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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 CENTOS

ng_fec

NG_FEC(4)						   BSD Kernel Interfaces Manual 						 NG_FEC(4)

NAME

     ng_fec -- netgraph Fast EtherChannel node

SYNOPSIS

     #include <netgraph/ng_fec.h>

DESCRIPTION

     The fec node implements Ethernet port trunking using the ``Cisco Fast EtherChannel'' protocol.  Upon creation, a fec node creates a network
     interface associated with it.  Interfaces are named ``fec0'', ``fec1'', etc.  New nodes take the first available unit.

HOOKS

     The fec node accepts any hooks.  However it does not use them.  Under normal operation, a fec node should not have any hooks.

CONTROL MESSAGES

     Interface membership in the FEC group is configured with the following control messages:

     NGM_FEC_ADD_IFACE (``add_iface'')
	     Attach interface to the FEC group.  The target interface name is passed as a string argument.

     NGM_FEC_DEL_IFACE (``del_iface'')
	     Remove interface from the trunk.  The target interface name is passed as a string argument.

     The following control messages define the forwarding method for a node:

     NGM_FEC_SET_MODE_MAC (``set_mode_mac'')
	     Forwarding decisions will be based on the link-layer MAC address of the destination.

     NGM_FEC_SET_MODE_INET (``set_mode_inet'')
	     Forwarding decisions will be based on the IP address of the destination.

SHUTDOWN

     This node shuts down upon receipt of a NGM_SHUTDOWN control message.

EXAMPLES

     The following example script creates an fec node, attaches four Ethernet interfaces to it and sets the forwarding method to be IP-address
     based:

	   /usr/sbin/ngctl -f- << SEQ
		   mkpeer fec dummy fec
		   msg fec0: add_iface "dc0"
		   msg fec0: add_iface "dc1"
		   msg fec0: add_iface "dc2"
		   msg fec0: add_iface "dc3"
		   msg fec0: set_mode_inet
	   SEQ

SEE ALSO

     netgraph(4)

HISTORY

     The fec node type was implemented in FreeBSD 5.0.

AUTHORS

     The fec node was written by Bill Paul <wpaul@FreeBSD.org>.  This manual page was written by Gleb Smirnoff <glebius@FreeBSD.org>.

BSD
								   July 22, 2004							       BSD
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