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Commit message:
Migrated tool version 0.1 from old tool shed archive to new tool shed repository |
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._nupop_0.1 nupop_0.1/._Npred.f90 nupop_0.1/._NuPoP.py nupop_0.1/._NuPoP.xml nupop_0.1/._changePath.pl nupop_0.1/._profile nupop_0.1/._test_nupop_chr1.fa nupop_0.1/._test_nupop_pred_chr1.txt nupop_0.1/._test_nupop_pred_chr1.wig nupop_0.1/Npred.f90 nupop_0.1/NuPoP.py nupop_0.1/NuPoP.xml nupop_0.1/README nupop_0.1/changePath.pl nupop_0.1/profile/.DS_Store nupop_0.1/profile/._.DS_Store nupop_0.1/profile/._146-149freqN4.txt nupop_0.1/profile/._146-149tranN4.txt nupop_0.1/profile/._147freqN.txt nupop_0.1/profile/._147tranN.txt nupop_0.1/profile/._freqL.txt nupop_0.1/profile/._tranL.txt nupop_0.1/profile/._tranL2.txt nupop_0.1/profile/._tranL3.txt nupop_0.1/profile/._tranL4.txt nupop_0.1/profile/146-149freqN4.txt nupop_0.1/profile/146-149tranN4.txt nupop_0.1/profile/147freqN.txt nupop_0.1/profile/147tranN.txt nupop_0.1/profile/freqL.txt nupop_0.1/profile/tranL.txt nupop_0.1/profile/tranL2.txt nupop_0.1/profile/tranL3.txt nupop_0.1/profile/tranL4.txt nupop_0.1/test_nupop_chr1.fa nupop_0.1/test_nupop_pred_chr1.txt nupop_0.1/test_nupop_pred_chr1.wig |
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| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/Npred.f90 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/Npred.f90 Tue Jun 07 17:41:06 2011 -0400 |
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| b"@@ -0,0 +1,930 @@\n+program main\r\n+\r\n+ implicit none\r\n+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\r\n+\r\n+ integer i,lfn,mlL,rep,species,order,p,q,n; character*280 cmd_str; character*98 outFile; character*1 letter; character*98 fileName; character*3 tpc\r\n+ real*8 freqL1(4),tranL1(4,4),tranL2(16,4),tranL3(64,4),tranL4(256,4)\r\n+ real*8 freqN4(64,4),tranN4((147-4)*256,4),freqN1(147,4),tranN1(584,4)\r\n+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\r\n+\r\n+ open(1,file='/home/galaxy/software/NuPoP_F/profile/freqL.txt')\n+ read(1,*) freqL1; close(1)\r\n+ open(1,file='/home/galaxy/software/NuPoP_F/profile/tranL.txt')\n+ do i=1,4; read(1,*) tranL1(i,:); end do; close(1)\r\n+ open(1,file='/home/galaxy/software/NuPoP_F/profile/tranL2.txt')\n+ do i=1,16; read(1,*) tranL2(i,:); end do; close(1)\r\n+ open(1,file='/home/galaxy/software/NuPoP_F/profile/tranL3.txt')\n+ do i=1,64; read(1,*) tranL3(i,:); end do; close(1)\r\n+ open(1,file='/home/galaxy/software/NuPoP_F/profile/tranL4.txt')\n+ do i=1,256; read(1,*) tranL4(i,:); end do; close(1)\r\n+\r\n+ open(1,file='/home/galaxy/software/NuPoP_F/profile/147freqN.txt')\n+ do i=1,147; read(1,*) freqN1(i,:); end do\r\n+ close(1)\r\n+ open(1,file='/home/galaxy/software/NuPoP_F/profile/147tranN.txt')\n+ do i=1,584; read(1,*) tranN1(i,:); end do\r\n+ close(1)\r\n+\r\n+ open(1,file='/home/galaxy/software/NuPoP_F/profile/146-149freqN4.txt')\n+ do i=1,64; read(1,*) freqN4(i,:); end do; close(1)\r\n+ open(1,file='/home/galaxy/software/NuPoP_F/profile/146-149tranN4.txt')\n+ do i=1,(147-4)*256; read(1,*) tranN4(i,:); end do; close(1)\r\n+\r\n+ !write(*,'(a)') 'Please input'\r\n+ call get_command(cmd_str)\n+ n=1\n+ q=1\n+ do p=1, len_trim(cmd_str)\n+ letter=cmd_str(p:p)\n+ if (letter .eq. ' ') then\n+ if (n==2) fileName=cmd_str(q:p-1)\n+ if (n==3) read(cmd_str(q:p-1), '(I10)') mlL\n+ if (n==4) read(cmd_str(q:p-1), '(I10)') order\n+ if (n==5) read(cmd_str(q:p-1), '(I10)') rep\n+ if (n==6) read(cmd_str(q:p-1), '(I10)') species\n+ q=p+1\n+ n=n+1\n+ end if\n+ if (p==len_trim(cmd_str)) then \n+ outFile=cmd_str(q:p)\n+ end if\n+ end do \n+ if(order/=1.and.order/=4) then; print*,'Order of Markov model 1 or 4 should be inputed! Program terminated.'; stop; end if\r\n+ if(rep/=0.and.rep/=1.and.rep/=2.and.rep/=3.and.rep/=4.and.rep/=5) then\r\n+ print*,'Linker length distribution update times value should be one of 0, 1, 2, 3, 4, 5! Program terminated.'; stop\r\n+ end if; rep=rep+1\r\n+\r\n+ lfn=len_trim(fileName)\r\n+ if(order==1) then\r\n+ call vtbfb(lfn,trim(fileName),freqL1,tranL1,freqN1,tranN1,mlL,rep,species,outFile)\r\n+ else if(order==4) then\r\n+ call vtbfbNL4(lfn,trim(fileName),freqL1,tranL1,tranL2,tranL3,tranL4,freqN4,tranN4,mlL,rep,species,outFile)\r\n+ end if\r\n+ \r\n+ !write(*,'(a)') ' Done.'\r\n+end\r\n+!