From bfaf4a250a90fed8c2df71651bbdd0d519e2137e Mon Sep 17 00:00:00 2001 From: YaqiangCao Date: Mon, 18 Sep 2023 15:39:36 -0400 Subject: [PATCH] updates --- build/scripts-3.10/tracPre2.py | 4 +++- dist/cLoops2-0.0.5-py3.10.egg | Bin 386428 -> 386435 bytes scripts/tracPre2.py | 4 +++- 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/build/scripts-3.10/tracPre2.py b/build/scripts-3.10/tracPre2.py index 49346b06..c1a852d8 100755 --- a/build/scripts-3.10/tracPre2.py +++ b/build/scripts-3.10/tracPre2.py @@ -1,7 +1,7 @@ #!/home/caoy7/anaconda3/envs/astroBoy/bin/python #--coding:utf-8-- """ -tracPre.py +tracPre2.py Pre-processing code for Hi-Trac data, implemented with cLoops2, from fastq to bedpe files and qc report. 2020-02-27: finished and well tested. 2020-06-30: add linker filter, new stat, and changing mapping to end-to-end @@ -357,9 +357,11 @@ def main(): Batch converting from bam to bedpe. """ #prepare everything + global logger op = help() date = time.strftime(' %Y-%m-%d', time.localtime(time.time())) logger = getLogger(fn=op.output + "/" + date.strip() + "_" + os.path.basename(__file__) + ".log") + for t in ["bowtie2", "samtools", "bamToBed"]: if not isTool(t): logger.error("%s not exits! Please install through conda." % t) diff --git a/dist/cLoops2-0.0.5-py3.10.egg b/dist/cLoops2-0.0.5-py3.10.egg index 1dbbe0446b1a3329061de56736ece91bf9987dbb..1c4d0a9920411c0ddd3c41c486dbdae3a56b7315 100644 GIT binary patch delta 3790 zcmZ8jc|2768$L60j(v@cZR`wVsjOipi6Yr5OGIQVBx`P#+gR!niffERLZyW^TZOpx zB}rMs$iBtpT0+;>{hcHC-d}hAd7gRR_kG^)dC&VfpYP^dd~^$*!}1soZ_bo*+Z-)C+Ez0D>;V9DwX zPUULZgk7VF3Z^77bW%_3rd^7R(y=chXCxYv@nS7&$~1SXRj9gJ<;^9<`=JCM%|BWB z7s!jpM(UVHLua|EOGY{SXyq$9q}5x(a={ZGwnb(&w$nt1SYmxTtwD-`nTl(OGD`~# zStM>KG9DHr;0(eE57LG8S#u*tXzdFvQ+i9DAN>zcDX#h=*6e1_0H;wgPftwfm|$37|L;~LXzAw53kqXcFn$3r|ssuyjEWN z`p`sdWa`&2RtD+OA-BB*ZGLytr6O=8iTFq;GAoxmX-r&diby1~Iu&|5$LI=X@BP!j zy81&)6pm;Y(pt0kU}V4vV`mw`LxpiJ?xg)nV^RYVsr|)#&j%k$8PVH)7r7J6kJ07u z?aJ~V)D&Ymo7skjjp@@qhZg9w3!}TNMN;T^a$?A}sko_Ou9U+n4L<2hNgM`BE%L3b zUsZ-4>b@V`^d{~8WK$@nnG#*~hU5UjAs66c4u_(kUYh&z=0g_^C%%&m#+XIsVN%odzyDJkuOKR+PSifr*)kG-S* zAZ5pzS>jW=xN06Ge7IwJHO@S9K}ouKUt4)RwBFqib3lGEX%teG=Q~Nn;r< zzJB*6{msm}-GEI{OE7QO3^mQ0YWg6&deDtryK!6l&%g?Dm}Bg~ZdTdrxr!Yf;FDF| zwjc)h#3!I&V~J$s(XDPQGwL{SwY_u0%giyY{RS&gClX#=5mQsdA(`lzX{l~IH+bVQ zOica#_i`8Le&6!)IdQKQ1H)Cd!(T~U>f`S&`#L>OAIg91E#3Oc`9^KXXX+{IYh^|f z%t`K?VH(i^ci-D&dRj#kWrXKeLd+eVwrqcfp8TUwqE}7+3S0IJ+Z&sn^~vDjpn~Ms zxyBodvNNx4C{xX}wNqV3eV&eNN=AtJDJ8ixm~UI9^cvkd?{-dgzsv=LqxmU{7FJ)5 z%t2TC68K+lxm^tTwD9v-vXMm?wInrXU__($nIcijv;VKcZ@xwouPM%s^pxLFX@Pc7pI>rd_L)@96#u-6{BJ=3-(rMCJD|pZN6%Dj-#>iX#0+P(5V+wb&R4n z!G6wx(Z=Hrwz{dHz-rWu^Rxc*r;J@K>|LFd)_%!q9^04@zPadEr}N&rshlUZo3eQ4 zwM+56tIPu%z z+z_szkzyzD17emj^Cu#Nn0%-)C*({^y$1DGP2c8}^F9l{e&Hv@nZ+w-DPqO=UXPk5 zG~t)^51*F}nAn;eH8EkEl|1>$a!ZhsKyMK~t=~9CYCQhaeC+h(jMb?3xR+Kc(?w;l zbzd@J)$ETwN?5RnMRuYy(DC7eIolzHlf}l$y#`4Ins@Ba^bMcotGKtnnkp=7;b7Qn zTJo6CB{5PVq_q*?*Fw`<^dod9_vnS4?JsqrWhDp&^M15a%~SB*<4rj+5HHO7WuId$ zQ&&1!D-MPN z@dGn!){(GmRWikdkmYnKglc8m^ot$6jhR!=BlsdWwflYc-6^|0g>F`QXLL));Pv3t zwdTw|X@LssRZsb_@!NW28h2itwywi;nm|kkBg{X-jfGs~YTwO7ppJ-KSU z)kU*jOuyU`5&P&vO_!jSlFSyu8nn8t3=U>Qs0fg~BcrqvznW9NX09yty2Vx;9&fS? 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