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Top Forums Shell Programming and Scripting Count and search by sequence in multiple fasta file Post 302892115 by ahamed101 on Tuesday 11th of March 2014 05:03:50 AM
Old 03-11-2014
a bash approach
Code:
#!/bin/bash

query=query.txt
file_list=(*.txt)
declare -A pattern

printf "%-10s\t%-10s\t" "" "Sequence"
for file in ${file_list[@]}
do
  printf "%-10s\t" $file
  while read line
  do
    [[ "$line" =~ ">" ]] && continue
    ((pattern[$file,$line]+=1))
  done < $file
done
echo

while read line
do
  [[ "$line" =~ ">" ]] && printf "%-10s\t" ${line/>/} && continue
  printf "%-10s\t" $line
  for file in ${file_list[@]}
  do
    printf "%-10s\t" ${pattern[$file,$line]:-0}
  done
  echo
done < $query

 

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echo(1) 							   User Commands							   echo(1)

NAME
echo - echo arguments SYNOPSIS
/usr/bin/echo [string...] DESCRIPTION
The echo utility writes its arguments, separated by BLANKs and terminated by a NEWLINE, to the standard output. If there are no arguments, only the NEWLINE character will be written. echo is useful for producing diagnostics in command files, for sending known data into a pipe, and for displaying the contents of environ- ment variables. The C shell, the Korn shell, and the Bourne shell all have echo built-in commands, which, by default, will be invoked if the user calls echo without a full pathname. See shell_builtins(1). sh's echo, ksh's echo, and /usr/bin/echo understand the back-slashed escape charac- ters, except that sh's echo does not understand a as the alert character. In addition, ksh's echo, does not have an -n option. sh's echo and /usr/bin/echo only have an -n option if the SYSV3 environment variable is set (see ENVIRONMENT VARIABLES below). If it is, none of the backslashed characters mentioned above are available. csh's echo and /usr/ucb/echo, on the other hand, have an -n option, but do not under- stand the back-slashed escape characters. OPERANDS
The following operand is supported: string A string to be written to standard output. If any operand is "-n", it will be treated as a string, not an option. The following character sequences will be recognized within any of the arguments: a Alert character.  Backspace. c Print line without new-line. All characters following the c in the argument are ignored. f Form-feed. New-line. Carriage return. Tab. v Vertical tab. \ Backslash. n Where n is the 8-bit character whose ASCII code is the 1-, 2- or 3-digit octal number representing that character. USAGE
Portable applications should not use -n (as the first argument) or escape sequences. The printf(1) utility can be used portably to emulate any of the traditional behaviors of the echo utility as follows: o The Solaris 2.6 operating environment or compatible version's /usr/bin/echo is equivalent to: printf "%b " "$*" o The /usr/ucb/echo is equivalent to: if [ "X$1" = "X-n" ] then shift printf "%s" "$*" else printf "%s " "$*" fi New applications are encouraged to use printf instead of echo. EXAMPLES
Example 1: Finding how far below root your current directory is located You can use echo to determine how many subdirectories below the root directory (/) is your current directory, as follows: o Echo your current-working-directory's full pathname. o Pipe the output through tr to translate the path's embedded slash-characters into space-characters. o Pipe that output through wc -w for a count of the names in your path. example% /usr/bin/echo $PWD | tr '/' ' ' | wc -w See tr(1) and wc(1) for their functionality. Below are the different flavors for echoing a string without a NEWLINE: Example 2: /usr/bin/echo example% /usr/bin/echo "$USER's current directory is $PWDc" Example 3: sh/ksh shells example$ echo "$USER's current directory is $PWDc" Example 4: csh shell example% echo -n "$USER's current directory is $PWD" Example 5: /usr/ucb/echo example% /usr/ucb/echo -n "$USER's current directory is $PWD" ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of echo: LANG, LC_ALL, LC_CTYPE, LC_MES- SAGES, and NLSPATH. SYSV3 This environment variable is used to provide compatibility with INTERACTIVE UNIX System and SCO UNIX installation scripts. It is intended for compatibility only and should not be used in new scripts. EXIT STATUS
The following error values are returned: 0 Successful completion. >0 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWcsu | +-----------------------------+-----------------------------+ |CSI |enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ SEE ALSO
echo(1B), printf(1), shell_builtins(1), tr(1), wc(1), ascii(5), attributes(5), environ(5), standards(5) NOTES
When representing an 8-bit character by using the escape convention n, the n must always be preceded by the digit zero(0). For example, typing: echo 'WARNING:7' will print the phrase WARNING: and sound the "bell" on your terminal. The use of single (or double) quotes (or two backslashes) is required to protect the "" that precedes the "07". Following the , up to three digits are used in constructing the octal output character. If, following the n, you want to echo addi- tional digits that are not part of the octal representation, you must use the full 3-digit n. For example, if you want to echo "ESC 7" you must use the three digits "033" rather than just the two digits "33" after the . 2 digits Incorrect: echo"0337 | od -xc produces: df0a (hex) 337 (ascii) 3 digits Correct: echo "00337" | od -xc produces: lb37 0a00 (hex) 033 7 (ascii) For the octal equivalents of each character, see ascii(5). SunOS 5.10 20 Jan 2000 echo(1)
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