From 6f18e3caa922aa8e9ed423584b615a16561257e3 Mon Sep 17 00:00:00 2001 From: Kevinzjy Date: Fri, 8 Sep 2023 14:05:26 +0800 Subject: [PATCH] fixed bug in CIRI-full Pipeline --- bin/CIRI_Full2$1.class | Bin 1455 -> 1455 bytes bin/CIRI_Full2$2.class | Bin 1455 -> 1455 bytes bin/CIRI_Full2$3.class | Bin 1452 -> 1452 bytes bin/CIRI_Full2$4.class | Bin 1452 -> 1452 bytes bin/CIRI_Full2.class | Bin 16234 -> 16602 bytes src/CIRI_Full2.java | 30 ++++++++++++++++++++++-------- 6 files changed, 22 insertions(+), 8 deletions(-) diff --git a/bin/CIRI_Full2$1.class b/bin/CIRI_Full2$1.class index 222b630a75fd77d6d5aec468e5a54a56135804f5..83bf4105ba38520394662178dc8b5d8e8263a433 100644 GIT binary patch delta 75 zcmV-R0JQ(F3$F{Xb_4;mlXnEIIko^30Ji`!0Js1%0J;D@0KNb~0J{J}0KEW50KWiH h0KfoL0Kx!h0LB1o0K))n0L1`u0LK7#0LYVF1yWDf77YLZ delta 75 zcmV-R0JQ(F3$F{Xb_4;YlXnEIIj8^=0I2{m0IC2p0IUE#0I&c+0IdK*0IvW?0I>j3 h0I~p70JH#T0Js2a0JQ*Z0Ji{g0J#8n0J@W11yV5^6)gY& diff --git a/bin/CIRI_Full2$2.class b/bin/CIRI_Full2$2.class index 0daf67c3e5b17d6fd04bee2600cd8dbca695cb74..a694e71d1b2f38a3c206ba80c258c304385ebd14 100644 GIT binary patch delta 75 zcmV-R0JQ(F3$F{Xb_4;;lXnEIInDqR0M7t10MGz40MY0K@=20LTD90L1`80LK7F0LcJR h0LlPV0L%br0MGzy0L=hx0M7t&0MP(<0Me6P1yW_p7OemP diff --git a/bin/CIRI_Full2$3.class b/bin/CIRI_Full2$3.class index d5376ed69c72ec9e125cd086727d6eaf755b7c98..e2e5cd3f097078e505c24538d9e41beeacd1f696 100644 GIT binary patch delta 75 zcmV-R0JQ(C3#<#Ua|8kHlXL{FIqv`y0Pp}Y0Pz4b0P_Gn0QUeu0Q3Mt0QLY!0Qdk= h0Qmq^0Q&%F0RI4M0Q>-L0R8}S0RRAZ0RfX*1yZ}O7mxq| delta 75 zcmV-R0JQ(C3#<#Ua|8k3lXL{FIpF{k0O9~K0OJ5N0ObHZ0O35epL|>*NxaHCBx548n{Y42F!H491My47QB?3=WJu3{H%E4DO5q41tV- g3?Yod3>l2#4B3n#47rSA3`L9*4CRcHlcQLJ0M(TX9smFU delta 77 zcmV~$K?*=X0EW@;X9%-&64@yw8*8$10wo(M2XT#AxSbGr&sk@W#dw_iYFxoZ%1y>Y f&Pyp#@lgvJd9?EB6)-AhQpl``MG2eiJ_Owl{)-Se diff --git a/bin/CIRI_Full2.class b/bin/CIRI_Full2.class index 99901fc55d67b1ab6d67d4844dab3715de40c1bc..e5d549c40b6b49ea0513b499fb99f748c60cf9c3 100644 GIT binary patch delta 1422 zcmYj~d2mlx6vyxPM3T4N_wIZ5MMQ)WOF}7Pmk?2c1d+t3rj}GGO#~IPX#FO(3W^bH zsJ&vBHfabQLz|A;sx7J$YZ3d>3MvyFjWIg?>zw&~&S%b@>E$^n%m~(kf|Ud9IadX+LiVux65$G?Qt$(LdOM*%fxm9`^+i!+<0vokDJ+`R zEE=lg1ij4IwY*~?8HBLBb0NcPmoQPndKIt}HDUi(;W{?DM#cCimN3iDEn$6}!8P0K z!(lI7{r}u691vK-dI!9Ikd?PHbh1|gORbqPMQDD~@M?*$rhGyQ!RKx0EaFwo2@dYOuSi%kHUx?7rI4 z1245TYN;LJt@cHr8jE^rJc87fsIRU=19darP>-UKdJ4hn88lX_&_v5XQ*An$X)_U` z?Lw$lh!)yDw9*cswRRY7w4-RNokEy)4(+syXs=bEgLW4kwMul-s?b>ny67sp>Ndi4 zPXHqHhUlh;qPyM(k$PwJ(7Pi_k48^D4$=B3^wB4xubz&6dM0A@g^1OcpufHX1N3~v z=>-_1A4I%<5()ZU4ACp`j{X$y8eT{;>f${k6vK>YBpUr9D2*qXb7Osen_(MeCs_2DlA_mt*0xCojZirF1DN=AtOvY{T3GRzUcpyA$ z@KCJBpJFrq5?k>|>_nv~#A8v6Ct@$2iZc8y&f}T5gDP9WKeixd2NCRcM0QW|vWJtm zJ&hE5CaLxuGVDC!