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Top Forums Shell Programming and Scripting parse fasta file to tabular file Post 302584581 by yifangt on Friday 23rd of December 2011 07:02:32 PM
Old 12-23-2011
Thanks! It worked except the OFS is missing, which is the header and the sequence are not delimited as needed. I added the OFS="\t", but it did not work.
Code:
awk 'BEGIN{RS=">"; OFS="\t"}{gsub("\n","",$0); print ">"$0}' file
-----------------------------
output is:
>seq0FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
>seq1KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKKIEKFHSQLMRLME LKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq2EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK
>seq3MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK
>YAL069W-1.334 Putative promoter sequenceCCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACAC

Any clue?
YF
 

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awk(1)							      General Commands Manual							    awk(1)

Name
       awk - pattern scanning and processing language

Syntax
       awk [-Fc] [-f prog] [-] [file...]

Description
       The  command scans each input file for lines that match any of a set of patterns specified in prog.  With each pattern in prog there can be
       an associated action that will be performed when a line of a file matches the pattern.  The set of patterns may appear literally  as  prog,
       or in a file specified as -f prog.

       Files  are  read  in  order;  if there are no files, the standard input is read.  The file name `-' means the standard input.  Each line is
       matched against the pattern portion of every pattern-action statement; the associated action is performed for each matched pattern.

       An input line is made up of fields separated by white space.  (This default can be changed by using FS, as described  below.)   The  fields
       are denoted $1, $2, ... ; $0 refers to the entire line.

       A pattern-action statement has the form

	    pattern { action }

       A missing { action } means print the line; a missing pattern always matches.

       An action is a sequence of statements.  A statement can be one of the following:

	    if ( conditional ) statement [ else statement ]
	    while ( conditional ) statement
	    for ( expression ; conditional ; expression ) statement
	    break
	    continue
	    { [ statement ] ... }
	    variable = expression
	    print [ expression-list ] [ >expression ]
	    printf format [ , expression-list ] [ >expression ]
	    next # skip remaining patterns on this input line
	    exit # skip the rest of the input

       Statements  are terminated by semicolons, new lines or right braces.  An empty expression-list stands for the whole line.  Expressions take
       on string or numeric values as appropriate, and are built using the operators +, -, *, /, %,  and concatenation	(indicated  by	a  blank).
       The  C operators ++, --, +=, -=, *=, /=, and %= are also available in expressions.  Variables may be scalars, array elements (denoted x[i])
       or fields.  Variables are initialized to the null string.  Array subscripts may be any string, not necessarily numeric; this allows  for  a
       form of associative memory.  String constants are quoted "...".

       The  print  statement prints its arguments on the standard output (or on a file if >file is present), separated by the current output field
       separator, and terminated by the output record separator.  The statement formats its expression list according to the format.  For  further
       information, see

       The  built-in  function	length	returns the length of its argument taken as a string, or of the whole line if no argument.  There are also
       built-in functions exp, log, sqrt, and int.  The last truncates its argument to an integer.  substr(s, m, n) returns the  n-character  sub-
       string  of  s that begins at position m.  The function sprintf(fmt, expr, expr, ...)  formats the expressions according to the format given
       by fmt and returns the resulting string.

       Patterns are arbitrary Boolean combinations (!, ||, &&, and parentheses)  of  regular  expressions  and	relational  expressions.   Regular
       expressions  must be surrounded by slashes and are as in egrep.	Isolated regular expressions in a pattern apply to the entire line.  Regu-
       lar expressions may also occur in relational expressions.

       A pattern may consist of two patterns separated by a comma; in this case, the action is performed for all lines between	an  occurrence	of
       the first pattern and the next occurrence of the second.

       A relational expression is one of the following:

	    expression matchop regular-expression
	    expression relop expression

       where a relop is any of the six relational operators in C, and a matchop is either ~ (for contains) or !~ (for does not contain).  A condi-
       tional is an arithmetic expression, a relational expression, or a Boolean combination of these.

       The special patterns BEGIN and END may be used to capture control before the first input line is read and after the last.   BEGIN  must	be
       the first pattern, END the last.

       A single character c may be used to separate the fields by starting the program with

	    BEGIN { FS = "c" }

       or by using the -Fc option.

       Other  variable	names  with special meanings include NF, the number of fields in the current record; NR, the ordinal number of the current
       record; FILENAME, the name of the current input file; OFS, the output field separator (default blank); ORS,  the  output  record  separator
       (default new line); and OFMT, the output format for numbers (default "%.6g").

Options
       -	 Used for standard input file.

       -Fc	 Sets interfield separator to named character.

       -fprog	 Uses prog file for patterns and actions.

Examples
       Print lines longer than 72 characters:
	    length > 72

       Print first two fields in opposite order:
	    { print $2, $1 }

       Add up first column, print sum and average:
		 { s += $1 }
	    END  { print "sum is", s, " average is", s/NR }

       Print fields in reverse order:
	    { for (i = NF; i > 0; --i) print $i }

       Print all lines between start/stop pairs:
	    /start/, /stop/

       Print all lines whose first field is different from previous one:
	    $1 != prev { print; prev = $1 }

Restrictions
       There  are  no explicit conversions between numbers and strings.  To force an expression to be treated as a number add 0 to it; to force it
       to be treated as a string concatenate "" to it.

See Also
       lex(1), sed(1)
       "Awk - A Pattern Scanning and Processing Language" ULTRIX Supplementary Documents Vol. II: Programmer

																	    awk(1)
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