diff options
Diffstat (limited to 'test')
| -rw-r--r-- | test/ChangeLog | 5 | ||||
| -rw-r--r-- | test/Makefile.am | 5 | ||||
| -rw-r--r-- | test/Makefile.in | 10 | ||||
| -rw-r--r-- | test/Maketests | 5 | ||||
| -rwxr-xr-x | test/arrayind1.awk | 99 | ||||
| -rw-r--r-- | test/arrayind1.in | 2 | ||||
| -rw-r--r-- | test/arrayind1.ok | 9 |
7 files changed, 133 insertions, 2 deletions
diff --git a/test/ChangeLog b/test/ChangeLog index 11908b40..e9ea5770 100644 --- a/test/ChangeLog +++ b/test/ChangeLog @@ -1,3 +1,8 @@ +2016-05-12 Arnold D. Robbins <arnold@skeeve.com> + + * Makefile.am (arrayind1): New test. + * arrayind1.awk, arrayind1.in, arrayind1.ok: New files. + 2016-04-27 Arnold D. Robbins <arnold@skeeve.com> * Makefile.am (rscompat): New test. diff --git a/test/Makefile.am b/test/Makefile.am index 844c87fb..07637e12 100644 --- a/test/Makefile.am +++ b/test/Makefile.am @@ -52,6 +52,9 @@ EXTRA_DIST = \ argarray.ok \ argtest.awk \ argtest.ok \ + arrayind1.awk \ + arrayind1.in \ + arrayind1.ok \ arrayparm.awk \ arrayparm.ok \ arrayprm2.awk \ @@ -1041,7 +1044,7 @@ CLEANFILES = core core.* fmtspcl.ok # try to keep these sorted. each letter starts a new line BASIC_TESTS = \ - addcomma anchgsub argarray arrayparm arrayprm2 arrayprm3 \ + addcomma anchgsub argarray arrayind1 arrayparm arrayprm2 arrayprm3 \ arrayref arrymem1 arryref2 arryref3 arryref4 arryref5 arynasty \ arynocls aryprm1 aryprm2 aryprm3 aryprm4 aryprm5 aryprm6 aryprm7 \ aryprm8 aryprm9 arysubnm asgext awkpath \ diff --git a/test/Makefile.in b/test/Makefile.in index 5e55b1b6..cb42bfed 100644 --- a/test/Makefile.in +++ b/test/Makefile.in @@ -309,6 +309,9 @@ EXTRA_DIST = \ argarray.ok \ argtest.awk \ argtest.ok \ + arrayind1.awk \ + arrayind1.in \ + arrayind1.ok \ arrayparm.awk \ arrayparm.ok \ arrayprm2.awk \ @@ -1297,7 +1300,7 @@ CLEANFILES = core core.* fmtspcl.ok # try to keep these sorted. each letter starts a new line BASIC_TESTS = \ - addcomma anchgsub argarray arrayparm arrayprm2 arrayprm3 \ + addcomma anchgsub argarray arrayind1 arrayparm arrayprm2 arrayprm3 \ arrayref arrymem1 arryref2 arryref3 arryref4 arryref5 arynasty \ arynocls aryprm1 aryprm2 aryprm3 aryprm4 aryprm5 aryprm6 aryprm7 \ aryprm8 aryprm9 arysubnm asgext awkpath \ @@ -2598,6 +2601,11 @@ anchgsub: @AWKPATH="$(srcdir)" $(AWK) -f $@.awk < "$(srcdir)"/$@.in >_$@ 2>&1 || echo EXIT CODE: $$? >>_$@ @-$(CMP) "$(srcdir)"/$@.ok _$@ && rm -f _$@ +arrayind1: + @echo $@ + @AWKPATH="$(srcdir)" $(AWK) -f $@.awk < "$(srcdir)"/$@.in >_$@ 2>&1 || echo EXIT CODE: $$? >>_$@ + @-$(CMP) "$(srcdir)"/$@.ok _$@ && rm -f _$@ + arrayparm: @echo $@ @AWKPATH="$(srcdir)" $(AWK) -f $@.awk >_$@ 2>&1 || echo EXIT CODE: $$? >>_$@ diff --git a/test/Maketests b/test/Maketests index 16b1e826..7f9fe1c5 100644 --- a/test/Maketests +++ b/test/Maketests @@ -10,6 +10,11 @@ anchgsub: @AWKPATH="$(srcdir)" $(AWK) -f $@.awk < "$(srcdir)"/$@.in >_$@ 2>&1 || echo EXIT CODE: $$? >>_$@ @-$(CMP) "$(srcdir)"/$@.ok _$@ && rm -f _$@ +arrayind1: + @echo $@ + @AWKPATH="$(srcdir)" $(AWK) -f $@.awk < "$(srcdir)"/$@.in >_$@ 2>&1 || echo EXIT CODE: $$? >>_$@ + @-$(CMP) "$(srcdir)"/$@.ok _$@ && rm -f _$@ + arrayparm: @echo $@ @AWKPATH="$(srcdir)" $(AWK) -f $@.awk >_$@ 2>&1 || echo EXIT CODE: $$? >>_$@ diff --git a/test/arrayind1.awk b/test/arrayind1.awk new file mode 100755 index 00000000..29fe80bc --- /dev/null +++ b/test/arrayind1.awk @@ -0,0 +1,99 @@ +#!