#################################################################################################\r\n+\r\n+subroutine vtbfb(lfn,filename,freqL,tranL,freqN,tranNN,mlL,rep,species,out1)\r\n+\r\n+ implicit none\r\n+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\r\n+\r\n+ integer t,d,i,j,k,l,m,n,z,mlL,lfn,rep,nvt,species\r\n+ integer zt,np,zp(100),q,st(100),ed(100),ext,rts(100),rte(100)\r\n+ integer ztt,nsec,x,base; integer,allocatable:: nrcv(:),nbrk(:)\r\n+ real*8 tempN,tempL,temp,tp,sc(4)\r\n+ real*8 freqL(4),tranL(4,4),freqN(147,4),tranN(146,4,4),tranNN(584,4),Pd(mlL),tmp(mlL)\r\n+\r\n+ character*80 seqName,out1,out2; character*2 tpc\r\n+ character(len=lfn) filename\r\n+ character(len=10000000),allocatable:: a(:)\r\n+\r\n+ integer*1,allocatable:: wt(:),w(:),c(:)\r\n+ integer,allocatable:: change(:),Nst(:)\r\n+ real*8,allocatable:: r(:),hatFN(:),hatFL(:),ra(:),hatAN(:),hatAL(:),rb(:),hatBN(:),hatBL(:)\r\n+ real*8,allocatable:: ppEndN(:),ppN(:),asc(:),aas(:)\r\n+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\r\n+\r\n+ do i=1,146; do j=1,4; tranN(i,j,:)=tranNN(4*(i-1)+j,:); end do; end do\r\n+\r\n+ if(spe"..b"d+2),c(z-t-d+3),c(z-t-d+4))*Pd(d)*hatBL(t+d)\r\n+ end if\r\n+\r\n+ tempN=tempN+temp\r\n+ end do\r\n+\r\n+ rb(t)=tempN+tempL\r\n+ if(rb(t)==0.0) then\r\n+ rb(t)=1.0/16.0; hatBN(t)=0.0; hatBL(t)=0.0\r\n+ else\r\n+ hatBN(t)=tempN/rb(t); hatBL(t)=tempL/rb(t)\r\n+ end if\r\n+\r\n+ end do\r\n+ !BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\r\n+ end if\r\n+ !^^^^^^^^^^^^^^^^^^^ end of backward ^^^^^^^^^^^^^^^^^^^\r\n+\r\n+ if(l<rep) then\r\n+ n=z; m=change(z)\r\n+ do while(m>0)\r\n+ tmp(n-m)=tmp(n-m)+1.0\r\n+ n=m-147; m=change(n)\r\n+ end do\r\n+ end if\r\n+\r\n+ deallocate(r,hatFN,hatFL,hatAL,hatBL); allocate(ppEndN(z+146),ppN(z),asc(74:z-73),aas(74:z-73),Nst(0:z/147))\r\n+ if(l==rep) then\r\n+\r\n+ ppEndN=0.0; ppN=0.0; temp=1.0\r\n+ do t=z-1,1,-1; temp=temp*rb(t)/ra(t+1); ppEndN(t)=hatAN(t)*hatBN(t)*temp; end do\r\n+ do t=1,z; do i=t,t+146; ppN(t)=ppN(t)+ppEndN(i); end do; end do\r\n+\r\n+ do t=74,z-73\r\n+ asc(t)=freqN4(w(t-73),w(t-72),w(t-71),w(t-70))/freqL4(w(t-73),w(t-72),w(t-71),w(t-70))&\r\n+ &*freqN4(c(z-t-72),c(z-t-71),c(z-t-70),c(z-t-69))/freqL4(c(z-t-72),c(z-t-71),c(z-t-70),c(z-t-69))\r\n+ do i=5,147\r\n+ asc(t)=asc(t)*tranN4(i,w(t-78+i),w(t-77+i),w(t-76+i),w(t-75+i),w(t-74+i))&\r\n+ &/tranL4(w(t-78+i),w(t-77+i),w(t-76+i),w(t-75+i),w(t-74+i))&\r\n+ &*tranN4(i,c(z-t-77+i),c(z-t-76+i),c(z-t-75+i),c(z-t-74+i),c(z-t-73+i))&\r\n+ &/tranL4(c(z-t-77+i),c(z-t-76+i),c(z-t-75+i),c(z-t-74+i),c(z-t-73+i))\r\n+ end do\r\n+ asc(t)=log(asc(t))\r\n+ end do; i=27\r\n+ if(z-73-i>=74+i+1) then\r\n+ do t=74,74+i; aas(t)=sum(asc(74:t+i))/(t+i-73.0); end do\r\n+ do t=74+i+1,z-73-i; aas(t)=aas(t-1)+(asc(t+i)-asc(t-1-i))/(2*i+1.0); end do\r\n+ do t=z-73-i+1,z-73; aas(t)=sum(asc(t-i:z-73))/(z-72.0-t+i); end do\r\n+ else\r\n+ aas=asc\r\n+ end if\r\n+ temp=sum(aas(:))/real(z-146); tp=sqrt(sum((aas(:)-temp)**2)/(z-147.0))\r\n+ aas=(aas-temp)/tp\r\n+\r\n+ n=z; m=change(z); k=0; w=0\r\n+ do while(m>0)\r\n+ k=k+1; Nst(k)=m-146; w(m-146:m)=1\r\n+ n=m-147; m=change(n)\r\n+ end do; nvt=k; Nst(0)=z+1\r\n+\r\n+ open(1,file=out1,position='append')\r\n+ do t=1+rts(q),z-rte(q)\r\n+ if(t<74.or.z-73<t) then\r\n+ write(1,'(i9,2x,f5.3,3x,f5.3,3x,i1,4x,a)') base+st(q)-1+t,ppEndN(t+146),ppN(t),w(t),tpc\r\n+ else\r\n+ write(1,'(i9,2x,f5.3,3x,f5.3,3x,i1,1x,f8.3)') base+st(q)-1+t,ppEndN(t+146),ppN(t),w(t),aas(t)\r\n+ end if\r\n+ end do\r\n+ close(1)\r\n+\r\n+ !open(2,file=out2(1:lfn+17),position='append')\r\n+ !do i=nvt,1,-1; if(1+rts(q)<=Nst(i).and.Nst(i)<=z-rte(q)) then \r\n+ ! write(2,'(a,3x,i9,8x,f8.5,8x,i4)') trim(seqName),base+st(q)-1+Nst(i)+73,ppEndN(Nst(i)+146),Nst(i-1)-Nst(i)-147\r\n+ !end if; end do\r\n+ !close(2)\r\n+\r\n+ end if\r\n+ deallocate(w,c,change,ra,hatAN,rb,hatBN,ppEndN,ppN,asc,aas,Nst)\r\n+\r\n+ !-----------------------\r\n+ end do !end of partition\r\n+ !-----------------------\r\n+\r\n+ if(l==rep) then; open(1,file=out1,position='append')\r\n+ temp=-0.05; t=0\r\n+ if(x<nsec) then\r\n+ do i=nbrk(x),nrcv(x+1)-1; write(1,'(i9,2x,f5.2,3x,f5.2,3x,i1,4x,a)') i,temp,temp,t,tpc; end do\r\n+ else if(x==nsec) then\r\n+ if(nbrk(nsec)<ztt+1) then\r\n+ do i=nbrk(nsec),ztt; write(1,'(i9,2x,f5.2,3x,f5.2,3x,i1,4x,a)') i,temp,temp,t,tpc; end do\r\n+ end if\r\n+ end if\r\n+ close(1); end if\r\n+\r\n+ !=====================\r\n+ end do !end of section\r\n+ !=====================\r\n+\r\n+ if(l<rep) then\r\n+ Pd=0.1\r\n+ do k=1,mlL; do i=1,mlL\r\n+ if(0.5*((k-i)/1.5)**2<20) Pd(k)=Pd(k)+tmp(i)*exp(-0.5*((k-i)/1.5)**2)\r\n+ end do; end do\r\n+ temp=sum(Pd); Pd=Pd/temp \r\n+\r\n+ !out2(1:lfn)=filename; out2(lfn+1:lfn+9)='_Lld4.txt'\r\n+ !open(2,file=out2(1:lfn+9))\r\n+ !do i=1,mlL; write(2,'(f7.5)') Pd(i); end do\r\n+ !close(2); !stop\r\n+ end if\r\n+\r\n+ !!!!!!!!\r\n+ end do !\r\n+ !!!!!!!!\r\n+\r\n+ deallocate(wt,nrcv,nbrk)\r\n+\r\n+end subroutine vtbfbNL4\r\n+!^^^^^^^^^^^^^^^^^^^^^^^^^^^^ end of program ^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n" |
