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Top Forums Shell Programming and Scripting Problem with writing to output - awk, echo Post 302716533 by pamu on Tuesday 16th of October 2012 02:30:04 PM
Old 10-16-2012
You can print both variables in awk itself...Smilie


Code:
while read BAM REGION;  
do
var=$(vasamtools view $BAM $REGION | awk '{if ($2==0) print $0}' | wc -l)
echo "$REGION $var" >> log.txt
done<regions.txtt


Last edited by pamu; 10-16-2012 at 03:40 PM.. Reason: corrected..
 

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awk(1)																	    awk(1)

NAME
awk - pattern scanning and processing language SYNOPSIS
/usr/bin/awk [-f progfile] [-Fc] [ ' prog '] [parameters] [filename...] /usr/xpg4/bin/awk [-FcERE] [-v assignment...] 'program' -f progfile... [argument...] The /usr/xpg4/bin/awk utility is described on the nawk(1) manual page. The /usr/bin/awk utility scans each input filename for lines that match any of a set of patterns specified in prog. The prog string must be enclosed in single quotes ( ') to protect it from the shell. For each pattern in prog there can be an associated action performed when a line of a filename matches the pattern. The set of pattern-action statements can appear literally as prog or in a file specified with the -f progfile option. Input files are read in order; if there are no files, the standard input is read. The file name '-' means the standard input. The following options are supported: -f progfile awk uses the set of patterns it reads from progfile. -Fc Uses the character c as the field separator (FS) character. See the discussion of FS below. USAGE
Input Lines Each input line is matched against the pattern portion of every pattern-action statement; the associated action is performed for each matched pattern. Any filename of the form var=value is treated as an assignment, not a filename, and is executed at the time it would have been opened if it were a filename. Variables assigned in this manner are not available inside a BEGIN rule, and are assigned after previ- ously specified files have been read. An input line is normally made up of fields separated by white spaces. (This default can be changed by using the FS built-in variable or the -Fc option.) The default is to ignore leading blanks and to separate fields by blanks and/or tab characters. However, if FS is assigned a value that does not include any of the white spaces, then leading blanks are not ignored. The fields are denoted $1, $2, ...; $0 refers to the entire line. Pattern-action Statements A pattern-action statement has the form: pattern { action } Either pattern or action can be omitted. If there is no action, the matching line is printed. If there is no pattern, the action is per- formed on every input line. Pattern-action statements are separated by newlines or semicolons. Patterns are arbitrary Boolean combinations ( !, ||, &&, and parentheses) of relational expressions and regular expressions. A relational expression is one of the following: expression relop expression expression matchop regular_expression where a relop is any of the six relational operators in C, and a matchop is either ~ (contains) or !~ (does not contain). An expression is an arithmetic expression, a relational expression, the special expression var in array or a Boolean combination of these. Regular expressions are as in egrep(1). In patterns they must be surrounded by slashes. Isolated regular expressions in a pattern apply to the entire line. Regular expressions can also occur in relational expressions. A pattern can consist of two patterns separated by a comma; in this case, the action is performed for all lines between the occurrence of the first pattern to the occurrence of the second pattern. The special patterns BEGIN and END can be used to capture control before the first input line has been read and after the last input line has been read respectively. These keywords do not combine with any other patterns. Built-in Variables Built-in variables include: FILENAME name of the current input file FS input field separator regular expression (default blank and tab) NF number of fields in the current record NR ordinal number of the current record OFMT output format for numbers (default %.6g) OFS output field separator (default blank) ORS output record separator (default new-line) RS input record separator (default new-line) An action is a sequence of statements. A statement can be one of the following: if ( expression ) statement [ else statement ] while ( expression ) statement do statement while ( expression ) for ( expression ; expression ; expression ) statement for ( var in array ) statement break continue { [ statement ] ... } expression # commonly variable = expression print [ expression-list ] [ >expression ] printf format [ ,expression-list ] [ >expression ] next # skip remaining patterns on this input line exit [expr] # skip the rest of the input; exit status is expr Statements are terminated by semicolons, newlines, or right braces. An empty expression-list stands for the whole input line. Expressions take on string or numeric values as appropriate, and are built using the operators +, -, *, /, %, ^ and concatenation (indicated by a blank). The operators ++, --, +=, -=, *=, /=, %=, ^=, >, >=, <, <=, ==, !