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debug-wrapper.scm
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;
; debug-wrapper.scm
;
; A quick hacky wrapper around the MOZI annotation-scheme code,
; used to debug performance issues in that code-base. This just
; provides a medium-sized list of genes, and then some small
; wrapprs to trigger processing of this list.
;
; ----------------------------------------------------------
;
; Basic list of 681 genes.
; See also lmpd-genes.scm for a list of 1482
;
; These are genes that are active in youth/young (human) adults, but
; whose activty disappears in sixty-year-olds.
;
(define gene-list (list "TSPAN6" "NDUFAF7" "RBM5" "SLC7A2" "NDUFAB1"
"DVL2" "SKAP2" "DHX33" "MSL3" "BZRAP1" "GTF2IRD1" "IL32" "RPS20" "SCMH1"
"CLCN6" "RNF14" "ATP2C1" "IGF1" "GLRX2" "FAS" "ATP6V0A1" "FBXO42" "JADE2"
"PREX2" "NOP16" "LMO3" "R3HDM1" "ERCC8" "HOMER3" "USE1" "OPN3" "SZRD1"
"ATG5" "CAMK2B" "MPC1" "MRPS24" "ZNF275" "TAF2" "TAF11" "IPO5" "NDUFB4"
"DIP2B" "MPPED2" "IARS2" "ERLEC1" "UFD1L" "PDCD2" "ACADVL" "ENO1" "FRYL"
"SEC31B" "KIFAP3" "NT5C2" "GPC4" "ITGA8" "PPP2R5C" "RBFOX1" "ITM2A"
"NRD1" "VDAC3" "CBFA2T2" "FKBP7" "SAR1A" "DUSP13" "PGR" "EPB41L3" "OXCT1"
"SLC27A5" "WBP11" "NCOA1" "MAPRE3" "MGST2" "DIMT1" "RBM22" "TMED2"
"HUWE1" "NLK" "UIMC1" "GNAS" "COQ9" "NSFL1C" "TASP1" "MRPS33" "NDUFB2"
"TXNL1" "MYL6" "HDAC6" "DHPS" "CREM" "PSMD8" "CIRBP" "HNRNPM" "SF3A1"
"POLR2F" "HMGXB4" "CHKB" "ZMAT5" "RBM23" "VTI1B" "TIMM9" "GSTZ1"
"RPS6KA5" "PSMB5" "PFDN4" "PSMA7" "NDUFAF5" "ATP1B4" "ALG13" "SUV39H1"
"SCML2" "PGK1" "KLF5" "TSC22D1" "MGRN1" "SLC7A6" "CMC2" "CPPED1" "MYEF2"
"CPQ" "LEPROTL1" "PPP2CB" "KLHDC4" "POP4" "AKT2" "RABAC1" "CARD8" "PON2"
"SSBP1" "BUD31" "MEST" "CHCHD3" "COA1" "BLVRA" "PLGRKT" "BAG1" "EXOSC3"
"RASSF4" "KAZALD1" "PITRM1" "EBF3" "LGI1" "MTMR4" "CDK5RAP3" "ENO3"
"ICAM2" "EZH1" "MRPL27" "HDAC5" "DUSP3" "DCUN1D4" "NDUFC1" "ZBTB16"
"COMMD9" "ATP5B" "ELK3" "ALDH2" "STX2" "GPR133" "MRPL51" "GAPDH" "TPI1"
"TMEM14C" "GCNT2" "NCOA7" "FANCE" "E2F3" "ACOT13" "COX7A2" "ENPP5"
"PCDHB2" "TMCO6" "TTC1" "POLR3G" "BNIP1" "TIMMDC1" "BCL6" "FAM162A"
"PRKAR2A" "TUSC2" "SSR3" "MOB1A" "NCL" "MPV17" "HSPE1" "ZNF142" "ID2"
"PNO1" "TMEM59" "LAMTOR2" "LEPR" "CTH" "TMEM9" "MRPS15" "SDHB" "FAAH"
"DPH5" "ANKRD13C" "VAMP8" "NDUFB3" "GDA" "MAPKAP1" "YPEL5" "RCL1" "GRIA2"
"PCMT1" "KIAA1217" "PAIP2" "ARL1" "SOCS2" "ECHDC2" "A1BG" "ZNF211"
"GTDC1" "CCDC18" "HNRNPA2B1" "FAM126A" "CLTA" "CISD1" "CDKN2C" "RASSF8"
"ATP7B" "ITIH5" "SMUG1" "NDUFAF4" "PLA2G12A" "PFKFB2" "ATP5E" "STAMBP"
"SNRNP27" "NQO2" "EMC3" "TMTC4" "SNRPD2" "ID1" "KDM5C" "ST3GAL3" "EMC1"
