bash - Calculating mean from values in columns specified on the first line using awk -


i have huge file (hundreds of lines, ca. 4,000 columns) structured this

locus   1   1   1   2   2   3   3   3 exon    1   2   3   1   2   1   2   3 data1   17.07   7.11    10.58   10.21   19.34   14.69   3.32    21.07 data2   21.42   11.46   7.88    9.89    27.24   12.40   0.58    19.82

and need calculate mean values (on each data line separately) same locus number (i.e., same number in first line), i.e.

data1: mean first 3 values (three columns locus '1': 17.07, 7.11, 10.58), next 2 values (10.21, 19.34) , next 3 values (14.69, 3.32, 21.07)

i have output this

data1   mean1   mean2   mean3 data1   mean1   mean2   mean3

i thinking using bash , awk... thank advice.

if me, use r, not awk:

library(data.table) x = fread('data.txt')  #> x #      v1    v2    v3    v4    v5    v6    v7   v8    v9 #1: locus  1.00  1.00  1.00  2.00  2.00  3.00 3.00  3.00 #2:  exon  1.00  2.00  3.00  1.00  2.00  1.00 2.00  3.00 #3: data1 17.07  7.11 10.58 10.21 19.34 14.69 3.32 21.07 #4: data2 21.42 11.46  7.88  9.89 27.24 12.40 0.58 19.82  # save first column of names later cnames = x$v1  # remove first column x[,v1:=null]  # matrix transpose: makes rows columns x = t(x)  # convert matrix data.table x = data.table(x,keep.rownames=f)  # set column names colnames(x) = cnames  #> x #   locus exon data1 data2 #1:     1    1 17.07 21.42 #...  # ditch useless column x[,exon:=null]  #> x #   locus data1 data2 #1:     1 17.07 21.42  # apply mean() function each column, grouped locus x[,lapply(.sd,mean),locus]  #   locus    data1    data2 #1:     1 11.58667 13.58667 #2:     2 14.77500 18.56500 #3:     3 13.02667 10.93333

for convenience, here's whole thing again without comments:

library(data.table) x = fread('data.txt') cnames = x$v1 x[,v1:=null] x = t(x) x = data.table(x,keep.rownames=f) colnames(x) = cnames x[,exon:=null] x[,lapply(.sd,mean),locus]

Comments

Post a Comment

Popular posts from this blog

Is there a better way to structure post methods in Class Based Views -

i'm using class based views in django , never specify url in ajax calls , omit action parameter in form because know these requests go through post method of class based view. notice view - profile page make many requests depending on user updating on page - post method become convoluted , if/else mess example: def post(self, request, *args, **kwargs): # handle user changing available date if request.post.get('availabledate') != none: self.updateavailabledate(request) return jsonresponse({'result':'success'}) if request.post.get('newprojectname') != none: creative_user = creativeuserprofile.objects.get(id = request.user.id) project = project.create_project(creative_user, request.post['newprojectname']) project.save() return jsonresponse({'projectid': project.id }) if request.post.get('projectimage') != none , request.files['file']: proj
Read more

performance - Why is XCHG reg, reg a 3 micro-op instruction on modern Intel architectures? -

i'm doing micro-optimization on performance critical part of code , came across sequence of instructions (in at&t syntax): add %rax, %rbx mov %rdx, %rax mov %rbx, %rdx i thought had use case xchg allow me shave instruction , write: add %rbx, %rax xchg %rax, %rdx however, dimay found agner fog's instruction tables , xchg 3 micro-op instruction 2 cycle latency on sandy bridge, ivy bridge, broadwell, haswell , skylake. 3 whole micro-ops , 2 cycles of latency! 3 micro-ops throws off 4-1-1-1 cadence , 2 cycle latency makes worse original in best case since last 2 instructions in original might execute in parallel. now... cpu might breaking instruction micro-ops equivalent to: mov %rax, %tmp mov %rdx, %rax mov %tmp, %rdx where tmp anonymous internal register , suppose last 2 micro-ops run in parallel latency 2 cycles. given register renaming occurs on these micro-architectures, though, doesn't make sense me done way. why wouldn't register renamer
Read more

jquery - Responsive Navbar with Sub Navbar -

good day, forgive me nav vocabulary not best. if question confusing apologize. i'm working on navigation bar needs centered on page @ 768px , above. items in nav open (or perhaps toggle) subnav lives directly below. these nav should appear centered on page. i have been able work through responsive portion of nav bar, having main items align vertically , sub nav menu of each item roll out below, , gave them indent separation. working well. however, issue not responsive side, behavior @ width greater 768px. happens toggling menu's sub navigation pushes other main items down page below sub nav. here's code: $(document).ready(function () { //stick in fixed 100% height behind navbar don't wrap $('#slide-nav.navbar-inverse').after($('<div class="inverse" id="navbar-height-col"></div>')); $('#slide-nav.navbar-default').after($('<div id="navbar-height-col"></d
Read more