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Full Discussion: Retrieving sequences corresponding to start and end position
Top Forums Shell Programming and Scripting Retrieving sequences corresponding to start and end position Post 303023756 by RudiC on Friday 21st of September 2018 04:28:29 PM
Old 09-21-2018
Unfortunately, this can't be tested with the data given. Howsoever, try
Code:
awk '
NR == 1         {print "seq_id            Start   End     sequence"
                 next}
NR == FNR       {SEQ = SEQ $0
                 next
                }
                {print $0, substr (SEQ, $2, $3-$2+1)
                }
' fastafile position.txt

 

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LEARN ABOUT DEBIAN

nysynopt

NYSYNOPT(1)						      General Commands Manual						       NYSYNOPT(1)

NAME

       nysynopt - tool to list contents of specialized-format patches

SYNOPSIS

       nysynopt pam options cradle [ print ] [ .go ]

DESCRIPTION

       nysynopt  is  a	tool in the Nypatchy suite of programs for working with Patchy Master Files (PAM files); see nypatchy(1).  Like nylist, it
       can print a listing (including line numbers) of the contents of these files.  However, it permits fine-tuning of the output through the use
       of a cradle file whose syntax is a subset of the nypatchy instruction set.  It also expands sequences inline.

USAGE

       The parameter pam is the name of the PAM file (a default extension of ".car" is assumed), print is the output file to write to (the default
       is standard output if omitted), and options is a sequence of single-character flags.  cradle is the set of instructions for  nysynopt.	If
       cradle is not given (or is replaced with "-"), standard input is assumed.  This argument may also be replaced by the three characters "EOF"
       to indicate that there is no cradle.

       The command should be ended with ".go" unless one wants to enter the Nypatchy interactive shell.

OPTIONS

       Note that options should be given as a single string of characters with no space separation and no use of the - character (except  that	it
       can be used in place of the options field if no options are desired).  Alphabetic options are not case-sensitive.

       E      Page ejects forced in the PAM file with +SEQ,QEJECT are honored (only if the S option is also given).

       H      Print help information only.

       I      Line numbers for individual PAM files should each start at zero.

       M      Missing sequences should be signalled.

       S      Start each new deck on a new page.

       X      Do not signal actions.

       Y      Do not expand sequences called by +CDE.

       Z      Do not expand sequences called by +SEQ.

       n      For  n  a  number  from  0 to 4 inclusive, assume 58, 62, 74, 84, or 98 lines per page in the output.  (The default is 110 lines per
	      page.)  For n a number greater than or equal to 20, use that specific number of lines per page.

       +      Inhibit the initial page-eject.

SEE ALSO

       fcasplit(1), nycheck(1), nydiff(1), nyindex(1), nylist(1), nymerge(1), nypatchy(1), nyshell(1), nytidy(1), yexpand(1)

       The reference manual for the Nypatchy suite of programs is available in compressed PostScript format at the following URL:
       http://wwwasdoc.web.cern.ch/wwwasdoc/psdir/p5refman.ps.gz

       Running the command "nysynopt help .no" also gives some brief help on usage.

AUTHOR

       This manual page was written by Kevin McCarty <kmccarty@debian.org> for the Debian GNU/Linux system (but may be used  by  others).   It	is
       licensed under the GNU General Public License, version 2 or later (at your choice).

COPYRIGHT

       Copyright (C) Kevin B. McCarty, 2008.

								   Mar 12, 2008 						       NYSYNOPT(1)
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