"UQCR11" "RNF6" "SHFM1" "STEAP4" "RBM48" "TUBGCP6" "EMC4" "RABL5" "MTX2"
"TXNDC17" "DAD1" "ECSIT" "CDC16" "RPL36" "MRPL34" "LSM4" "CYP2E1"
"ZNF337" "PRRC2B" "COX4I1" "NFATC1" "PDLIM4" "PSME3" "NDUFA2" "RAF1"
"ENOSF1" "MRPL35" "SERPINF1" "GRSF1" "WBP2" "PRMT7" "POMP" "MYH8" "BEX2"
"ACTR3B" "ARL8B" "EMC7" "LAMTOR5" "KCTD1" "DDB2" "PUM1" "NREP" "CTSL"
"FAM189A2" "MDFIC" "CAPRIN1" "CD63" "TSPAN31" "MRPL44" "NDUFB5" "TANK"
"VPS45" "PSMB7" "UBAP2" "GRHPR" "BPHL" "UQCC2" "NUMA1" "DCUN1D5" "UNC13C"
"TUBGCP4" "SLC28A2" "CYP1B1" "COX17" "PARP16" "HERC5" "PPA2" "LGR5"
"NEDD1" "SLAIN1" "GRTP1" "TMX1" "SERF2" "SRP14" "WDR61" "TPM1" "SEC11A"
"PMM2" "MYLK3" "CLTC" "GAREM" "GREB1L" "RNF165" "TXNL4A" "NFIC" "PSMB6"
"PSMA5" "CELSR2" "TIPRL" "UFC1" "SETDB1" "ADAMTSL4" "JTB" "HAX1" "ACP1"
"NVL" "DEGS1" "PSEN2" "PDIA6" "SFXN5" "ZNF385B" "UBR3" "GULP1" "ATG3"
"SRPRB" "TMEM108" "SLIT2" "DDIT4L" "PAM" "TSLP" "ATG12" "BOD1" "MYLK4"
"DYNLT1" "PSPH" "ATXN7L1" "ZMYM3" "ARHGAP36" "HMBOX1" "PXDNL" "GOLGA7"
"POLR2K" "EIF3H" "NDUFB9" "TATDN1" "FAM171A1" "FAM188A" "GSTO1" "EIF3M"
"ARFGAP2" "DAK" "CPSF7" "CABLES2" "SAP18" "HNMT" "TIMM8B" "PTS" "NDUFC2"
"BICD1" "ZNF385D" "GEMIN6" "ATP5A1" "CCDC50" "UTRN" "ZNF117" "RASSF3"
"HNRNPU" "TRIP12" "LGI4" "MSI2" "UCHL1" "ATP5G3" "TCEB1" "PSMA8" "DPH3"
"ACSS1" "TMEM55A" "GOLGA7B" "CNOT8" "NUP205" "KCNMA1" "SCAF4" "MALSU1"
"PDE6D" "MUM1L1" "AFAP1L1" "WDR19" "MRPL17" "CNNM4" "ZFAND2B" "AGPAT6"
"SNF8" "CBR1" "TPPP3" "CCDC28B" "SSU72" "PCNT" "PCYT1A" "COX7A1" "BCL6B"
"POLR3K" "NXF1" "OLFML2B" "MRPL55" "RFTN2" "VSNL1" "RPRD2" "BOLA3"
"MRPS18C" "ARPC2" "SUCLG1" "PPM1L" "ADAMTS9" "ELP6" "SMIM12" "SFMBT1"
"RAD54L2" "HPGD" "ARFIP1" "UQCRQ" "HCN1" "IQUB" "SUN1" "DCAF13" "NDUFB6"
"CFL2" "KLHDC2" "TRUB1" "ZFYVE1" "PSMC3" "DPCD" "ALKBH3" "CCT2" "ZNF202"
"USP54" "NDST2" "SEC11C" "CENPV" "HSP90B1" "AP1G1" "PPIB" "FAM96A"
"SMAD3" "PDIA3" "FBXO22" "ATP5L" "GPX4" "ATP5H" "POLR2G" "COPS6" "RAB4A"
"DNAJC7" "COA6" "MMADHC" "MPLKIP" "HEXIM2" "COL3A1" "CNNM3" "USP39"
"RNF181" "LRRC28" "PPIC" "STXBP6" "MFF" "ATP5I" "PARM1" "NSMCE1" "EFNA1"
"CRADD" "SIN3A" "CNBP" "ZNF32" "TOR1AIP2" "BRD3" "SF3B5" "STX8" "UBB"
"DNAJC18" "NUDCD2" "GPR27" "KBTBD2" "TRIAP1" "MTSS1" "ZNF160" "FEZ2"
"FAM86JP" "RBKS" "EXOSC1" "PDE7B" "MRPL36" "BPTF" "ZNF540" "EXOSC10"
"FRMD3" "TP53RK" "SYNPO2" "MYEOV2" "MRPL52" "TMEM134" "BNC2" "KDM2A"
"RHOD" "COMMD1" "GLRX" "DMRT2" "FAM86B3P" "MINOS1" "UQCRH" "PHC3" "USMG5"
"HOXB2" "NRROS" "MSRB3" "SNAPC5" "MRPL11" "IL20RB" "AKIRIN1" "TMEM167A"
"NDUFA11" "CADM2" "LSM1" "TMEM9B" "SCUBE2" "UCP3" "PAAF1" "MRPL48" "RTTN"
"KCMF1" "RMDN1" "IRX5" "MAMSTR" "POLE" "FAM210A" "ATOX1" "KIAA0195"