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| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/NuPoP.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/NuPoP.py Tue Jun 07 17:41:06 2011 -0400 |
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| @@ -0,0 +1,118 @@ +#!/usr/bin/python + +## Description: A pythonic wrapper for Nucleosome position prediction tool called NuPoP_F. It can handle multiple sequence in a FASTA file. Further details can be found at http://nucleosome.stats.northwestern.edu/ +## Written by Vipin T Sreedharan, Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen Germany. + +import os, re, sys, struct, time +from Bio import SeqIO + +def __main__(): + stime = time.asctime( time.localtime(time.time()) ) + print '----------------------------------------' + print 'NuPoP started on ' + stime + print '----------------------------------------' + print'\nStep:1 Checking input parameters\n' + try: + fasta_file = sys.argv[1] + linker_len = sys.argv[2] + order_mm = sys.argv[3] + linker_up = sys.argv[4] + organism = sys.argv[5] + res_format = sys.argv[6] + pred_file = sys.argv[7] + pred_file_path = sys.argv[8] + except: + sys.stderr.write("Check input parameters:\n\t1. A valid FASTA file\n\t2. Linker DNA length (100-500)\n\t3. Order of HMM (1 or 4)\n\t4. Linker length distribution (0-5)\n\t") + sys.stderr.write("5. Species (1 : Homo sapiens, 2 : Mus musculus, 3 : Rattus norvegicus, 4 : Danio rerio, 5 : Drosophila melanogaster, 6 : Caenorhabditis elegans, 7 : Saccharomyces cerevisiae, 8 : Candida albicans, 9 : Schizosaccharomyces pombe, 10 : Arabidopsis thaliana, 11 : Zea mays)\n\t") + sys.stderr.write("6. Result format (wig or text)\n\t7. Prediction result file name\n\t8. Temporory path\n") + sys.exit(-1) + ## species available for NuPoP program + species = {'1' : "Homo sapiens", '2' : "Mus musculus", '3' : "Rattus norvegicus", '4' : "Danio rerio", '5' : "Drosophila melanogaster", '6' : "Caenorhabditis elegans", '7' : "Saccharomyces cerevisiae", '8' : "Candida albicans", '9' : "Schizosaccharomyces pombe", '10' : "Arabidopsis thaliana", '11' : "Zea mays"} + os.system("mkdir -p " + pred_file_path) + ## log message + print "Reading FASTA file : " + fasta_file + "\n" + print "Maximum length of linker DNA : " + linker_len + "\n" + print "Order of Markov Model : " + order_mm + "\n" + print "Linker length distribution update times : " + linker_up + "\n" + print "Species selected : " + species[organism] + "\n\n" + pred_file_handle = open(pred_file, "w+") + if res_format == 'wig': pred_file_handle.write("track type=wiggle_0 name=\"Nucleosome_Position_Prediction\" description=\"Genome source " + species[organism] + "\"\n") + print 'Step:2 Processing FASTA file\n' + fasta_handle = open(fasta_file, "rU") + for record in SeqIO.parse(fasta_handle, "fasta"): + print 'Sequence identifier: ' + record.id + '\n' + print 'Sequence length: '+ str(len(record.seq)) + '\n' + fasta_in = pred_file_path + "/" + record.id + ".fa" + fasta_outhand = open(fasta_in, "w+") + fasta_outhand.write(record.format("fasta")) + fasta_outhand.close() + # Npred result file + npred_out = pred_file_path + "/"+record.id + # compile NPred program + print 'Compiling NuPoP for chromosome/contig: ' + str(record.id) + try: + ## TODO Please add the right path to Npred.f90, It can be found in nupop_0.1/. + os.system("/usr/bin/gfortran Npred.f90 -w -o " + pred_file_path + "/" + record.id + "Npred") + except: + sys.stderr.write("Compile NPred failed. Please make sure the path of your gfortran compiler and Npred.f90 program, Cannot continue, Program terminating.....