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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 303023753 by Ibk on Friday 21st of September 2018 03:45:18 PM
Old 09-21-2018
Retrieving sequences corresponding to start and end position
Hi all,

I have a fasta file of a reference sequnce, I will like to retrieve sequences corresponding to a list of start and end position in another file

Code:
>my_ref_seq
GCCCTATAAGGGCAGAAGCTTGTCCTTCTTGTGCCAGTTATGACGTTTGTCCTAACTGCACATCTGGTAG
CATCCCCGATGATGGGTCTTCCAAAGGACAGATCCCCTCCTGGGAAGATGTTACAAAAACTTCTACCTAC
TCTCTCTTGTTGTCTGAGGACACATCCGACGAACTGCACCCTGACGACCTGGTTAACGTTGCTGCTCATA
TCCGAAAGGCCTTGTCCACTCAGTCTCACCCGGCAAATGTTGATATGTGCAAAGAACAGCTCACATCTCT
GTTGGTTATGGCTGAAGCAATGCTACCCCAACGCTCTAGGTCGACACTCCCACTACACCAAAAATATGTG

position.txt
Code:
my_ref_seq    1550   1590    
my_ref_seq    2399   2429    
my_ref_seq    3008   3038

expected result
Code:
seq_id            Start   End     sequence
my_ref_seq    1550   1590    TCCGAAAGGCCTTGTCCACTCAGTCTCACC
my_ref_seq    2399   2429    TCTCTCTTGTTGTCTGAGGACACATCCGAC
my_ref_seq    3008   3038    GAACTGTCCGAAAGGCCTTGTCCACTCAAA

Thank you for the help.
Last edited by Scrutinizer; 09-21-2018 at 05:09 PM.. Reason: code tags
 

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LEARN ABOUT DEBIAN

irsend

IRSEND(1)							   User Commands							 IRSEND(1)

NAME

       irsend - basic LIRC program to send infra-red commands

SYNOPSIS

       irsend [options] DIRECTIVE REMOTE CODE [CODE...]

DESCRIPTION

       Asks the lircd daemon to send one or more CIR (Consumer Infra-Red) commands. This is intended for remote control of electronic devices such
       as TV boxes, HiFi sets, etc.

       DIRECTIVE can be:
	  SEND_ONCE	    - send CODE [CODE ...] once
	  SEND_START	    - start repeating CODE
	  SEND_STOP	    - stop repeating CODE
	  LIST		    - list configured remote items
	  SET_TRANSMITTERS  - set transmitters NUM [NUM ...]
	  SIMULATE	    - simulate IR event

       REMOTE is the name of a remote, as described in the lircd configuration file.

       CODE is the name of a remote control key of REMOTE, as it appears in the lircd configuration file.

       NUM is the transmitter number of the hardware device.

       For the LIST DIRECTIVE, REMOTE and/or CODE can be empty:

	  LIST	 ""    ""   - list all configured remote names
	  LIST REMOTE  ""   - list all codes of REMOTE
	  LIST REMOTE CODE  - list only CODE of REMOTE

       The SIMULATE command only works if it has been explicitly enabled in lircd.

       -h --help
	      display usage summary

       -v --version
	      display version

       -d --device
	      use given lircd socket [/var/run/lirc/lircd]

       -a --address=host[:port]
	      connect to lircd at this address

       -# --count=n
	      send command n times

EXAMPLES

	  irsend LIST DenonTuner ""
	  irsend SEND_ONCE  DenonTuner PROG-SCAN
	  irsend SEND_ONCE  OnkyoAmpli VOL-UP VOL-UP VOL-UP VOL-UP
	  irsend SEND_START OnkyoAmpli VOL-DOWN ; sleep 3
	  irsend SEND_STOP  OnkyoAmpli VOL-DOWN
	  irsend SET_TRANSMITTERS 1
	  irsend SET_TRANSMITTERS 1 3 4
	  irsend SIMULATE "0000000000000476 00 OK TECHNISAT_ST3004S"

FILES

       /etc/lirc/lircd.conf
	      Default lircd configuration file.  It should contain all the remotes, their infra-red codes and the corresponding timing	and  wave-
	      form details.

DIAGNOSTICS

       If lircd is not running (or /var/run/lirc/lircd lacks write permissions) irsend aborts with the following diagnostics:
       "irsend: could not connect to socket"
       "irsend: Connection refused" (or "Permission denied").

SEE ALSO

       The documentation for lirc is maintained as html pages. They are located under html/ in the documentation directory.

       lircd(8), mode2(1), smode2(1), xmode2(1), irrecord(1), irw(1), http://www.lirc.org.

irsend 0.9.0-pre1						   October 2010 							 IRSEND(1)
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