"MLF1" "GRAMD1C" "BOLA1" "TMEM11" "RIIAD1" "SEPW1" "MAGED1" "FCER1A"
"PSMG4" "SSR4" "TRAPPC5" "PLAG1" "LSM10" "COA4" "NEUROG1" "MRPS11"
"MRPS16" "FAM104B" "SATB1" "NDN" "CNOT10" "ZNF662" "CEP57L1" "SFXN4"
"FAM162B" "DENND5A" "UBE2F" "PCDH9" "MROH7" "NDUFA12" "APOO" "PTRHD1"
"RPS27L" "ADSSL1" "UBALD2" "ROR1" "NR2F2" "PSMD13" "ANKFY1" "ZNF529"
"POLR1D" "TOR3A" "PPP1CC" "RGS9BP" "KRT10" "GPATCH8" "RPS19BP1" "CMC1"
"MAGI2" "EXD3" "MORN2" "COL4A5" "COMMD6" "S100A16" "RNFT1" "HN1"
"BLOC1S2" "LCOR" "XPNPEP3" "ACN9" "TECPR2" "TOMM7" "ADA" "NOP9" "CASP4"
"METTL9" "ZNF398" "ZNF682" "MRPL21" "HTT" "COL4A6" "PHF2" "FAM118B"
"FAM49A" "MRPL42" "UBL5" "CCDC69" "NCOA6" "MT-ND5" "ZNF521" "MT-ND3"
"SELT" "OSTC" "TSEN15" "MT-ND4" "DCLRE1A" "CCDC167" "DMD" "SNORA63"
"TATDN3" "FAM229B" "INPP5B" "COL15A1" "ZBTB48" "ZNF783" "FLJ00104"
"SARNP" "DNAJC19" "SNORA12" "U3" "U3" "SUPT4H1" "ANKRD39" "NDUFS3"
"SLC23A3" "ARL16" "ZSWIM7" "COL28A1" "SLC35E2" "TENM3" "FAM19A5" "TPI1P1"
"OST4" "EEF1DP3" "HSBP1" "MCTS1" "DICER1-AS1" "CDKN2AIPNL" "FAM200B"
"GOLGA2P5" "MRPL33" "NME1-NME2" "UBE2V1" "SMIM20" "APOPT1" "CUX1"
"UBE2F-SCLY" "GOLGA7B" "NCBP2-AS2"))
(use-modules (annotation biogrid))
(use-modules (annotation gene-go))
(use-modules (annotation gene-pathway))
(use-modules (annotation functions))
(use-modules (annotation util))
; (load "inst.scm")
; (define smpdb-ctr (accum-time "smpdb"))
; (define reactome-ctr (accum-time "reactome"))
; (define find-pathway-genes-ctr (accum-time "find-pathway-genes"))
; (define add-pathway-genes-ctr (accum-time "add-pathway-genes"))
; (define find-go-term-ctr (accum-time "find-go-term"))
; (define find-memberln-ctr (accum-time "find-memberln"))
; (define add-go-info-ctr (accum-time "add-go-info"))
; (define find-parent-ctr (accum-time "find-parent"))
; (load "report.scm")
(define (old-report)
; top-level stuff
(biogrid-ctr #:report? #t)
(biowrite-ctr #:report? #t)
(gene-go-anno-ctr #:report? #t)
(gene-go-write-ctr #:report? #t)
(gene-path-anno-ctr #:report? #t)
(gene-path-write-ctr #:report? #t)
(smpdb-ctr #:report? #t)
(reactome-ctr #:report? #t)
; pathway stuff
(find-pathway-genes-ctr #:report? #t)
(add-pathway-genes-ctr #:report? #t)
(find-pathway-member-ctr #:report? #t)
(pathway-gene-interactors-ctr #:report? #t)
(generate-interactors-ctr #:report? #t)
(pathway-hierarchy-ctr #:report? #t)
(check-pathway-ctr #:report? #t)
(find-protein-ctr #:report? #t)
(find-mol-ctr #:report? #t)
(find-go-term-ctr #:report? #t)
; grid stuff
(match-gene-interactors-ctr #:report? #t)
(find-output-interactors-ctr #:report? #t)
(generate-result-ctr #:report? #t)
(build-interaction-ctr #:report? #t)
