From 4214cdc90c12a76ce24e565ed9379b100da45563 Mon Sep 17 00:00:00 2001 From: Robert Edgar Date: Mon, 19 Aug 2024 15:35:01 -0700 Subject: [PATCH] Update convert test & check --- src/Makefile | 6 ++-- test_data/chains.fa | 61 ----------------------------------- test_scripts/check_convert.py | 5 ++- test_scripts/convert.bash | 2 ++ 4 files changed, 9 insertions(+), 65 deletions(-) diff --git a/src/Makefile b/src/Makefile index 7e75b26..d6dd391 100644 --- a/src/Makefile +++ b/src/Makefile @@ -8,13 +8,13 @@ OBJDIR := o BINPATH := $(BINDIR)/reseek CC = gcc -CFLAGS := $(CFLAGS) -ffast-math -march=native --std=c++17 -O3 -DNDEBUG -fopenmp +CFLAGS := $(CFLAGS) -ffast-math -march=native -O3 -DNDEBUG CXX = g++ -CXXFLAGS := $(CFLAGS) -ffast-math -march=native --std=c++17 -O3 -DNDEBUG -fopenmp +CXXFLAGS := $(CFLAGS) -ffast-math -march=native -O3 -DNDEBUG UNAME_S := $(shell uname -s) -LDFLAGS := $(LDFLAGS) -ffast-math -march=native -O3 -fopenmp +LDFLAGS := $(LDFLAGS) -ffast-math -march=native -O3 ifeq ($(UNAME_S),Linux) LDFLAGS += -static endif diff --git a/test_data/chains.fa b/test_data/chains.fa index 859fe7c..10ca89e 100644 --- a/test_data/chains.fa +++ b/test_data/chains.fa @@ -215,20 +215,6 @@ IYRALEQSALPIHAVQLIEDTSRETAKELFTLNDGLDVLIPRGGKKLIDLVVRESTVPVLETGAGNCHIFIDETAKPQMA EKVVVNAKTQRPSVCNAIESLLIHKAWARQHGKELLDQLENAGVEIRGDELVCELHPSSKQASKEDWETEFLAPVLSVKT VENVQEAVKHIQQYGTNHSEAILTENDKNAVYFQTAVDAAAVYHNASTRFTDGFEFGYGAEIGISTQKLHARGPMGLPAL TSTKYIIKGTGQIRE ->AFDB_Q839W3:A -MKVTDLKQLGQQAKEASYTLGLMDTRQKNTLLNKMAAAIEANAPRILQANALDLEQAATHGISETMQDRLRLTEERITAM -AEGIRQVATLPDPIGEVDKMWRNEAGLLIGQQRVPLGVIGIIYESRPNVTTDAASLCFKSGNAVILRGGKEAFHSNQILV -TILQEALIQEAVSPHLIQFVDDTSRETAQQLMRLNDYLDVLIPRGGANLIKTVLTTATVPVIETGTGNCHIYVDKDAQLT -MATEIIVNAKCQRPSVCNAAETLLIHQEVAEAFLPTIEKALKEFHVELRADERALAIFEEAIPATEQDWETEFLDFILAV -KVVDSLDEAIQHINRYNTKHSESIISDNYFATQQFLQQVDAAAVYANASTRFTDGFEFGFGAEIGISTQKLHARGPMGLA -ELTSTKYVIYGNGQARS ->AFDB_Q890J4:A -MVDLEQLGQQAQQASYTLGLLSTAQKNQVLTAMATALTSHQDEILAANAQDLENPQVPVKFVDRLRLTADRIQDMAIGLK -QVVSLPDPIGNVDRAWRNEAGLMIAKERVPLGVIGMIFEARPNVTVDASALCFKTGNAVILRGGKEALHSNQALVQVLRG -ALRAEAVDENAIQLITDTSHATAAKFMQLTDYVDVLIPRGSARLIQTVLAKATVPVIETGAGNCHVYVDKDAQLQMATDI -VINGKVQRPSVCNATEKLLIHREVAADYLPSMIQALREQGVEVRGDAATQAIVPDVVPATDADWGTEYNDLIIAVKVVDS -EAAAITHINRYNTQHSEAIVTDNYQAGKLFQQRVNAACVYINASTRFTDGFEFGFGAEIGISTQKLHARGPMGLAELTSY -KYVIDGNGQIRH >AFDB_Q896G4:A MDDLNKYLINKGKKAKEASRFLSSVDSNFKNKALHKMGEDLKANMNKIIAANKIDMEKGKEKGLSKSLLDRLLIDEKRVN DMVNGLIEVAELPDPIGEVLNMWKRPNGINIGVKRVPLGVIGIIYEARPNVTVDATALCLKSGNAVILRGGSEAINTNKA @@ -236,13 +222,6 @@ IGKILENSAIESGLPEGTIQLIETTDREIVNKMLKLNEYIDVLIPRGGRGLIDNVVKNSTVPVIQTGVGLCHVYVDGSAN LKMAQDIIVNAKTQRPGVCNALETLLVHKDVANSFLPEIVSEISKYGVESKLCEKSFEVVKGSIKDAKVLSLISEATEED WDTEYLDLILSIKIVNSLDEALNHIYDHGTKHSEAIITENYTNSQRFLNEVDAAAVYVNASTRFTDGSQFGFGAEIGIST QKLHARGPMGLTQLTTTKYIIYGNGQIR ->AFDB_Q8CUQ4:A -MSEVIEKAKRAKQASFKMALSTTDDKNEALQLISQAIINHKQEILTANALDIEEGKKKGLSEAVIDRIRLNEERLQDIAD -AILQVTILTDPIGEALEIIEKDNGLFITKKRVPIGVIGMVYEARPNVTVDAASLAIKTGNSVVLRGSSSAIESNKALIQV -IHQSLASSSIPKEAVQLIEDTRREVANQFFQLNEYLDVLIPRGGKQLIDTVIKQSTVPVIETGAGNCHVYLDESAKVEMA -TEIVLNAKLQRPSVCNAIESLIIHRQWFEDHGLELLKTMQSHDIKIHGDSVVMEKFPPAIKAVERDWEKEYLSSEISVKI -VDSVSEAIDHINRYGTRHSEAIITENKMNAEQFQLQVDAAAVYHNASTRFTDGFEFGYGAEIGISTQKLHARGPMGLEAL -TSTKFVISGSGQIRE >PDB_1hhs:A PRRAPAFPLSDIKAQMLFANNIKAQQASKRSFKEGAIETYEGLLSVDPRFLSFKNELSRYLTDHFPANVDEYGRVYGNGV RTNFFGMRHMNGFPMIPATWPLASNLKKRADADLADGPVSERDNLLFRAAVRLMFSDLEPVPLKIRKGSSTCIPYFSNDM @@ -273,14 +252,6 @@ MGTLLMSITYLVMQLDHTAPHLNSRIKDMPSACRFLDSYWQGHEEIRQISKSDDAMLGWTKGRALVGGHRLFEMLKEGKV NPSPYMKISYEHGGAFLGDILLYDSRREPGSAIFVGNINSMLNNQFSPEYGVQSGVRDRSKRKRPFPGLAWASMKDTYGA CPIYSDVLEAIERCWWNAFGESYRAYREDMLKRDTLELSRYVASMARQAGLAELTPIDLEVLADPNKLQYKWTEADVSAN IHEVLMHGVSVEKTERFLRSVMPR ->PDB_2ckw:A -DEFQWKGLPVVKSGLDVGGMPTGTRYHRSPAWPEEQPGETHAPAPFGSGDKRYTFSQTEMLVNGLKPYTEPTAGVPPQLL -SRAVTHVRSYIETIIGTHRSPVLTYHQACELLERTTSCGPFVQGLKGDYWDEEQQQYTGVLANHLEQAWDKANKGIAPRN -AYKLALKDELRPIEKNKAGKRRLLWGCDAATTLIATAAFKAVATRLQVVTPMTPVAVGINMDSVQMQVMNDSLKGGVLYC -LDYSKWDSTQNPAVTAASLAILERFAEPHPIVSCAIEALSSPAEGYVNDIKFVTRGGLPSGMPFTSVVNSINHMIYVAAA -ILQAYESHNVPYTGNVFQVETIHTYGDDCMYSVCPATASIFHTVLANLTSYGLKPKPTNTPVFLKRTFTQTPHGIRALLD -ITSITRQFYWLKANRTSDPSSPPAFDRQARSAQLENALAYASQHGPVMFDTVRQIAIKTAQGEGLVLVNTNYDQALATYN -AWFIGGT >PDB_3h5y:A KGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLE AAKKTIINVLEQTIDPPDKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGA @@ -288,35 +259,3 @@ LKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKTHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYS RWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEV TNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQS SILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELDFYVPRQEPMFRWMRFS ->PDB_4gzk:A -HAETRIVTDAPRNSESVGDHLFNGGVNHHDEDPDAYTKMYGPLVGYDPRNPTTLFANARQTGTQLVAPRKAREILTGIYS -FEPTVLAFQREFVKRANAVAQPDLNSDGFSLNGLHTTFDSIRSVSGYPQWPVSALPKSNVGLLRDDLKLQERMTARQVVI -AREIWKRVWGHMKPTAIKIPKMMSTSGPPRNVNDAEMKLQYALALFSGNRYNGYLDAFKSGDLSRFYRDYEAAVIMGTTN -NVRWQVDNNPGKKRDDYWAQADIERELAPSKRPITTKVEINGTVYDDFAAMRTRLLVNAGPWTINVALQQPFATTGCMNA -MFELYRATWHPDEDKIAGFLEGKHAFFGDVSSYDHSFSEEKIDLSLEVGKEFISPEIMELASSLFYAAYFTRPLGPDDGP -QLVGNPNRYLEKQVKAGNRSGHAFTSLFAKVWKVIDTVSKFDQMGYDVVANMDAILKGDMPFGCINNGDDEIVWFKSERD -YRLFLRLLETQPQEQRMFKVGPEEGAVFSGSVYQLIGPLKYQAVERITTPFQRIICPERSIGGNFRKFWPLGILERYNKR -NSHPVLEEVWRVFDDDTYATLMEPHYGSFLGIVQRAHKEIPFSVDDLSWKEIMVLDDPNKMYHRFTDEEIRDQVQESAFR -KLQPIFFERMFKEHYKGNYV ->PDB_5amq:A -MDYQEYQQFLARINTARDACVAKDIDVDLLMARHDYFGRELCKSLNIEYRNDVPFIDIILDIRPEVDPLTIDAPHITPDN -YLYINNVLYIIDYKVSVSNESSVITYDKYYELTRDISDRLSIPIEIVIIRIDPVSRDLHINSDRFKELYPTIVVDINFNQ -FFDLKQLLYEKFGDDEEFLLKVAHGDFTLTAPWCKTGCPEFWKHPIYKEFKMSMPVPERRLFEESVKFNAYESERWNTNL -VKIREYTKKDYSEHISKSAKNIFLASGFYKQPNKNEISEGWTLMVERVQDQREISKSLHDQKPSIHFIWGAHNPGNSNNA -TFKLILLSKSLQSIKGISTYTEAFKSLGKMMDIGDKAIEYEEFCMSLKSKARSSWKQIMNKKLEPKQINNALVLWEQQFM -INNDLIDKSEKLKLFKNFCGIGKHDLEVSKPKILDFDDANMYLASLTMMEQSKKILSKSNGLKPDNFILNEFGSRIKDAN -KETYDNMHKIFETGYWQCISDFSTLMKNILSVSQYNRHNTFRIAMCANNNVFAIVFPSADTVVYSIIVLHKEEENIFNPG -CLHGTFKCMNGYISISRAIRLDKERCQRIVSSPGLFLTTCLLFKHDNPTLVMSDIMNFSIYTSLSITKSVLSLTEPARYM -IMNSLAISSNVKDYIAEKFSPYTKTLFSVYMTRLIKNACFDAYDQRQRVQLRQKGIKDNRELTSIWFPGSVTLKEYLTQI -YLPFYFNAKGLHEKHHVMVDLAKTILEIECEQRENIKEIWSTNCTKQTVNLKILIHSLCKNLLADTSRHNHLRNRIENRN -NFRRSITTISTFTSSKSCLKIGDFRKEKELQSVKQKKILEVQSRKMRLANNYEMLRNAMPNYTDYISTKVFDRLYELLDK -KVLTDKPVIEQIMDMMIDHKKFYFTFFNKGQKTSKDREIFVGEYEAKMCMYAVERIAKERCKLNPDEMISEPGDGKLKVL -EQKSEQEIRFLVETTRQKNREIDEAIEALATEGYESNLGKIEKLSLGKAKGLKMEINADMSKWSAQDVFYKYFWLIALDP -ILYPQEKERILYFMCNYMDKELILPDELLFNLLDQKVAYQNDIIATMTNQLNSNTVLIKRNWLQGNFNYTSSYVHSCAMS -VYKEILKEAITLLDGSILVNSLVHSDDNQTSITIVQDKMENDKIIDFAMKEFERACLTFGCQANMKKTYVTNCIKEFVSL -FNLYGEPFSIYGRFLLTSVGDCAYIGPYEDLASRISSAQTAIKHGCPPSLAWVSIAISHWMTSLTYNMLPGQSNDPIDYF -PAENRKDIPIELNGVLDAPLSMISTVGLESGNLYFLIKLLSKYTPVMQKRESVVNQIAEVKNWKVEDLTDNEIFRLKILR -YLVLDASILTPRKFTTAGSLRKLYSFSKYQDRLSSPGGMVELFTYLLEKPELLVTKGEDMKDYMESVIFRYNSKRFKESL -SIQNPAQLFIEQILFSHKPVIDFSGIRDKYINGKVTFTEAYRLLMRDLSSLELTNDDIQVIYSYIILNDPMMITIANTHI -LSIYGSPQRRMGMSCSTMPEFRNSPALVLRAYSKNNPDIQGAPTEMARDLVHLKEFVENTNLEEKMKVRIAMNEAEKGQR -DIVFELKEMTRFYQVCYEYVKSTEHKIKVFILPAKSYTTTDFCSLMQGNLIKDKEWYTVHYLKQIL diff --git a/test_scripts/check_convert.py b/test_scripts/check_convert.py index 3f7f32e..8224d03 100644 --- a/test_scripts/check_convert.py +++ b/test_scripts/check_convert.py @@ -30,7 +30,10 @@ def check_fasta(fn): errors += 1 print("ERROR %s not found in %s" % (label, fn)) return - if seq != seq2: + if seq == seq2: + if 0: + print("seq ok %s" % label) + else: errors += 1 print("ERROR %s different %s" % (label, fn)) return diff --git a/test_scripts/convert.bash b/test_scripts/convert.bash index 7c378be..18dc54c 100644 --- a/test_scripts/convert.bash +++ b/test_scripts/convert.bash @@ -11,6 +11,7 @@ ls ../test_structures/* \ -fasta files.fa \ -cal files.cal \ -bca files.bca \ + -chainsep : \ -log convert_files.log ../bin/reseek \ @@ -18,6 +19,7 @@ ls ../test_structures/* \ -fasta dir.fa \ -cal dir.cal \ -bca dir.bca \ + -chainsep : \ -log convert_dir.log function cvt() {