\n") + os.system("rm -rf " + pred_file_path) + sys.exit(-1) + print 'Done.' + # run NuPoP + print 'Predicting Nucleosome positioning for chromosome/contig: ' + str(record.id) + try: + os.system(pred_file_path + "/" + record.id + "Npred " + fasta_in + " " + linker_len + " " + order_mm + " " + linker_up + " " + organism + " " + npred_out) + except: + sys.stdout.write("NuPoP execution failed for chromosome/contig " + str(record.id) + ".\n") + os.system("rm -rf " + fasta_in) + os.system("rm -rf " + pred_file_path + '/' + record.id + "Npred") + continue + print 'Done.' + try: + npred_res_handle = open(npred_out, "r") + except: + sys.stderr.write("NuPoP prediction result file fail to open.") + sys.exit(-1) + print 'Writing result files' + ## create binary files with nucleosome occupancy score and feature position + nos = open(pred_file_path + "/" + record.id + ".nos", "wb") + pos = open(pred_file_path + "/" + record.id + ".pos", "wb") + if res_format == 'text': + pred_file_handle.write("Chromosome/Contig = " + record.id + "\n") + for line in npred_res_handle: + line = line.strip() + if re.search(r'^\s*Position', line): + pred_file_handle.write(line + "\n") + continue + pred_file_handle.write(line + "\n") + parts = line.split(" ") + parts[2] = parts[2].lstrip() + nos.write(struct.pack('f', float(parts[2]))) + pos.write(struct.pack('i', int(parts[0]))) + elif res_format == 'wig': + pred_file_handle.write("fixedStep chrom=" + record.id + " start=1 step=1 span=1\n") + for line in npred_res_handle: + line = line.strip() + if re.search(r'^\s*Position', line): continue + parts = line.split(" ") + parts[2] = parts[2].lstrip() + pred_file_handle.write(parts[2] + "\n") + nos.write(struct.pack('f', float(parts[2]))) + pos.write(struct.pack('i', int(parts[0]))) + npred_res_handle.close() + nos.close() + pos.close() + # clean up the contig based fasta and npred result file + os.system("rm -rf " + fasta_in + " " + npred_out ) + os.system("rm -rf " + pred_file_path +'/'+ record.id + "Npred") + print " Saving feature postion to (" + pred_file_path + '/' + record.id + '.pos' + ")\n" + print " Saving nucleosome occupancy score to (" + pred_file_path + '/' + record.id + '.nos' + ")\n" + print 'Done.' + fasta_handle.close() + pred_file_handle.close() + etime = time.asctime( time.localtime(time.time()) ) + print '----------------------------------------' + print 'NuPoP finished on ' + etime + print '----------------------------------------' + +if __name__=='__main__':__main__() |
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| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/NuPoP.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/NuPoP.xml Tue Jun 07 17:41:06 2011 -0400 |
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| @@ -0,0 +1,129 @@ +<tool id="nupop_0.1" name="NuPoP" version="0.1"> + <description>Predict nucleosome positioning for DNA sequences of any length</description> + <command interpreter="python">NuPoP.py + $fasta_input + $linker_length + $order_mm + $linker_update + $species + #if $types.format_type == "text": + text $np_text $np_text.extra_files_path + #elif $types.format_type == "wig": + wig $np_wig $np_wig.extra_files_path + #end if + > $Log_File + </command> + <inputs> + <param format="fasta" name="fasta_input" type="data" label="DNA sequence" help="The FASTA file contains DNA sequence."> + </param> + <param name="linker_length" type="integer" size="4" value="100" label="Maximum length of Linker (bp)" help="An integer for the maximum allowable linker DNA length. Typical values are between 100 and 500."> + </param> + <param name="order_mm" type="integer" size="4" value="1" label="Order of Markov model" help="An integer 1 or 4, represents the first or fourth order Markov chain."> + </param> + <param name="linker_update" type="integer" size="4" value="0" label="Linker length distribution update times" help="An integer 0-5. If a sequence is shorter than 200K, this option is coerced as ”0” as sequence may be not long enough to provide meaningful estimate of the distribution."> + </param> + <param name="species" type="select" label="Species" help="Select species according to the source sequence. If your intented species is not listed, choose a species on the list that is evolutionary closest to the one under prediction."