_I5JuQnKuGB<;)O+E>Znen@p39|~~%sIC)6^_{NN(CI^sJkAIT zcG9S^vw%XJrPSQnKrNho^rmx!S~?Zf#<@>n64XxCqK;CfPO=_#mci6THl=XciXvn? z>L$afyNsep*^he2IC@(qP;Z$;(K4C($Z^zHPN04=gJR^T6f0*_e>tB9$UGV-SCc1B zZlXbQ2gS=GN{|OAQI^qAd5VU~vy?1*18FMDO zi$c~66D&aTI>7vh9c5jFe+}!p)o%TN1w5+~B{e`2{s&kfF)EWip19ueUgVSQdB5K{ zxEn*45zBG6gl1?p%&K8y1G?3)q-XYZmkr4De*+GbL?|R6Wisu#|}H%S*@dk9g$>qUeZ{jG@M0nYxl5Fdx*uljMsD%uj>L!^*}7sdtkX9iUNHQ-qeTVEqx4D=!tk+ zpMXMr3f|FYz@^W@yZQnY=}YjQz5*ZU>#z=3%s(b@7PhS(hxX+Nc*!kdN*iAD;O zMhQQP5Cj*qKwi+CA}i5Xoje!ba9AgisLj(oTdzMmNLa<$`UO!Til^J;y%q4 zk11Pp(yLC1<~a?@ar#lNGl=Fp`_KaCK+1CtqkLyHEp#T(8|)5aG@d1QvYt$qSev)x ePKjCUb)0o~N5u7ax5xDKp4;ga?dcJF5dQ(ZoK~^` diff --git a/src/CIRI_Full2.java b/src/CIRI_Full2.java index bae2dfa..e1ddbd2 100644 --- a/src/CIRI_Full2.java +++ b/src/CIRI_Full2.java @@ -149,15 +149,29 @@ public static void main(String[] args) throws InterruptedException, IOException writeStream1.newLine(); writeStream1.write("bwa mem -T 19 -t "+t+" "+ref+" "+read1+" "+read2+" > "+workdir+"/sam/"+prefix+"_ciri.sam"); writeStream1.newLine(); - if(z.indexOf("-0")!=-1){ - writeStream1.write("perl "+cdir+ciri+" -I "+workdir+"/sam/"+prefix+"_ciri.sam -O "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -A "+anno+" -T "+t+" -0"); - } - else{ - writeStream1.write("perl "+cdir+ciri+" -I "+workdir+"/sam/"+prefix+"_ciri.sam -O "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -A "+anno+" -T "+t); - - } + + if (!anno.equals("")) { + if(z.indexOf("-0")!=-1){ + writeStream1.write("perl "+cdir+ciri+" -I "+workdir+"/sam/"+prefix+"_ciri.sam -O "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -A "+anno+" -T "+t+" -0"); + } + else { + writeStream1.write("perl "+cdir+ciri+" -I "+workdir+"/sam/"+prefix+"_ciri.sam -O "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -A "+anno+" -T "+t); + } + } else { + if(z.indexOf("-0")!=-1){ + writeStream1.write("perl "+cdir+ciri+" -I "+workdir+"/sam/"+prefix+"_ciri.sam -O "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -T "+t+" -0"); + } + else { + writeStream1.write("perl "+cdir+ciri+" -I "+workdir+"/sam/"+prefix+"_ciri.sam -O "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -T "+t); + } + } + writeStream1.newLine(); - writeStream1.write("perl "+cdir+as+" -S "+workdir+"/sam/"+prefix+"_ciri.sam -C "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -A "+anno+" -O "+workdir+"/CIRI-AS_output/"+prefix+" -D yes"); + if (!anno.equals("")) { + writeStream1.write("perl "+cdir+as+" -S "+workdir+"/sam/"+prefix+"_ciri.sam -C "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -A "+anno+" -O "+workdir+"/CIRI-AS_output/"+prefix+" -D yes"); + } else { + writeStream1.write("perl "+cdir+as+" -S "+workdir+"/sam/"+prefix+"_ciri.sam -C "+workdir+"/CIRI_output/"+prefix+".ciri -F "+ref+" -O "+workdir+"/CIRI-AS_output/"+prefix+" -D yes"); + } writeStream1.close(); String[] ciri_c={"sh",workdir+"/tmp1.sh"}; Process cirip= Runtime.getRuntime().exec(ciri_c);