From 92f5b1d4e6e77f6342a320db7014f12bba8da217 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Tue, 30 Mar 2021 13:27:35 +0300 Subject: [PATCH] On branch v0.5b Changes to be committed: new file: doc/README.results new file: end.sh new file: examples/negatome_mouse.tsv new file: examples/negatome_mouse_pairs.tsv new file: examples/raftsProteins.tsv new file: examples/separate/CTT new file: negatome_mouse_pairs.tsv new file: patches/extraVerbose.patch new file: proteins/TLR --- doc/README.results | 29 + end.sh | 149 ++ examples/negatome_mouse.tsv | 406 ++++++ examples/negatome_mouse_pairs.tsv | 1991 ++++++++++++++++++++++++++ examples/raftsProteins.tsv | 346 +++++ examples/separate/CTT | 5 + negatome_mouse_pairs.tsv | 2171 +++++++++++++++++++++++++++++ patches/extraVerbose.patch | 43 + proteins/TLR | 4 + 9 files changed, 5144 insertions(+) create mode 100644 doc/README.results create mode 100644 end.sh create mode 100644 examples/negatome_mouse.tsv create mode 100644 examples/negatome_mouse_pairs.tsv create mode 100644 examples/raftsProteins.tsv create mode 100644 examples/separate/CTT create mode 100644 negatome_mouse_pairs.tsv create mode 100644 patches/extraVerbose.patch create mode 100644 proteins/TLR diff --git a/doc/README.results b/doc/README.results new file mode 100644 index 0000000..341b2be --- /dev/null +++ b/doc/README.results @@ -0,0 +1,29 @@ +Name1: Protein 1 name +msa1: Protein 1 UniProt ID +Name2: Protein 2 name +msa2: Protein 2 Uniprot ID +colA: Position of residue "A" from Protein 1 in the MSA +realA: Position of residue "A" from Protein 1 in the non-aligned sequence of the reference organism +colB: Position of residue "B" from Protein 2 in the MSA +realB: Position of residue "B" from Protein 3 in the non-aligned sequence of the reference organism +seq1: Position and amino-acid of residue "A" from Protein 1 in the non-aligned, non-filtered by gblocks sequence of the reference organism +seq2: Position and amino-acid of residue "A" from Protein 1 in the non-aligned, non-filtered by gblocks sequence of the reference organism +meanA: meanA +meanB: meanB +corr: Co-evolutionary correlation (non corrected) +boot: Bootstrap value of the correlation +corrT: Correlation threshold for each pair of proteins +cCoev: Co-evolutionary correlation (corrected, normalized to threshold) +pvalA: Correlation p-value for A->B (non-corrected) +pvalB: Correlation p-value for B->A (non-corrected) +pMean: Mean correlation p-value (non-corrected) +pDiff: Difference between pvalA-pvalB (absolute value) +corr1: Correlation for A->B (non-corrected) +corr2: Correlation for B->A (non-corrected) +bonferroni: Bonferroni corrected pMean +GapA: MSA column gaps (-) for residue "A" +GapB: MSA column gaps (-) for residue "B" +GapAB: Mean value of GapA and GapB +DivA: Diversity within MSA column for residue "A" +DivB: Diversity within MSA column for residue "B" +DivAB: Mean value of DivA and DivB diff --git a/end.sh b/end.sh new file mode 100644 index 0000000..d4d4a45 --- /dev/null +++ b/end.sh @@ -0,0 +1,149 @@ +#!/bin/bash + +# Export all +set -a + +# What date and time is it? +DATESTAMP=$(date) + +# Current work dir +CWD=$(pwd) + +# Load settings first +. $CWD/settings.conf + +# Load functions +. $CWD/functions/databases.sh +. $CWD/functions/retrieval.sh +. $CWD/functions/blast.sh +. $CWD/functions/msa.sh +. $CWD/functions/trees.sh +. $CWD/functions/pairing.sh +. $CWD/functions/caps.sh +. $CWD/functions/results.sh +. $CWD/functions/network.sh +. $CWD/functions/check.sh + +EGAPS="0.8" # Gaps score cut +EPDIF="0.0011" + +ETSV="$TMP/$RESULTS/pairs-P${PVALUE}-B${BONFERRONI}.tsv" +EOUT="filtered-P${PVALUE}-pDiff${EPDIF}-Bonf${BONFERRONI}.tsv" +ENET="FILTERED-P${PVALUE}-pDiff${EPDIF}-Bonf${BONFERRONI}.xml" + +# Let user change work dir here as well +read -p "Change working dir or press ENTER to accept: " -e -i $TMP TMP +mkdir -p $TMP + +# Specify the input file +echo -e "\n\e[96mEnter the full path to the pairs-P${PVALUE}-B${BONFERRONI}.tsv file:\e[39m" +read -e -i $ETSV ETSV + +rm -rf $TMP/$RESULTS/pairs-P${PVALUE}-B${BONFERRONI} +mkdir -p $TMP/$RESULTS/pairs-P${PVALUE}-B${BONFERRONI} + +sed 1d "$ETSV" | while read -r Name1 msa1 Name2 msa2 colA realA colB realB seq1 seq2 flt1 flt2 meanA meanB corr boot corrT cCoev pvalA pvalB pMean pDiff corr1 corr2 bonferroni GapA GapB GapAB DivA DivB DivAB ; do + if [ "$flt1" = "#" ] && [ "$flt2" = "#" ]; then + echo "Pair from a good quality MSA" + if (( $(echo "$GapA > $EGAPS" |bc -l) && $(echo "$GapB > $EGAPS" |bc -l) && $(echo "$pDiff < $EPDIF" |bc -l) )); then + echo "$Name1 $msa1 $Name2 $msa2 $cCoev $pvalA $pvalB $pMean $bonferroni $boot" >> $TMP/$RESULTS/pairs-P${PVALUE}-B${BONFERRONI}/$msa1-$msa2.tsv + echo "Consider $Name1 $msa1 <-> $Name2 $msa2" + else + echo "Skipping $Name1 $msa1 <-> $Name2 $msa2" + fi + else + echo "pair from a bad quality MSA" + fi +done + +cd $TMP/$RESULTS/pairs-P${PVALUE}-B${BONFERRONI} + for pair in * ; do + namesIDs=$(head -n 1 $pair | awk '{print $1,$2,$3,$4}') + coevNumber=$(awk '{print $5}' $pair | datamash count 1) + + cCoevMAX=$(awk '{print $5}' $pair | datamash max 1) + cCoevMEAN=$(awk '{print $5}' $pair | datamash mean 1) + cCoevMIN=$(awk '{print $5}' $pair | datamash min 1) + cCoevSDEV=$(awk '{print $5}' $pair | datamash sstdev 1) + + bootMAX=$(awk '{print $10}' $pair | datamash max 1) + bootMEAN=$(awk '{print $10}' $pair | datamash mean 1) + bootMIN=$(awk '{print $10}' $pair | datamash min 1) + bootSDEV=$(awk '{print $10}' $pair | datamash sstdev 1) + + pMeanMIN=$(awk '{print $8}' $pair | datamash min 1) + pMeanMEAN=$(awk '{print $8}' $pair | datamash mean 1) + pMeanMAX=$(awk '{print $8}' $pair | datamash max 1) + pMeanSDEV=$(awk '{print $8}' $pair | datamash sstdev 1) + + BonferroniMIN=$(awk '{print $9}' $pair | datamash min 1) + BonferroniMEAN=$(awk '{print $9}' $pair | datamash mean 1) + BonferroniMAX=$(awk '{print $8}' $pair | datamash max 1) + BonferroniSDEV=$(awk '{print $8}' $pair | datamash sstdev 1) + + echo "$namesIDs $coevNumber $cCoevMIN $cCoevMAX $cCoevMEAN $cCoevSDEV $bootMIN $bootMEAN $bootMAX $bootSDEV $pMeanMIN $pMeanMAX $pMeanMEAN $pMeanSDEV $BonferroniMIN $BonferroniMAX $BonferroniMEAN $BonferroniSDEV" >> $TMP/$RESULTS/$EOUT + echo "Processed $pair" +done + +sed -i "1i Name1 msa1 Name2 msa2 coevNumber cCoevMIN cCoevMAX cCoevMEAN cCoevSDEV bootMIN bootMEAN bootMAX bootSDEV pMeanMIN pMeanMAX pMeanMEAN pMeanSDEV BonferroniMIN BonferroniMAX BonferroniMEAN BonferroniSDEV" $TMP/$RESULTS/$EOUT + +# Prepare the XML header +cat << EOF >> $TMP/$RESULTS/$ENET + + + + + + Protein-Protein Interaction + N/A + N/A + $DATE + CAPS + http://www.cytoscape.org/ + Cytoscape-XGMML + + + + + + + + +EOF + +# Add nodes. +sed 1d $TMP/tsv/proteinsFound.tsv | while read -r idxml namexml attribute; do +echo -e "Adding node $idxml $namexml $attribute in $TMP/$RESULTS/$ENET" +cat << EOF >> $TMP/$RESULTS/$ENET + + + + + + +EOF +done + +# Add edges +sed 1d $TMP/$RESULTS/$EOUT | \ +while read -r Name1 msa1 Name2 msa2 coevNumber cCoevMIN cCoevMAX cCoevMEAN cCoevSDEV bootMIN bootMEAN bootMAX bootSDEV pMeanMIN pMeanMAX pMeanMEAN pMeanSDEV BonferroniMIN BonferroniMAX BonferroniMEAN BonferroniSDEV ; do +echo -e "Adding edge: $msa1-$msa2 in $TMP/$RESULTS/$ENET" +cat << EOF >> $TMP/$RESULTS/$ENET + + + + + + + + + + + + + + + +EOF +done +echo "" >> $TMP/$RESULTS/$ENET diff --git a/examples/negatome_mouse.tsv b/examples/negatome_mouse.tsv new file mode 100644 index 0000000..90af958 --- /dev/null +++ b/examples/negatome_mouse.tsv @@ -0,0 +1,406 @@ +Q64343 Abcg1 +Q7TMS5 Abcg2 +Q9DBM0 Abcg8 +P21836 Ache +Q9QZQ1 Afdn +A2ASQ1 Agrn +O08915 Aip +O08715 Akap1 +P31750 Akt1 +Q920R0 Als2 +Q8VHG2 Amot +Q02357 Ank1 +Q3UMR0 Ankrd27 +Q6DQH2 Apbb2 +P62331 Arf6 +Q6Y5D8 Arhgap10 +Q91YM2 Arhgap35 +P53762 Arnt +Q9WTL8 Arntl +Q6NXK8 Asic1 +O35625 Axin1 +O08734 Bak1 +Q07813 Bax +P21237 Bdnf +P25916 Bmi1 +P21274 Bmp2 +O55003 Bnip3 +Q9ESU6 Brd4 +Q7TSA3 Btla +O70355 Btnl2 +P98086 C1qa +P28651 Ca8 +P28652 Camk2b +Q8VHK1 Caskin2 +Q08024 Cbfb +P30658 Cbx2 +Q6PDY0 Ccdc85b +Q5SNZ0 Ccdc88a +P10855 Ccl3 +P14097 Ccl4 +P30882 Ccl5 +Q9QWV9 Ccnt1 +P51680 Ccr4 +P31041 Cd28 +P27512 Cd40 +P27548 Cd40lg +P60766 Cdc42 +P09803 Cdh1 +Q03147 Cdk7 +P46414 Cdkn1b +P53566 Cebpa +P28033 Cebpb +Q00322 Cebpd +Q03059 Chat +O08785 Clock +Q9JJZ9 Cngb3 +Q01147 Creb1 +P45481 Crebbp +P27699 Crem +P01587 Csf2 +P26955 Csf2rb +P50462 Csrp3 +P56546 Ctbp2 +P09793 Ctla4 +Q02248 Ctnnb1 +Q9WTX6 Cul1 +P98078 Dab2 +P31786 Dbi +Q8VHZ5 Ddit4l +Q62108 Dlg4 +Q09163 Dlk1 +P97465 Dok1 +Q99N11 Dusp22 +P51141 Dvl1 +Q61501 E2f1 +Q8R0K9 E2f4 +Q61502 E2f5 +Q61508 Ecm1 +P57776 Eef1d +Q8BPB5 Efemp1 +Q9WVJ9 Efemp2 +P01132 Egf +Q01279 Egfr +B2RWS6 Ep300 +Q8BGS1 Epb41l5 +Q03137 Epha4 +P07321 Epo +P14753 Epor +P25446 Fas +P41047 Faslg +Q08879 Fbln1 +P37889 Fbln2 +Q9WVH9 Fbln5 +P26151 Fcgr1 +Q61559 Fcgrt +P15655 Fgf2 +P54130 Fgf9 +P16092 Fgfr1 +P21803 Fgfr2 +Q03142 Fgfr4 +O70433 Fhl2 +P35917 Flt4 +P11276 Fn1 +P70339 Frat1 +Q8C180 Frs2 +Q61584 Fxr1 +Q9WVR4 Fxr2 +Q9Z1S8 Gab2 +P17679 Gata1 +P48540 Gdnf +P03995 Gfap +Q9Z0G0 Gipc1 +Q9JMB0 Gkap1 +P27601 Gna13 +P08752 Gnai2 +Q6R0H7 Gnas +P62880 Gnb2 +P63213 Gng2 +O89100 Grap2 +P23818 Gria1 +Q9WV60 Gsk3b +Q8R4I4 Gtf2a1l +O88895 Hdac3 +Q9Z2V6 Hdac5 +Q8C2B3 Hdac7 +Q6I6G8 Hecw2 +Q62424 Hoxa13 +P70217 Hoxd13 +O08983 Hps1 +Q99KG7 Hps4 +P38532 Hsf1 +Q05793 Hspg2 +Q9WVS0 Icos +Q61635 Ifi47 +P05017 Igf1 +Q9QZ85 Iigp1 +P01582 Il1a +Q61730 Il1rap +P04351 Il2 +P01586 Il3 +P04401 Il5 +P21183 Il5ra +P15247 Il9 +P15208 Insr +Q8K4N8 Irak1 +P70671 Irf3 +P70434 Irf7 +P52332 Jak1 +Q62120 Jak2 +P05627 Jun +Q02257 Jup +P23299 Kcne1 +Q9WTW2 Kcne3 +P35918 Kdr +Q60749 Khdrbs1 +P33175 Kif5a +Q61768 Kif5b +P28738 Kif5c +P70188 Kifap3 +P05532 Kit +O08584 Klf6 +Q6TDP3 Klhl17 +P00756 Klk1b3 +P00757 Klk1b4 +Q61097 Ksr1 +P11627 L1cam +P63006 Lhx1 +P09056 Lif +Q91XD2 Lims2 +Q8C129 Lnpep +Q8BFW7 Lpp +Q924X6 Lrp8 +P09225 Lta +P41155 Ltb +P20917 Mag +Q9ESN9 Mapk8ip3 +Q6PER3 Mapre3 +Q03141 Mark3 +P28574 Max +P97287 Mcl1 +P25206 Mcm3 +P49717 Mcm4 +Q61881 Mcm7 +P23804 Mdm2 +Q924H2 Med15 +Q80YQ2 Med23 +Q9CQA5 Med4 +Q9CZB6 Med7 +Q9D7W5 Med8 +Q60954 Meis1 +P55002 Mfap2 +Q9QZJ6 Mfap5 +A2AM29 Mllt3 +Q91V27 Mlph +Q3UPW8 Mlxip +Q61391 Mme +P50538 Mxd1 +Q80US8 Mxd3 +Q60948 Mxd4 +P50540 Mxi1 +P06876 Myb +Q7TPV4 Mybbp1a +P01108 Myc +P10166 Mycl +P03966 Mycn +Q99104 Myo5a +Q9JK37 Myoz1 +P13595 Ncam1 +Q60974 Ncor1 +Q9WU42 Ncor2 +Q9CZA6 Nde1 +P08553 Nefm +O35657 Neu1 +Q62414 Neurod2 +P46662 Nf2 +P01139 Ngf +P42586 Nkx2-2 +P97503 Nkx3-2 +Q99MA9 Nkx6-1 +Q01705 Notch1 +O35516 Notch2 +Q61982 Notch3 +P31695 Notch4 +Q99J85 Nptxr +Q62227 Nr0b2 +Q505F1 Nr2c1 +P06537 Nr3c1 +Q8CJ26 Nradd +Q8CBD1 Nrip1 +Q9JHR9 Nrip2 +Q8R4G0 Ntng1 +Q9QXX8 Nufip1 +Q61146 Ocln +Q9EQW6 Olig2 +Q63912 Omg +Q61206 Pafah1b2 +Q61205 Pafah1b3 +Q8CIN4 Pak2 +P11103 Parp1 +Q2EMV9 Parp14 +Q71VB4 Pbx1 +O35984 Pbx2 +O88689 Pcdha4 +P17918 Pcna +P63239 Pcsk1 +Q02242 Pdcd1 +P26450 Pik3r1 +Q66T02 Plekhg5 +Q8CGN5 Plin1 +Q07832 Plk1 +Q60953 Pml +Q62009 Postn +P35396 Ppard +P37238 Pparg +P63330 Ppp2ca +Q76MZ3 Ppp2r1a +Q99K43 Prc1 +Q5M9N9 Prdx2 +P05132 Prkaca +P31324 Prkar2b +P16054 Prkce +P0C605 Prkg1 +Q61410 Prkg2 +Q9JIF0 Prmt1 +P05143 Prp2 +P15331 Prph +P15499 Prph2 +P41593 Pth1r +Q9QVP9 Ptk2b +P29351 Ptpn6 +Q62132 Ptprr +Q8K094 Pvr +P61027 Rab10 +P62492 Rab11a +P35292 Rab17 +P35293 Rab18 +P62821 Rab1A +P35295 Rab20 +P35285 Rab22a +P35288 Rab23 +Q9WTL2 Rab25 +Q9ERI2 Rab27a +Q99KL7 Rab28 +P53994 Rab2a +Q64008 Rab34 +Q9JKM7 Rab37 +P63011 Rab3a +P56371 Rab4a +Q9CQD1 Rab5a +P35279 Rab6a +P51150 Rab7a +P55258 Rab8a +Q9R0M6 Rab9a +O35551 Rabep1 +P63001 Rac1 +Q9WTJ5 Ramp1 +Q99JI6 Rap1b +Q922H7 Rasl11b +P13405 Rb1 +Q60972 Rbbp4 +Q64701 Rbl1 +O08674 Rbpjl +Q8BP92 Rcn2 +P15307 Rel +Q04207 Rela +Q04863 Relb +Q60841 Reln +P97428 Rgs16 +Q78NN4 Rgs19 +O08849 Rgs2 +P61588 Rnd3 +Q9D0C1 Rnf115 +P70336 Rock2 +P47708 Rph3a +P18653 Rps6ka1 +Q8K0T0 Rtn1 +O70622 Rtn2 +Q9ES97 Rtn3 +Q99P72 Rtn4 +Q99PI8 Rtn4r +Q8K0S5 Rtn4rl1 +Q7M6Z0 Rtn4rl2 +P43407 Sdc2 +O35988 Sdc4 +P63300 Selenow +P42208 Septin2 +O55131 Septin7 +O88974 Setdb1 +P97797 Sirpa +P53986 Slc16a1 +P13808 Slc4a2 +Q62432 Smad2 +Q8BUN5 Smad3 +P97471 Smad4 +P97454 Smad5 +O35182 Smad6 +O35253 Smad7 +O35717 Socs2 +O35718 Socs3 +Q62417 Sorbs1 +O89090 Sp1 +Q58A65 Spag9 +Q9JM90 Stap1 +P42225 Stat1 +Q00262 Stx2 +Q64704 Stx3 +P70452 Stx4 +Q8K1E0 Stx5 +O08599 Stxbp1 +Q548T0 Stxbp2 +Q60770 Stxbp3 +Q9D666 Sun1 +Q99N80 Sytl1 +Q99N50 Sytl2 +Q99N48 Sytl3 +Q549X6 Sytl4 +Q9R0Q1 Sytl4 +Q80T23 Sytl5 +Q8CF89 Tab1 +Q8R0L9 Tada3 +P70323 Tbx1 +P70371 Terf1 +Q64092 Tfe3 +P04202 Tgfb1 +Q62219 Tgfb1i1 +Q64729 Tgfbr1 +Q62312 Tgfbr2 +P21981 Tgm2 +P39447 Tjp1 +P26039 Tln1 +B9EKI3 Tmf1 +Q9D8D0 Tnfrsf13c +P50592 Tnfsf10 +P43488 Tnfsf4 +P32972 Tnfsf8 +P41274 Tnfsf9 +Q6PFX9 Tnks +Q3UES3 Tnks2 +O88346 Tnnt1 +P02340 Tp53 +P39429 Traf2 +P70196 Traf6 +O55055 Trdmt1 +Q9ERP3 Trim54 +Q9QUQ5 Trpc4 +Q9EP53 Tsc1 +Q61037 Tsc2 +P62500 Tsc22d1 +P25976 Ubtf +Q8CGY6 Unc45b +Q8K1S4 Unc5a +Q8K1S3 Unc5b +O08747 Unc5c +Q00731 Vegfa +P97946 Vegfd +Q8BH43 Wasf2 +P22561 Wt1 +O70373 Xirp1 +P62960 Ybx1 +P62259 Ywhae +P68254 Ywhaq +P63101 Ywhaz +Q80X44 Zbtb24 +Q8BN78 Zbtb33 +P17141 Zfp37 +Q62523 Zyx diff --git a/examples/negatome_mouse_pairs.tsv b/examples/negatome_mouse_pairs.tsv new file mode 100644 index 0000000..1a6c806 --- /dev/null +++ b/examples/negatome_mouse_pairs.tsv @@ -0,0 +1,1991 @@ +Q6ZNK6 Q9Y4K3 +Q9NR31 Q15797 +P11627 P53986 +P33176 Q96EK5 +Q9NPY3 P02745 +P03211 Q15796 +Q9SYQ8 O80809 +Q99576 O43524 +P55196 Q9NYB0 +Q7L7X3 O60566 +Q9BZM4 P16757 +Q29983 P16757 +Q8TD07 P16757 +Q61508 P36888 +Q9SYQ8 O80809 +O80809 Q9SYQ8 +P11799-3 P62149 +Q09472 P16070 +P54130 P16092 +P54130 Q03142 +O12161 P08047 +P02769 P04840 +P41593 Q9WTJ5 +Q6ZP65 Q6QLM7 +P11655 P48415 +P04003 P25942 +B3VK31 Q95JH1 +Q8IUD6 Q7Z434 +Q8IUD6 Q9BYX4 +O60423 Q3MIR4 +O60423 Q3MIR4 +Q8TF62 Q3MIR4 +Q9Y2Q0 Q3MIR4 +Q9NTI2 Q3MIR4 +Q16512 Q15418 +Q16513 Q15418 +Q16513 P51812 +Q16512 P51812 +P38431 P32481 +Q99575 Q96P20 +Q7JWH5 Q8IP45 +Q7JWH5 Q24311 +O00482 Q96EB6 +P52603 P08956 +F6IB71 P08956 +P52603 P08957 +F6IB71 P08957 +Q8QHK8 Q7ZX24 +O15360 Q00597 +P35872 Q5SJE9 +P10999 Q91783 +P35968 P17948 +Q5M9N9 P60484 +Q920R0 P00441 +P42212 P08238 +Q91XD2 Q15404 +Q9GZX6 Q13651 +Q14526 P51531 +O15151-4 P04637 +Q04863 P15307 +Q04863 Q04207 +Q13586 Q13507 +Q13586 Q9Y210 +O95999 Q13489 +Q86Y07 P51452 +Q86Y07-2 P49116 +Q86Y07-2 O14733 +P34741 P05230 +Q9QXX8 Q61584 +Q9QXX8 Q9WVR4 +Q61206 Q924X6 +Q61205 Q924X6 +P07203 P09917 +Q96UP3 Q96TL7 +Q8CBD1 Q9JIF0 +Q8CBD1 P68254 +Q8TEW0 P53667 +Q61559 P27512 +Q8AVZ3 Q91783 +P03073 P02340 +Q15750-2 P49116 +P35917 P35918 +P35917 Q00731 +O12161 Q9QWV9 +Q9ULX6 P13861 +Q9ULX6 O43823 +P80370 P46531 +Q7L3B6 P04049 +Q8IRY7 Q9W2K2 +Q9VEN9 Q9VVI2 +Q9VEN9 Q9VTZ0 +Q15797 Q9UM13 +Q13485 Q9UM13 +Q9WTW2 P23299 +P08047 P04608 +P08047 P04608 +Q56P03 Q16254 +Q9JM90 O60674 +Q9JM90 Q9QVP9 +Q62417-3 P18206 +Q9FEG2 P18064 +Q9FEG2 P18064 +Q39128 P18064 +O89100 Q9Z1S8 +P00918 P40879 +P35570 P62994 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+Q02248 Q8BN78 +P16520 Q6Y2X3 +P63239 Q58A65 +Q8NI70 Q9H213 +P18848 Q9H6S3 +Q16828 Q9H9D4 +P17036 Q92730 +P17679 Q924H2 +P19490 Q62936 +P83876 Q53GS9 +P42285 Q9NPD3 +Q06330 Q06587 +P25963 Q9H6S3 +P55854 Q16891 +P02765 P07384 +P20917 Q8K0S5 +Q15024 Q9Y2L1 +Q8TAU0 Q9NQX6 +O75175 P41240 +O75400 P55854 +P51693 Q8NI70 +P62879 Q8TBX8 +P42285 Q9NQT4 +P56589 Q9Y5Y5 +P62821 Q91V27 +Q16828 Q9NQX6 +Q9Y2I6 Q9Y6D9 diff --git a/patches/extraVerbose.patch b/patches/extraVerbose.patch new file mode 100644 index 0000000..be20d60 --- /dev/null +++ b/patches/extraVerbose.patch @@ -0,0 +1,43 @@ +diff -pruN orig/caps.cpp new/caps.cpp +--- orig/caps.cpp 2021-03-23 14:36:09.044861000 +0200 ++++ new/caps.cpp 2021-03-23 17:21:39.432706915 +0200 +@@ -15,8 +15,8 @@ + #include + #include + #include +- +- ++#include ++#include + + #include + #include +@@ -680,6 +680,10 @@ int main(int argc, char *argv[]){ + + threshold = totaltemp[value]; + totaltempnew = totaltemp; ++ ++ // This is shamelessly taken from: https://stackoverflow.com/a/39746650 ++ std::ofstream outFile("totaltemp.txt"); ++ for (const auto &e : totaltemp) outFile << e << "\n"; + + + /*=======================================================*/ +@@ -910,8 +914,6 @@ double getIndex(std::vector cons + } + + +- +- + /* + * === FUNCTION ====================================================================== + * Name: print_inter +@@ -926,7 +928,7 @@ int print_inter(vector& Correl1, + int cor=0, pairs=0; + + output << endl << endl; +- ++ + output << "Coevolving Pairs of amino acid sites\n"; + output << "================================================================================================================================\n"; + output << "Col1(real)\tCol2(real)\tDmean1\t\tDmean2\t\tCorrelation\tBootstrap value\tP-value1\tP-value2\tMean P-value\tCorrelation1\tCorrelation2\n\n"; diff --git a/proteins/TLR b/proteins/TLR new file mode 100644 index 0000000..cbe8cbd --- /dev/null +++ b/proteins/TLR @@ -0,0 +1,4 @@ +Q9EPQ1 Tlr1 TLR +Q9QUN7 Tlr2 TLR +Q9QUK6 Tlr4 TLR +Q9EPW9 Tlr6 TLR