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Full Discussion: Inserting IDs from a text file into a sequence alignment file
Top Forums Shell Programming and Scripting Inserting IDs from a text file into a sequence alignment file Post 302925806 by nans on Wednesday 19th of November 2014 11:44:39 AM
Old 11-19-2014
Well, usually, when we have multiple files, we put everything into a variable and that would work. For my issue above, after going through several forums I understood that I have to make $file (full of IDs) into a variable to which I append each line in the while loop and then put bwa outside of the loop.. but I have just been struggling with the code..
 

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LEARN ABOUT BSD

break

break(1)                                                           User Commands                                                          break(1)

NAME

       break, continue - shell built-in functions to escape from or advance within a controlling while, for, foreach, or until  loop

SYNOPSIS

   sh
       break [n]

       continue [n]

   csh
       break

       continue

   ksh
       *break [n]

       *continue [n]

DESCRIPTION

   sh
       The break utility exits from the enclosing for or while loop, if any. If n is specified, break n levels.

       The continue utility resumes the next iteration of the enclosing for or while loop. If n is specified, resume at the n-th enclosing loop.

   csh
       The  break  utility  resumes  execution after the end of the nearest enclosing foreach or while loop. The remaining commands on the current
       line are executed. This allows multilevel breaks to be written as a list of break commands, all on one line.

       The continue utility continues execution of the next iteration of the nearest enclosing while or foreach loop.

   ksh
       The break utility exits from the enclosed for, while, until, or select loop, if any. If n is specified,  then  break  n  levels.  If  n  is
       greater than the number of enclosing loops, the outermost enclosing loop shall be exited.

       The  continue utility resumes the next iteration of the enclosed for, while, until, or select loop. If n is specified then resume at the n-
       th enclosed loop. If n is greater than the number of enclosing loops, the outermost enclosing loop shall be used.

       On this man page, ksh(1) commands that are preceded by one or two * (asterisks) are treated specially in the following ways:

       1.  Variable assignment lists preceding the command remain in effect when the command completes.

       2.  I/O redirections are processed after variable assignments.

       3.  Errors cause a script that contains them to abort.

       4.  Words that follow a command preceded by ** that are in the format of a variable assignment are expanded with the same rules as a  vari-
           able  assignment.  This means that tilde substitution is performed after the = sign, and also that word splitting and file name genera-
           tion are not performed.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE         |      ATTRIBUTE VALUE        |
       +-----------------------------+-----------------------------+
       |Availability                 |SUNWcsu                      |
       +-----------------------------+-----------------------------+

SEE ALSO

       csh(1), exit(1), ksh(1), sh( 1), attributes(5)

SunOS 5.10                                                          17 Jul 2002                                                           break(1)
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