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Top Forums Shell Programming and Scripting Parsing a fasta sequence with start and end coordinates Post 302514168 by michaelrozar17 on Friday 15th of April 2011 02:23:19 AM
Old 04-15-2011
Quote:
Originally Posted by empyrean
cut command is not working properly.. its splicing whole file in to 10 frament length lines
Yes.The given cut command is intended to work as you said. You would need to change the start and end character index accordingly. If you need to only match certain lines to extract characters, provide more information.
Code:
cut -c15-25 inputfile

 

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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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