From c21966c9a0a27646347dec4506e08f40afbe9e8c Mon Sep 17 00:00:00 2001 From: jo Date: Tue, 30 Jul 2024 18:50:07 +0200 Subject: [PATCH] added reduced pathway screening option to gapseq findRxn - use parameter `-p small|min` to use smaller or mininal pathway collection - reduced running time considerably - needs further testing --- src/gapseq_find.sh | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/src/gapseq_find.sh b/src/gapseq_find.sh index 126a9679..867a17be 100755 --- a/src/gapseq_find.sh +++ b/src/gapseq_find.sh @@ -323,6 +323,23 @@ case $pathways in core) pwyKey="Amino-Acid-Biosynthesis|Nucleotide-Biosynthesis|Cofactor-Biosynthesis|Carbohydrates-Degradation|CARBO-BIOSYNTHESIS|Polyamine-Biosynthesis|Fatty-acid-biosynthesis|Energy-Metabolism|Terpenoid-Biosynthesis|Chorismate-Biosynthesis" ;; + small) + pwyKey="Amino-Acid-Biosynthesis|Nucleotide-Biosynthesis|Cofactor-Biosynthesis|Energy-Metabolism|Sugars-And-Polysaccharides-Degradation" + ;; + min) + tca="\\|TCA\\||P105-PWY" + resp="PWY-7544|PWY0-1334" + ferm="PYR-TO-BUT-NADPH|2FLHYD|PWY-7385|PWY-6344|PWY-5938|PWY-5494|PWY-5497|P164-PWY|PWY-8086|PWY-5677|PWY-8014|P162-PWY|CENTFERM-PWY|P122-PWY|PWY-6130|P108-PWY|PYR-ACCOA-FROX|BIFIDOSHUNT2|LNT-DEGRADATION|PWY-6583|PWY-5437|FERMENTATION-PWY" + glyc="ANAGLYCOLYSIS-PWY|PWY-1042" + ppp="NONOXIPENT-PWY|OXIDATIVEPENT-PWY" + aasyn="PWY-4361|PWY-3941|ARGASEDEG-PWY|ASPARAGINESYN-PWY|PWY-2942|ALANINE-VALINESYN-PWY|PHESYN|PWY-2941|TRPSYN-PWY2|PWY-4341|SERSYN-PWY|GLYSYN-THR-PWY|ASPARAGINE-BIOSYNTHESIS|GLUTSYNIII-PWY|TRPSYN-PWY|PWY-3461|PWY-5101|LEUSYN-PWY|PWY-3081|PWY-5097|ILEUSYN-PWY|GLUTAMATE-SYN2-PWY|HOMOSERSYN-PWY|PWY-3982|PROSYN-PWY|PWY-5344|HOMOSER-THRESYN-PWY|GLNSYN-PWY|HOMOCYSDEGR-PWY|CYSTSYN-PWY|HISTSYN-PWY|GLYSYN-ALA-PWY|HOMOSER-METSYN-PWY|ARGSYNBSUB-PWY|PWY0-901|PWY490-4|DAPLYSINESYN-PWY" + cosyn="PWY-6148|PWY-8171|PWY0-1275|PWY-5443|MENAQUINONESYN-PWY|PWY-6892|PWY-6383|PWY-7761|PWY-7165|NADPHOS-DEPHOS-PWY|PWY-7377|PWY0-1507|PWY-5509|PWY-5837|PWY-6893|PWY-7356|NAD-BIOSYNTHESIS-II|PWY-7376|PWY-6151|RIBOSYN2-PWY|PWY-7962|PWY-7729|NADPHOS-DEPHOS-PWY-1|PWY-2161|PWY-6910|PYRIDNUCSYN-PWY|NADP-RED-FD-NADH|PWY-6890|PANTO-PWY|PWY-7378|P241-PWY|COA-PWY|PWY-6614|PWY-5653|PYRIDNUCSAL-PWY|PWY-5785|PYRIDOXSYN-PWY|PWY-6891|1CMET2-PWY" + nusyn="PWY-7199|IMPSYN-HIGH-HCO3|PWY-7193|PWY-6610|SALVPURINE2-PWY|PWY-7205|PWY-6599|PWY-7791|PWY-7790|PWY-7187|PWY-7210|P121-PWY|PWY-6545|PWY-7183|PWY-6121|PWY-5686|PWY-6556|PWY-6123|PWY-7221|PWY-7219|PWY-7197|PWY-7176" + carbodeg="PWY-6572|RIBOKIN-PWY|PWY-7077|PWY-7581|PWY-7247|PWY-5941|2FLHYD|PWY-6717|PWY-6507|PWY0-1314|ARABCAT-PWY|PWY-7242|RHAMCAT-PWY|LACTOSECAT-PWY|DARABITOLUTIL-PWY|PWY0-1309|TREDEGLOW-PWY|PWY0-1324|MANNCAT-PWY|PWY0-1301|PWY-7178|GLYCEROLMETAB-PWY|PWY-2221|PWY-7180|GALACTITOLCAT-PWY|PWY-621|GALACTUROCAT-PWY|PWY-3801|LACTOSEUTIL-PWY|PWY-5517|PWY-8121|PWY-4261|PWY-6130|DARABCATK12-PWY|GLUAMCAT-PWY|BIFIDOSHUNT2|EXC-STARCH-N27|LNT-DEGRADATION|GLUCOSE1PMETAB-PWY|GLYCOCAT-PWY|PWY-6906|PWY-6317" + carboxdeg="GLUCONSUPER-PWY|IDNCAT-PWY|PWY-7247|PWY-7948|2FLHYD|PWY0-1313|PROPIONMET-PWY|PWY0-42|PWY-7242|PWY-8134|PWY-5177|GALACTARDEG-PWY|GALACTUROCAT-PWY|GLYCOLATEMET-PWY|PWY-6518|GALACTCAT-PWY|BIFIDOSHUNT2|PWY-7754|LNT-DEGRADATION|PWY-6697" + pwyKey="$tca|$resp|$ferm|$glyc|$ppp|$aasyn|$cosyn|$nusyn|$carbodeg|$carboxdeg" + noSuperpathways=false # some listed pathways are superpathways + ;; kegg) pwyKey=kegg ;;