diff lipidmaps.conf @ 0:e8bd49794291 draft

Init repository with last lipidmaps_textsearch master version

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lipidmaps.conf	Tue Apr 11 03:47:06 2017 -0400
@@ -0,0 +1,130 @@
+## LIPIDMAPS CONF FILE
+## Version 2.1 -- edited by F.Giacomoni 
+## Build October 30th 2012
+## release October 22th 2013
+## release Nov 25th 2013
+## release Fev 17th 2014
+## release 2014-05-07
+## release 2016-06-09 / REST client implementation
+## release 2016-09-27 - clean and requirement
+#
+# Galaxy url for HTML JS and CSS path 
+JS_GALAXY_PATH=https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/scripts
+CSS_GALAXY_PATH=https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/style
+
+# HTML TEMPLATE PATH:
+HTML_ENTRIES_PER_PAGE=4
+
+## LIPIDMAPS SEARCH URL
+SEARCH_URL=http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessTextSearch&OutputColumnHeader=No&OutputMode=File&OutputType=TSV
+LM_ID_URL=http://www.lipidmaps.org/data/LMSDRecord.php?&LMID=
+REST_WS=http://www.lipidmaps.org/data/lm_rest.php
+
+#VALUE FOR loss /add atoms (loss/add_$ATOMS)
+O=15.9949
+2O=31.9898
+4O=63.9797
+hydroperoxide=34.0055
+water=18.0106
+
+## Annotation for loss /add atoms
+ANNOT_loss_O=+O
+ANNOT_loss_2O=+2O
+ANNOT_loss_4O=+4O
+ANNOT_loss_hydroperoxide=+H2O2
+ANNOT_loss_water=+H2O
+
+## ----------------******************-------SOME PARSING RULES to LM CLUSTERING---------------*******************---------------------##
+# RULE of '-' only
+RULE01=^\-$
+
+# RULE of XX-xx only -- Ex: PE-NMe2 or PC
+RULE02=^([A-Z|a-z|0-9|\-]*)$
+
+## *** ***  *** *** PG  *** *** *** *** ##
+# RULE of XX(16:1/16:1)
+RULE03=^([A-Z|a-z]{2,4})\((\d+):(\d+)\/(\d+):(\d+)\)$
+
+# RULE of XX(16:1/16:1(OHC)) OXYDED!!
+RULE04=^([A-Z|a-z]{2,4})\((\d+):(\d+)\/(\d+):(\d+)\(([OHC]*)\)\)$
+
+#RULE of XX(16:1(1Z,..)/16:1(1Z,..)(OHC)) OXYDED!! -- Ex: PE(16:0/22:6(54Z,7Z,10Z,12E,16Z,19Z)(14OH))
+RULE05=^([A-Z|a-z]{2,4})\((\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\(([OHCKe0-9]*)\)\)$
+
+# RULE of XX(16:1(1Z,..)/16:1(1Z,..))
+RULE06=^([A-Z|a-z]{2,4})\((\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)$
+
+# RULE of XX(16:1(1Z,...)) ou XX(16:1) ONLY
+RULE07=^([A-Z|a-z]{2,5})\((\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)$
+
+# RULE of XX(X-16:1(1Z,..)/16:1(1Z,..)) with(1Z,...) in option
+RULE08=^([A-Z|a-z]{2,4})\(([A-Z]{1})-(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)$
+
+# RULE of XX(16:1(1Z,..)/X-16:1(1Z,..)) with (1Z,...) in option
+RULE09=^([A-Z|a-z]{2,4})\((\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/([A-Z]{1})-(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)$
+
+# RULE of XX(X-16:1(1Z,..)/X-16:1(1Z,..)) with (1Z,...) in option
+RULE10=^([A-Z|a-z]{2,4})\(([A-Z]{1})-(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/([A-Z]{1})-(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)$
+
+# RULE of XX-xx(16:1(1Z,..)/16:1(1Z,..))  -- Ex: PE-NMe(16:0/16:0)
+RULE11=^([A-Z|a-z]*-[A-Z|a-z|0-9]*)\((\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)$
+
+# RULE of XX-xx(X-16:1(1Z,..)/X-16:1(1Z,..)) -- Ex: PE-NMe(O-16:0/O-16:0)
+RULE12=^([A-Z|a-z]*-[A-Z|a-z|0-9]*)\(([A-Z]{1})-(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/([A-Z]{1})-(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)$
+
+# RULE of XX-xx(16:1(1Z,)/16:1(1Z,)/16:1(1Z,...)) -- Ex: PS-NAc(18:0/18:1(9Z)/16:0)
+RULE13=^([a-z|A-Z|\-]*)\((\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)$
+
+# RULE of XX(16:1(1Z,..)/16:1(1Z,..))[Xx] -- Ex : PC(18:1(9Z)/0:0)[rac]
+RULE14=^([A-Z|a-z]{2,4})\((\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)(\[[A-Z|a-z|0-9]*\])$
+
+# RULE of XX(16:1(1Z,..)/16:1(1Z,..))(OHC[S]) -- Ex: PE(16:0/20:4(5Z,8Z,10E,14Z)(12OH[S]))  OXYDED!!
