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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 OPENDARWIN

seek

seek(n) 						       Tcl Built-In Commands							   seek(n)

__________________________________________________________________________________________________________________________________________________

NAME

       seek - Change the access position for an open channel

SYNOPSIS

       seek channelId offset ?origin?
_________________________________________________________________

DESCRIPTION

       Changes the current access position for channelId.

       ChannelId  must	be  an	identifier for an open channel such as a Tcl standard channel (stdin, stdout, or stderr), the return value from an |
       invocation of open or socket, or the result of a channel creation command provided by a Tcl extension.

       The offset and origin arguments specify the position at which the next read or write will occur for channelId. Offset must  be  an  integer
       (which may be negative) and origin must be one of the following:

       start	 The new access position will be offset bytes from the start of the underlying file or device.

       current	 The  new access position will be offset bytes from the current access position; a negative offset moves the access position back-
		 wards in the underlying file or device.

       end	 The new access position will be offset bytes from the end of the file or device.  A negative offset places  the  access  position
		 before the end of file, and a positive offset places the access position after the end of file.

       The origin argument defaults to start.

       The  command  flushes  all buffered output for the channel before the command returns, even if the channel is in nonblocking mode.  It also
       discards any buffered and unread input.	This command returns an empty string.  An error occurs if this	command  is  applied  to  channels
       whose underlying file or device does not support seeking.

       Note  that  offset  values  are	byte offsets, not character offsets.  Both seek and tell operate in terms of bytes, not characters, unlike |
       read.

SEE ALSO

       file(n), open(n), close(n), gets(n), tell(n), Tcl_StandardChannels(3)

KEYWORDS

       access position, file, seek

Tcl									8.1								   seek(n)
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