> + <option value="1" selected="true">Homo sapiens</option> + <option value="2">Mus musculus</option> + <option value="3">Rattus norvegicus</option> + <option value="4">Danio rerio</option> + <option value="5">Drosophila melanogaster</option> + <option value="6">Caenorhabditis elegans</option> + <option value="7">Saccharomyces cerevisiae</option> + <option value="8">Candida albicans</option> + <option value="9">Schizosaccharomyces pombe</option> + <option value="10">Arabidopsis thaliana</option> + <option value="11">Zea mays</option> + </param> + + <conditional name="types"> + <param name="format_type" type="select" label="Output format" help="See about format section."> + <option value="text">Text format</option> + <option value="wig">Wiggle fixedStep format</option> + </param> + <when value="text"></when> + <when value="wig"></when> + </conditional> + + </inputs> + + <outputs> + <data format="txt" name="np_text" label="NuPoP prediction in text format" > + <filter>types['format_type'] == "text"</filter> + </data> + <data format="wig" name="np_wig" label="NuPoP prediction in wiggle format" > + <filter>types['format_type'] == "wig"</filter> + </data> + <data format="txt" name="Log_File" label="NuPoP Log File"/> + </outputs> + + <tests> + <test> + <param name='fasta_input' value='test_nupop_chr1.fa' ftype='fasta' /> + <param name='linker_length' value='100' /> + <param name='order_mm' value='1' /> + <param name='linker_update' value='0' /> + <param name='species' value='1' /> + <param name='format_type' value='text' /> + <param name='format_type' value='wig' /> + <param name='np_text' file='test_nupop_pred_chr1.txt' ftype='txt' /> + <param name='np_wig' file='test_nupop_pred_chr1.wig' ftype='wig' /> + </test> +</tests> + + <help> + + +**What it does** + +NuPoP is a software tool for Nucleosome Positioning Prediction. For more information on NuPoP and the methods, please refer to `here`__ + .. __: http://nucleosome.stats.northwestern.edu/ + +------ + +**Example** + +- DNA sequence in FASTA format:: + + >CHR1 + CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAAAT + CTTTAAATCCTACATCCATGAATCCCTAAATACCTAATTCCCTAAACCCGAAACCGGTTT + CTCTGGTTGAAAATCATTGTGTATATAATGATAATTTTATCGTTTTTATGTAATTGCTTA + TTGTTGTGTGTAGATTTTTTAAAAATATCATTTGAGGTCAATACAAATCCTATTTCTTGT + GGTTTTCTTTCCTTCACTTAGCTATGGATGGTTTATCTTCATTTGTTATATTGGATACAA + +- Prediction result in text format:: + + Chromosome/Contig = CHR1 + Position P-start Occup N/L Affinity + 1 0.000 0.000 0 2.843 + 2 0.032 0.032 0 2.839 + 3 0.840 0.872 1 2.815 + 4 0.001 0.872 1 2.814 + +- or in Wiggle fixedStep format:: + + track type=wiggle_0 name="Nucleosome_Position_Prediction" description="Genome source Homo sapiens" + fixedStep chrom=CHR1 start=1 step=1 span=1 + 0.000 + 0.032 + 0.872 + 0.872 + +------ + +**About formats** + +**FASTA format** A sequence in FASTA format begins with a single-line +description, followed by lines of sequence data. The description line +is distinguished from the sequence data by a greater-than (">") symbol +in the first column. The token until the first space or the end of the +line is used as identifier for the sequence. The remainer of the +description line will be ignored. + +**Prediction result format** The prediction results including nucleosome occupancy score, Viterbi prediction and nucleosome affinity score with the corresponding position in the genome sequence. + +**Wiggle fixedStep format** The data is introduced by a line beginning with the keyword "fixedStep", and the arguments "chrom", "start", "step" and "span". The arguments are indicating the chromosome on which the features are located, starting position of the first feature, the spacing between each feature and the width of each feature in base pair respectively. + +</help> +</tool> |
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| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/README Tue Jun 07 17:41:06 2011 -0400 |
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| @@ -0,0 +1,47 @@ + +NuPoP is a software tool for Nucleosome Positioning Prediction. For more information on NuPoP please refer For more information on NuPoP and the methods, please refer http://nucleosome.stats.northwestern.edu/ + +For comments, please contact: jzwang@northwestern.edu + +Vipin T Sreedharan customized the fortran program and wrote a pythonic interface to integrate in Galaxy service. + +1) It can handle multiple fasta sequence in a query file to predict nucleosome positioning. + +2) Multiple output, Plain text based result and Wiggle fixedStep format based on users request. In addition to this it will create binary files of nucleosome occupency score and corresponding positions in the genomic