(find-protein-form-ctr #:report? #t)
; common to grid and path
(find-name-ctr #:report? #t)
(find-pubmed-id-ctr #:report? #t)
; ???
(find-memberln-ctr #:report? #t)
(add-go-info-ctr #:report? #t)
(find-parent-ctr #:report? #t)
(locate-node-ctr #:report? #t)
(add-loc-ctr #:report? #t)
)
(define (do-anno nparents)
(define start (current-time))
(define anno (gene-go-annotation gene-list
"my-go-anno-results"
#:parents nparents))
(define elapse (- (current-time) start))
(format #t "GO Annotation took ~A seconds\n" elapse)
*unspecified*
)
(define (do-path nparents)
(define start (current-time))
(define anno (gene-pathway-annotation gene-list
"path-results"
#:pathway "reactome smpdb"
; XXX if the pathway is set, then it crashes, see issue #91
; #:namespace "biological_process molecular_function cellular_component"
#:parents nparents))
(define elapse (- (current-time) start))
(format #t "Path Annotation (p=~A) took ~A seconds\n" nparents elapse)
*unspecified*
)
(define (do-path-ns nparents)
(define start (current-time))
(define anno (gene-pathway-annotation gene-list
"path-with-ns-results"
#:pathway "reactome smpdb"
#:namespace "biological_process molecular_function cellular_component"
#:parents nparents))
(define elapse (- (current-time) start))
(format #t "Path Annotation (p=~A) took ~A seconds\n" nparents elapse)
*unspecified*
)
(define (do-one-path gename)
(define start (current-time))
(define anno (gene-pathway-annotation (list gename)
"do-one-path-results"
#:pathway "reactome smpdb"
; XXX if the pathway is set, then it crashes, see issue #91
; #:namespace "biological_process molecular_function cellular_component"
#:parents 0))
(define elapse (- (current-time) start))
(format #t "Path Annotation for ~A took ~A seconds; got ~A annotations\n"
gename elapse (cog-arity anno))
*unspecified*
)
(define (do-grid-protein nparents)
(define start (current-time))
(define anno (biogrid-interaction-annotation gene-list
"my-biogrid-results"
#:namespace "biological_process molecular_function cellular_component"
#:interaction "Proteins"
; #:interaction "Genes"
#:parents nparents))
(define elapse (- (current-time) start))
(format #t "Grid Annotation took ~A seconds\n" elapse)
*unspecified*
)
(define (do-grid-gene nparents)
(define start (current-time))
(define anno (biogrid-interaction-annotation gene-list
"my-biogrid-results"
#:namespace "biological_process molecular_function cellular_component"
#:interaction "Genes"
#:parents nparents))
(define elapse (- (current-time) start))
(format #t "Grid Annotation took ~A seconds\n" elapse)
*unspecified*
)
; (start-cogserver "path.conf")
; (start-cogserver "grid.conf")