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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 SYNOPSIS
awk [ -Fc ] [ prog ] [ file ] ... DESCRIPTION
Awk 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 asso- ciated 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 file. 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, vide infra.) 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, newlines 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 printf statement formats its expression list according to the format (see printf(3)). 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 printf(3) for- mat 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 newline); and OFMT, the output format for numbers (default "%.6g"). 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 } SEE ALSO
lex(1), sed(1) A. V. Aho, B. W. Kernighan, P. J. Weinberger, Awk - a pattern scanning and processing language BUGS
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. AWK(1)
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