+RULE15=^([A-Z|a-z]{2,4})\((\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)\(([A-Z|a-z|0-9|\[\]]*)\)\)$
+
+# RULE des XX(X-16:1(1Z,..)/16:1(1Z,..))(OHC[S]) -- Ex: PE(P-18:0/20:4(6E,8Z,11Z,14Z)(5OH[S]))  OXYDED!!
+RULE16=^([A-Z|a-z]{2,4})\(([A-Z]{1})-(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)\(([A-Z|a-z|0-9|\[\]]*)\)\)$
+
+# RULE of XX[3',5'](16:1(1Z,..)/16:1(1Z,..))
+RULE17=^([A-Z|a-z|0-9|\[\]|,]*)\((\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)$
+
+## *** ***  *** *** SM  *** *** *** *** ##
+# RULE OF xx-XX(16:1(1z..)/16:0(1z..)(OH)) -- Ex: PE-Cer(d16:2(4E,6E)/24:1(15Z)(2OH))  OXYDED !!
+RULE18=^([A-Za-z0-9\-]*)\([a-z](\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\(([COH0-9\-]*)\)\)$
+
+# RULE OF xx-XX(16:1(1z..)/16:0(1z..)) -- Ex: GlcCer(d14:2(4E,6E)/18:1(9Z))
+RULE19=^([A-Za-z0-9\-]*)\([a-z]{0,1}(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/[a-z]{0,1}(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)$
+
+# RULE OF M(IP)2C(16:1(1z..)/16:0(1z..)) -- Ex: M(IP)2C(d18:0/18:0(2OH))   OXYDED !!
+RULE20=^(M\(IP\)2C)\([a-z]{0,1}(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/[a-z]{0,1}(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\(([COH0-9\-]*)\)\)$
+
+# RULE of M(IP)2C(16:1(1z..)/16:0(1z..)) -- Ex: M(IP)2C(t18:0/18:0)
+RULE21=^(M\(IP\)2C)\([a-z]{0,1}(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/[a-z]{0,1}(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)$
+
+# RULE of -- Ex: DG(22:3(10Z,13Z,16Z)/22:5(7Z,10Z,13Z,16Z,19Z)/0:0)[iso2]
+RULE22=^([A-Z|a-z]{2,4})\((\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\/(\d+):(\d+)[A-Z|a-z|0-9|,|\(\)]*\)(\[[A-Z|a-z|0-9]*\])$
+
+## ----------------******************-------SOME RECIPES to LM CLUSTERING---------------*******************---------------------##
+## give the array position of each part of the cluster name : 
+## $Gp1, $Gp2, $Gp3, $Ch1_C, $Ch1_i, $Ch2_C, $Ch2_i, $Ch3_C, $Ch3_i, $Ox, $Post (11 values)
+RECIPE01=1,0,0,0,0,0,0,0,0,0,0
+RECIPE02=1,0,0,0,0,0,0,0,0,0,0
+RECIPE03=1,0,0,2,3,4,5,0,0,0,0
+RECIPE04=1,0,0,2,3,4,5,0,0,6,0
+RECIPE05=1,0,0,2,3,4,5,0,0,6,0
+RECIPE06=1,0,0,2,3,4,5,0,0,0,0
+RECIPE07=1,0,0,2,3,0,0,0,0,0,0
+RECIPE08=1,2,0,3,4,5,6,0,0,0,0
+RECIPE09=1,4,0,2,3,5,6,0,0,0,0
+RECIPE10=1,2,5,3,4,6,7,0,0,0,0
+RECIPE11=1,0,0,2,3,4,5,0,0,0,0
+RECIPE12=1,2,5,3,4,6,7,0,0,0,0
+RECIPE13=1,0,0,2,3,4,5,6,7,0,0
+RECIPE14=1,0,0,2,3,4,5,0,0,0,6
+RECIPE15=1,0,0,2,3,4,5,0,0,6,0
+RECIPE16=1,2,0,3,4,5,6,0,0,7,0
+RECIPE17=1,0,0,2,3,4,5,0,0,0,0
+RECIPE18=1,0,0,2,3,4,5,0,0,6,0
+RECIPE19=1,0,0,2,3,4,5,0,0,0,0
+RECIPE20=1,0,0,2,3,4,5,0,0,6,0
+RECIPE21=1,0,0,2,3,4,5,0,0,0,0
+RECIPE22=1,0,0,2,3,4,5,6,7,0,8
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