[EMBOSS] Note about restrict -alphabetic

[Guy Bottu]

from : BEN

	Dear colleagues,
	
I just tried something with restrict under EMBOSS 2.7.1. The program sorts by 
default the cut sites from begin to end. With parameter -alphabetic it sorts 
instead the output line according to the name of the restriction enzyme. All 
well, but if there are several cut sites for one enzyme, these are apparently 
output randomly. Cf. this example for the command
restrict vec:puc18 -enzymes=haeiii,mboi -alphabetic
-------------------

########################################
# Program: restrict
# Rundate: Mon Sep 22 17:11:15 2003
# Report_format: table
# Report_file: puc18.restrict
########################################

#=======================================
#
# Sequence: PUC18     from: 1   to: 2686
# HitCount: 26
#
# Minimum cuts per enzyme: 1
# Maximum cuts per enzyme: 2000000000
# Minimum length of recognition site: 4
# Blunt ends allowed
# Sticky ends allowed
# DNA is linear
# Ambiguities allowed
#
#=======================================

  Start     End Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev
   2675    2678 HaeIII      GGCC               2676   2676         .         .
   1741    1744 HaeIII      GGCC               1742   1742         .         .
   1821    1824 HaeIII      GGCC               1822   1822         .         .
    389     392 HaeIII      GGCC                390    390         .         .
    287     290 HaeIII      GGCC                288    288         .         .
    646     649 HaeIII      GGCC                647    647         .         .
   2088    2091 HaeIII      GGCC               2089   2089         .         .
    820     823 HaeIII      GGCC                821    821         .         .
    831     834 HaeIII      GGCC                832    832         .         .
    849     852 HaeIII      GGCC                850    850         .         .
   1283    1286 HaeIII      GGCC               1284   1284         .         .
   2067    2070 MboI        GATC               2066   2070         .         .
   2325    2328 MboI        GATC               2324   2328         .         .
   2342    2345 MboI        GATC               2341   2345         .         .
   2378    2381 MboI        GATC               2377   2381         .         .
   1545    1548 MboI        GATC               1544   1548         .         .
    430     433 MboI        GATC                429    433         .         .
   1373    1376 MboI        GATC               1372   1376         .         .
   1448    1451 MboI        GATC               1447   1451         .         .
   1459    1462 MboI        GATC               1458   1462         .         .
   1467    1470 MboI        GATC               1466   1470         .         .
    277     280 MboI        GATC                276    280         .         .
   1557    1560 MboI        GATC               1556   1560         .         .
   1662    1665 MboI        GATC               1661   1665         .         .
   2003    2006 MboI        GATC               2002   2006         .         .
   2021    2024 MboI        GATC               2020   2024         .         .

#---------------------------------------
#---------------------------------------
------------------------------------------------------------------------------
IMHO it would be better if the lines were sorted by enzyme name AND for each 
enzyme by position from begin to end. Is this also your opinion ?

	Sinceely,
	Guy Bottu