sequence. The binary file path can be found in NuPoP Log file. + +How to integrate into your Galaxy: + +1. Unpack the compressed file and move the resulting folder to anywhere you want. + +2. Under the resulting folder run perl code by type "perl changePath.pl". This command set up the Fotran codes input file path according to the exact location. + +3. Please make sure that Biopython is installed in your machine. + +4. Edit the <command> tag in NuPoP.xml move into your Galaxy root. + +5. Set the correct path for fortran program(NPred.f90) in NuPoP.py. Always below the line of #TODO line number + +6. Move the test_nupop_* files to galaxy test-data folder. + +CONTENTS + +Npred.f90 : Fortran program (core). + +NuPoP.py : A pythonic interface to the core program. + +NuPoP.xml : Tool configuration file. + +changePath.pl : Seeting the CWD path in core program. + +profile/ : NuPoP dependencies. + +test_nupop_chr1.fa : genome sequence in FASTA format. + +test_nupop_pred_chr1.txt : prediction result in text format. + +test_nupop_pred_chr1.wig : prediction result in Wiggle format. + + +Please let me know if you find any difficulty to integrate into Galaxy. I can be reached at vipin.ts@tuebingen.mpg.de + + |
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| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/changePath.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/changePath.pl Tue Jun 07 17:41:06 2011 -0400 |
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| @@ -0,0 +1,61 @@ +#!/usr/local/bin/perl +#use strict; +use Cwd; + +#system('cp Npred.f90.back Npred.f90'); +my $cwd=getcwd(); +open (OLD,"Npred.f90"); +my @lines=<OLD>; +close(OLD); +open (NEW,">Npred.f90"); +my $i=0; +my $current; +for ($i==0;$i<=$#lines;$i++){ + if($lines[$i]=~m/freqL.txt/){ + $current=" open(1,file='".$cwd."/profile/freqL.txt')"; + $lines[$i] =$current; + print NEW $lines[$i],"\n"; + } + elsif ($lines[$i]=~m/tranL.txt/){ + $current=" open(1,file='".$cwd."/profile/tranL.txt')"; + $lines[$i] =$current; + print NEW $lines[$i],"\n"; + } + elsif ($lines[$i]=~m/tranL2.txt/){ + $current=" open(1,file='".$cwd."/profile/tranL2.txt')"; + $lines[$i] =$current; + print NEW $lines[$i],"\n"; + } + elsif ($lines[$i]=~m/tranL3.txt/){ + $current=" open(1,file='".$cwd."/profile/tranL3.txt')"; + $lines[$i] =$current; + print NEW $lines[$i],"\n"; + } + elsif ($lines[$i]=~m/tranL4.txt/){ + $current=" open(1,file='".$cwd."/profile/tranL4.txt')"; + $lines[$i] =$current; + print NEW $lines[$i],"\n"; + } + elsif ($lines[$i]=~m/147freqN.txt/){ + $current=" open(1,file='".$cwd."/profile/147freqN.txt')"; + $lines[$i] =$current; + print NEW $lines[$i],"\n"; + } + elsif ($lines[$i]=~m/147tranN.txt/){ + $current=" open(1,file='".$cwd."/profile/147tranN.txt')"; + $lines[$i] =$current; + print NEW $lines[$i],"\n"; + } + elsif ($lines[$i]=~m/146-149freqN4.txt/){ + $current=" open(1,file='".$cwd."/profile/146-149freqN4.txt')"; + $lines[$i] =$current; + print NEW $lines[$i],"\n"; + } + elsif ($lines[$i]=~m/146-149tranN4.txt/){ + $current=" open(1,file='".$cwd."/profile/146-149tranN4.txt')"; + $lines[$i] =$current; + print NEW $lines[$i],"\n"; + } + else{print NEW $lines[$i]}; +} +close NEW; |
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| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/profile/146-149tranN4.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/profile/146-149tranN4.txt Tue Jun 07 17:41:06 2011 -0400 |
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| b |
| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/profile/147freqN.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/profile/147freqN.txt Tue Jun 07 17:41:06 2011 -0400 |
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| b |
| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/profile/freqL.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/profile/freqL.txt Tue Jun 07 17:41:06 2011 -0400 |
| b |
| @@ -0,0 +1,1 @@ + 0.33853 0.16147 0.16147 0.33853 |
| b |
| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/profile/tranL.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/profile/tranL.txt Tue Jun 07 17:41:06 2011 -0400 |
| b |
| @@ -0,0 +1,4 @@ + 0.40013 0.13698 0.15945 0.30344 + 0.34441 0.18087 0.14195 0.33277 + 0.36436 0.16979 0.18051 0.28533 + 0.26215 0.17440 0.16453 0.39892 |
| b |
| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/profile/tranL2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/profile/tranL2.txt Tue Jun 07 17:41:06 2011 -0400 |
| b |
| @@ -0,0 +1,16 @@ + 0.43483 0.12783 0.16522 0.27212 + 0.34452 0.18799 0.15059 0.31690 + 0.38622 0.16322 0.17822 0.27234 + 0.31507 0.16047 0.16667 0.35779 + 0.38571 0.14181 0.16614 0.30634 + 0.36036 0.16977 0.14137 0.32850 + 0.33142 0.18758 0.17898 0.30201 + 0.23614 0.17682 0.17249 0.41455 + 0.44113 0.11956 0.16081 0.27850 + 0.33758 0.18696 0.15689 0.31857 + 0.35967 0.17552 0.16877 0.29604 + 0.30430 0.15258 0.17088 0.37224 + 0.33098 0.15952 0.14368 0.36582 + 0.33903 0.17907 0.12956 0.35234 + 0.35866 0.16692 0.18868 0.28574 + 0.21583 0.19244 0.15888 0.43286 |
| b |
| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/profile/tranL3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/profile/tranL3.txt Tue Jun 07 17:41:06 2011 -0400 |
| b |
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| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/profile/tranL4.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/profile/tranL4.txt Tue Jun 07 17:41:06 2011 -0400 |
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0.31888 0.16103 0.15375 0.36634\n+ 0.35946 0.15319 0.14906 0.33828\n+ 0.34495 0.15474 0.14373 0.35657\n+ 0.32436 0.17805 0.15942 0.33816\n+ 0.23323 0.18248 0.16586 0.41843\n+ 0.40968 0.14112 0.12719 0.32202\n+ 0.30777 0.21072 0.14370 0.33780\n+ 0.35360 0.16695 0.15325 0.32620\n+ 0.29825 0.16746 0.17703 0.35726\n+ 0.32716 0.18108 0.15271 0.33905\n+ 0.32507 0.18868 0.12827 0.35798\n+ 0.35205 0.16006 0.18474 0.30315\n+ 0.22594 0.19421 0.15652 0.42333\n+ 0.40776 0.13688 0.17402 0.28134\n+ 0.35483 0.17370 0.17016 0.30132\n+ 0.35997 0.16071 0.20507 0.27425\n+ 0.36189 0.13326 0.18451 0.32035\n+ 0.36223 0.14369 0.15844 0.33564\n+ 0.36417 0.19828 0.14847 0.28908\n+ 0.32970 0.17647 0.18591 0.30792\n+ 0.29767 0.13961 0.18884 0.37388\n+ 0.43438 0.11754 0.18773 0.26035\n+ 0.35028 0.18006 0.17055 0.29911\n+ 0.35257 0.14706 0.21103 0.28934\n+ 0.34850 0.12723 0.18594 0.33833\n+ 0.28978 0.14702 0.11892 0.44428\n+ 0.37883 0.16931 0.13811 0.31374\n+ 0.33020 0.16972 0.17880 0.32127\n+ 0.27894 0.16155 0.16167 0.39784\n+ 0.40372 0.14389 0.16730 0.28509\n+ 0.28665 0.22447 0.13701 0.35187\n+ 0.33692 0.18571 0.17675 0.30063\n+ 0.23787 0.23438 0.13338 0.39437\n+ 0.38631 0.15445 0.16025 0.29899\n+ 0.34249 0.15997 0.12141 0.37613\n+ 0.29418 0.20247 0.19474 0.30860\n+ 0.18118 0.21727 0.15228 0.44927\n+ 0.41340 0.12447 0.17505 0.28708\n+ 0.27934 0.21963 0.19574 0.30530\n+ 0.32223 0.20090 0.17438 0.30248\n+ 0.26047 0.19650 0.15261 0.39042\n+ 0.32855 0.17435 0.14504 0.35206\n+ 0.29929 0.19565 0.12388 0.38118\n+ 0.32233 0.19160 0.19096 0.29511\n+ 0.15778 0.24682 0.17136 0.42404\n+ 0.44075 0.12001 0.19050 0.24875\n+ 0.35362 0.17763 0.18531 0.28344\n+ 0.37647 0.16663 0.20768 0.24922\n+ 0.32905 0.14554 0.20839 0.31702\n+ 0.37687 0.12992 0.18900 0.30421\n+ 0.37081 0.16288 0.14440 0.32191\n+ 0.29577 0.19351 0.20616 0.30456\n+ 0.24087 0.17952 0.19238 0.38724\n+ 0.45628 0.10538 0.16386 0.27448\n+ 0.35574 0.17584 0.16217 0.30624\n+ 0.35669 0.17129 0.15976 0.31226\n+ 0.31914 0.13828 0.20065 0.34194\n+ 0.32797 0.16054 0.15058 0.36091\n+ 0.34903 0.16613 0.14286 0.34199\n+ 0.32605 0.16187 0.20443 0.30765\n+ 0.23515 0.18335 0.18067 0.40083\n+ 0.39374 0.15194 0.13908 0.31524\n+ 0.30673 0.23524 0.12822 0.32980\n+ 0.36241 0.17666 0.15628 0.30465\n+ 0.27005 0.17460 0.14164 0.41371\n+ 0.38879 0.13425 0.16339 0.31357\n+ 0.35152 0.17677 0.12164 0.35008\n+ 0.34581 0.17235 0.16726 0.31458\n+ 0.21229 0.17300 0.15656 0.45814\n+ 0.43301 0.12085 0.14822 0.29792\n+ 0.33154 0.19932 0.12903 0.34010\n+ 0.35800 0.18420 0.14174 0.31606\n+ 0.26409 0.16437 0.13490 0.43664\n+ 0.31075 0.17483 0.14277 0.37165\n+ 0.32370 0.19088 0.11772 0.36770\n+ 0.35645 0.16340 0.18840 0.29175\n+ 0.16960 0.20304 0.13446 0.49290\n' |
| b |
| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/test_nupop_chr1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/test_nupop_chr1.fa Tue Jun 07 17:41:06 2011 -0400 |
| b |
