless  specified, lines with no delimiters are passed through untouched.
		   Either the -c or -f option must be specified.

Examples
       Mapping of user IDs to names:
       cut -d: -f1,5 /etc/passwd
       To set name to the current login name for the csh shell:
       set name=`who am i | cut -f1 -d" "`
       To set name to the current login name for the sh, sh5, and ksh shells:
       name=`who am i | cut -f1 -d" "`

Diagnostics
       "line too long"	   A line can have no more than 511 characters or fields.

       "bad list for c/f option"
			   Missing -c or -f option or incorrectly specified list.  No error occurs if a line has fewer fields than the list  calls
			   for.

       "no fields"	   The list is empty.

See Also
       grep(1), paste(1)

																	    cut(1)
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