/usr/local/bin/awk -f +# this script renums pedigrees with metafounders +# so that they are added *before*regular animals +# mf are ascertained because they are not in the 1st column +# also ordered by generation assuming that all metafounders +# start at generation 1 +# +# + function maxval (a,b) { + max=b + if (a>b){max=a} + return max + } +BEGIN{ + pos[0]=0 # actual position in the original data file + changed=1 + posout[0]=0 # position in the new file + last=0 + cum[0]=0 #number of times it acts as parent + gen[0]=0 +} +# read and store pedigree file +{ + pos[$1]=NR + dam[$1]=$2 + sire[$1]=$3 + included[$1]=0 + gen[$1]=9999 +} +END{ + #printf("%10s%10s\n",NR,"animals") > "/dev/stderr" + # find out who is a genetic group + for (x in sire){ + if(! (sire[x] in pos)){ + is_group[sire[x]]=1 + #printf("%10s%10s\n","sire",sire[x]) > "/dev/stderr" + cum[sire[x],"sire"]++ + } + } + for (x in dam){ + if(! (dam[x] in pos)){ + is_group[dam[x]]=1 + #printf("%10s%10s\n","dam",dam[x]) > "/dev/stderr" + cum[dam[x],"dam"]++ + } + } + # compute numbers, but don't write them out + #printf("%16s\n","info on mf") > "/dev/stderr" + for (x in is_group){ + nmf++ + posout[x]=posout[last]+1 + printf("%16s%16s%16s%16s%16s%16s%16s\n", posout[x],0,0,x,0,0,0) + included[x]=1 + gen[x]=0 + last=x + cumgen[0]++ + #printf("%10s%16s%10s%16s%10s%10s%10s\n","group",last," included as",posout[x]," as sire, as dam",cum[x,"sire"],cum[x,"dam"]) > "/dev/stderr" + } + # regular individuals + printf("%16s\n","recoding animals") > "/dev/stderr" + iter=1 + #--> comment next line and this element of the associative array becomes null + #printf("%s%16s\n","at the beginning it should be empty: ",posout["00000779770060"]) > "/dev/stderr" + #--> + while (changed){ + changed=0 + for (x in pos){ + if(x!=0 && !included[x]){ + # change to number of generation + # if(included[dam[x]] && included[sire[x]]){ + if((gen[dam[x]]<iter) && (gen[sire[x]]<iter)){ + # the new code is actually the order animals are printed + posout[x]=posout[last]+1 + gen[x]=maxval(gen[dam[x]],gen[sire[x]])+1 + printf("%16s%16s%16s%16s%16s%16s%16s\n", posout[x],posout[dam[x]],posout[sire[x]],x,dam[x],sire[x],gen[x]) + included[x]=1 + changed=1 + last=x + nanim++ + cumgen[gen[x]]++ + } + # } + } + } + iter++ + #--> + printf("%s%16s\n","in the loop: ",posout["00000779770060"]) > "/dev/stderr" + #--> + #printf("%10s%10s%10s%10s%16s%16s\n","round",iter,"included",posout[last],"last ",last) > "/dev/stderr" + } + #printf("%10s%10s%10s%10s%10s%10s\n","metafounders:",nmf," animals",nanim," total",posout[last]) > "/dev/stderr" + #printf("%16s%16s\n","pseudogenerations:",gen[last]) > "/dev/stderr" + for (x in cumgen){ + #printf("%10s%16s%10s%16s\n","pseudogeneration:",x," including: ",cumgen[x]) > "/dev/stderr" + } + #--> this is the guilty line + printf("%s%16s\n","at the end: ",posout["00000779770060"]) > "/dev/stderr" + #--> +} diff --git a/test/arrayind1.in b/test/arrayind1.in new file mode 100644 index 00000000..915d8657 --- /dev/null +++ b/test/arrayind1.in @@ -0,0 +1,2 @@ +64000757790003 00000779770060 00000757740011 1979 2 1975 0 +00000779770060 1975su1du1 1975su1du1 1975 1 1975 1975su1du1 diff --git a/test/arrayind1.ok b/test/arrayind1.ok new file mode 100644 index 00000000..c68346ea --- /dev/null +++ b/test/arrayind1.ok @@ -0,0 +1,9 @@ +recoding animals +in the loop: 3 +in the loop: 3 +in the loop: 3 +at the end: 3 + 1 0 0 00000757740011 0 0 0 + 2 0 0 1975su1du1 0 0 0 + 3 2 2 00000779770060 1975su1du1 1975su1du1 1 + 4 3 1 64000757790003 00000779770060 00000757740011 2 |