=, and ?: are also available in expressions. Variables can be scalars, array elements (denoted x[i]), or fields. Variables are initialized to the null string or zero. Array subscripts can be any string, not necessarily numeric; this allows for a form of associative memory. String constants are quoted (""), with the usual C escapes recognized within. The print statement prints its arguments on the standard output, or on a file if >expression is present, or on a pipe if '|cmd' is present. The output resulted from the print statement is terminated by the output record separator with each argument separated by the current out- put field separator. The printf statement formats its expression list according to the format (see printf(3C)). Built-in Functions The arithmetic functions are as follows: cos(x) Return cosine of x, where x is in radians. (In /usr/xpg4/bin/awk only. See nawk(1).) sin(x) Return sine of x, where x is in radians. (In /usr/xpg4/bin/awk only. See nawk(1).) exp(x) Return the exponential function of x. log(x) Return the natural logarithm of x. sqrt(x) Return the square root of x. int(x) Truncate its argument to an integer. It is truncated toward 0 when x > 0. The string functions are as follows: index(s, t) Return the position in string s where string t first occurs, or 0 if it does not occur at all. int(s) truncates s to an integer value. If s is not specified, $0 is used. length(s) Return the length of its argument taken as a string, or of the whole line if there is no argument. split(s, a, fs) Split the string s into array elements a[1], a[2], ... a[n], and returns n. The separation is done with the regular expression fs or with the field separator FS if fs is not given. sprintf(fmt, expr, expr,...) Format the expressions according to the printf(3C) format given by fmt and returns the resulting string. substr(s, m, n) returns the n-character substring of s that begins at position m. The input/output function is as follows: getline Set $0 to the next input record from the current input file. getline returns 1 for successful input, 0 for end of file, and -1 for an error. Large File Behavior See largefile(5) for the description of the behavior of awk when encountering files greater than or equal to 2 Gbyte ( 2**31 bytes). Example 1: Printing Lines Longer Than 72 Characters The following example is an awk script that can be executed by an awk -f examplescript style command. It prints lines longer than seventy two characters: length > 72 Example 2: Printing Fields in Opposite Order The following example is an awk script that can be executed by an awk -f examplescript style command. It prints the first two fields in opposite order: { print $2, $1 } Example 3: Printing Fields in Opposite Order with the Input Fields Separated The following example is an awk script that can be executed by an awk -f examplescript style command. It prints the first two input fields in opposite order, separated by a comma, blanks or tabs: BEGIN { FS = ",[ ]*|[ ]+" } { print $2, $1 } Example 4: Adding Up the First Column, Printing the Sum and Average The following example is an awk script that can be executed by an awk -f examplescript style command. It adds up the first column, and prints the sum and average: { s += $1 } END { print "sum is", s, " average is", s/NR } Example 5: Printing Fields in Reverse Order The following example is an awk script that can be executed by an awk -f examplescript style command. It prints fields in reverse order: { for (i = NF; i > 0; --i) print $i } Example 6: Printing All lines Between start/stop Pairs The following example is an awk script that can be executed by an awk -f examplescript style command. It prints all lines between start/stop pairs. /start/, /stop/ Example 7: Printing All Lines Whose First Field is Different from the Previous One The following example is an awk script that can be executed by an awk -f examplescript style command. It prints all lines whose first field is different from the previous one. $1 != prev { print; prev = $1 } Example 8: Printing a File and Filling in Page numbers The following example is an awk script that can be executed by an awk -f examplescript style command. It prints a file and fills in page numbers starting at 5: /Page/ { $2 = n++; } { print } Example 9: Printing a File and Numbering Its Pages Assuming this program is in a file named prog, the following example prints the file input numbering its pages starting at 5: example% awk -f prog n=5 input See environ(5) for descriptions of the following environment variables that affect the execution of awk: LANG, LC_ALL, LC_COLLATE, LC_CTYPE, LC_MESSAGES, NLSPATH, and PATH. LC_NUMERIC Determine the radix character used when interpreting numeric input, performing conversions between numeric and string val- ues and formatting numeric output. Regardless of locale, the period character (the decimal-point character of the POSIX locale) is the decimal-point character recognized in processing awk programs (including assignments in command-line argu- ments). See attributes(5) for descriptions of the following attributes: /usr/bin/awk +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWesu | +-----------------------------+-----------------------------+ |CSI |Not Enabled | +-----------------------------+-----------------------------+ /usr/xpg4/bin/awk +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWxcu4 | +-----------------------------+-----------------------------+ |CSI |Enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ egrep(1), grep(1), nawk(1), sed(1), printf(3C), attributes(5), environ(5), largefile(5), standards(5) Input white space is not preserved on output if fields are involved. 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 an expression to be treated as a string, concatenate the null string ("") to it. 22 Jun 2005 awk(1)
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