| b'@@ -0,0 +1,3838 @@\n+>chr1\n+CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACA\n+CATCCTAACACTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTT\n+ACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAAC\n+CACCATCCATCCCTCTACTTACTACCACTCACCCACCGTTACCCTCCAATTACCCATATC\n+CAACCCACTGCCACTTACCCTACCATTACCCTACCATCCACCATGACCTACTCACCATAC\n+TGTTCTTCTACCCACCATATTGAAACGCTAACAAATGATCGTAAATAACACACACGTGCT\n+TACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTCACTTGTATACTGATTT\n+TACGTACGCACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTCAGATTC\n+CACTTCACTCCATGGCCCATCTCTCACTGAATCAGTACCAAATGCACTCACATCATTATG\n+CACGGCACTTGCCTCAGCGGTCTATACCCTGTGCCATTTACCCATAACGCCCATCATTAT\n+CCACATTTTGATATCTATATCTCATTCGGCGGTCCCAAATATTGTATAACTGCCCTTAAT\n+ACATACGTTATACCACTTTTGCACCATATACTTACCACTCCATTTATATACACTTATGTC\n+AATATTACAGAAAAATCCCCACAAAAATCACCTAAACATAAAAATATTCTACTTTTCAAC\n+AATAATACATAAACATATTGGCTTGTGGTAGCAACACTATCATGGTATCACTAACGTAAA\n+AGTTCCTCAATATTGCAATTTGCTTGAACGGATGCTATTTCAGAATATTTCGTACTTACA\n+CAGGCCATACATTAGAATAATATGTCACATCACTGTCGTAACACTCTTTATTCACCGAGC\n+AATAATACGGTAGTGGCTCAAACTCATGCGGGTGCTATGATACAATTATATCTTATTTCC\n+ATTCCCATATGCTAACCGCAATATCCTAAAAGCATAACTGATGCATCTTTAATCTTGTAT\n+GTGACACTACTCATACGAAGGGACTATATCTAGTCAAGACGATACTGTGATAGGTACGTT\n+ATTTAATAGGATCTATAACGAAATGTCAAATAATTTTACGGTAATATAACTTATCAGCGG\n+CGTATACTAAAACGGACGTTACGATATTGTCTCACTTCATCTTACCACCCTCTATCTTAT\n+TGCTGATAGAACACTAACCCCTCAGCTTTATTTCTAGTTACAGTTACACAAAAAACTATG\n+CCAACCCAGAAATCTTGATATTTTACGTGTCAAAAAATGAGGGTCTCTAAATGAGAGTTT\n+GGTACCATGACTTGTAACTCGCACTGCCCTGATCTGCAATCTTGTTCTTAGAAGTGACGC\n+ATATTCTATACGGCCCGACGCGACGCGCCAAAAAATGAAAAACGAAGCAGCGACTCATTT\n+TTATTTAAGGACAAAGGTTGCGAAGCCGCACATTTCCAATTTCATTGTTGTTTATTGGAC\n+ATACACTGTTAGCTTTATTACCGTCCACGTTTTTTCTACAATAGTGTAGAAGTTTCTTTC\n+TTATGTTCATCGTATTCATAAAATGCTTCACGAACACCGTCATTGATCAAATAGGTCTAT\n+AATATTAATATACATTTATATAATCTACGGTATTTATATCATCAAAAAAAAGTAGTTTTT\n+TTATTTTATTTTGTTCGTTAATTTTCAATTTCTATGGAAACCCGTTCGTAAAATTGGCGT\n+TTGTCTCTAGTTTGCGATAGTGTAGATACCGTCCTTGGATAGAGCACTGGAGATGGCTGG\n+CTTTAATCTGCTGGAGTACCATGGAACACCGGTGATCATTCTGGTCACTTGGTCTGGAGC\n+AATACCGGTCAACATGGTGGTGAAGTCACCGTAGTTGAAAACGGCTTCAGCAACTTCGAC\n+TGGGTAGGTTTCAGTTGGGTGGGCGGCTTGGAACATGTAGTATTGGGCTAAGTGAGCTCT\n+GATATCAGAGACGTAGACACCCAATTCCACCAAGTTGACTCTTTCGTCAGATTGAGCTAG\n+AGTGGTGGTTGCAGAAGCAGTAGCAGCGATGGCAGCGACACCAGCGGCGATTGAAGTTAA\n+TTTGACCATTGTATTTGTTTTGTTTGTTAGTGCTGATATAAGCTTAACAGGAAAGGAAAG\n+AATAAAGACATATTCTCAAAGGCATATAGTTGAAGCAGCTCTATTTATACCCATTCCCTC\n+ATGGGTTGTTGCTATTTAAACGATCGCTGACTGGCACCAGTTCCTCATCAAATATTCTCT\n+ATATCTCATCTTTCACACAATCTCATTATCTCTATGGAGATGCTCTTGTTTCTGAACGAA\n+TCATAAATCTTTCATAGGTTTCGTATGTGGAGTACTGTTTTATGGCGCTTATGTGTATTC\n+GTATGCGCAGAATGTGGGAATGCCAATTATAGGGGTGCCGAGGTGCCTTATAAAACCCTT\n+TTCTGTGCCTGTGACATTTCCTTTTTCGGTCAAAAAGAATATCCGAATTTTAGATTTGGA\n+CCCTCGTACAGAAGCTTATTGTCTAAGCCTGAATTCAGTCTGCTTTAAACGGCTTCCGCG\n+GAGGAAATATTTCCATCTCTTGAATTCGTACAACATTAAACGTGTGTTGGGAGTCGTATA\n+CTGTTAGGGTCTGTAAACTTGTGAACTCTCGGCAAATGCCTTGGTGCAATTACGTAATTT\n+TAGCCGCTGAGAAGCGGATGGTAATGAGACAAGTTGATATCAAACAGATACATATTTAAA\n+AGAGGGTACCGCTAATTTAGCAGGGCAGTATTATTGTAGTTTGATATGTACGGCTAACTG\n+AACCTAAGTAGGGATATGAGAGTAAGAACGTTCGGCTACTCTTCTTTCTAAGTGGGATTT\n+TTCTTAATCCTTGGATTCTTAAAAGGTTATTAAAGTTCCGCACAAAGAACGCTTGGAAAT\n+CGCATTCATCAAAGAACAACTCTTCGTTTTCCAAACAATCTTCCCGAAAAAGTAGCCGTT\n+CATTTCCCTTCCGATTTCATTCCTAGACTGCCAAATTTTTCTTGCTCATTTATAATGATT\n+GATAAGAATTGTATTTGTGTCCCATTCTCGTAGATAAAATTCTTGGATGTTAAAAAATTA\n+TTATTTTCTTCATAAAGAAGCTTTCAAGATATAAGATACGAAATAGGGGTTGATAATTGC\n+ATGACAGTAGCTTTAGATCAAAAAGGAAAGCATGGAGGGAAACAGTAAACAGTGAAAATT\n+CTCTTGAGAACCAAAGTAAACCTTCATTGAAGAGCTTCCTTAAAAAATTTAGAATCTCCC\n+ATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATCTTTTTTCAAAGAAACTTCAAA\n+TGCCTCTTTTATGCAAGGGGCAAAATCCTGAAATGACTTAAACTTAGCAGTTTCGTCTTT\n+TTTCAAAGAGAATGGTTGAAGAAGAATTGTTTTGGACGCTTATTGACAATCTGTTGCATT\n+GATAAAGTACCTACTATCCCAGACTATATTTGTATACAAGTACAAAATTAGGTTTGTTGA\n+AACAACTTTCCGATCATTGGTGCCCGTATCTGATGTTTTTTTAGTAATTTCTTTGTAAAT\n+ACAGGGAGTTGTTTCGAAAGCTTATGAGAAAAATACATGAATGACAGGTAAAAATATTGG\n+CTCGAAAAAGAGGACAAAAAGAGAAATCATAAATGAGTAAACCCACTTGCTGGACATTAT\n+CCAGTAAAGGCTTGGTAGTAACCATAATATTACCCAGGTACGAAACGCTAAGAACCTTGA\n+AAGA'..b'TATCAAACGGGACCAGGCTATGACGTCGTCAGATCCGTCGGT\n+GCCAACTTGTTCAACGCTTCAGTGAAACTACTAAAGGAAAGTGAGGTCCAGGACCAAAAG\n+GTTTGGTTGAGTTTCACCCACGATACCGATATTCTGAACTATTTGACCACTATCGGCATA\n+ATCGATGACAAAAATAACTTGACCGCCGAACATGTTCCATTCATGGAAAACACTTTCCAC\n+AGATCCTGGTACGTTCCACAAGGTGCTCGTGTTTACACTGAAAAGTTCCAGTGTTCCAAT\n+GACACCTATGTTAGATACGTCATCAACGATGCTGTCGTTCCAATTGAAACCTGTTCTACT\n+GGTCCAGGGTTCTCCTGTGAAATAAATGACTTCTACGACTATGCTGAAAAGAGAGTAGCC\n+GGTACTGACTTCCTAAAGGTCTGTAACGTCAGCAGCGTCAGTAACTCTACTGAATTGACC\n+TTTTTCTGGGACTGGAATACCAAGCACTACAACGACACTTTATTAAAACAGTAAATAGAT\n+AATATGATTATGTAATTTTAGAAACTAATTATGAATACCGATTTATTTTTTTTTTTTTTT\n+TTCACTTTTGCTGGCAAGAAATACGAAATTGCAATGACGATCACAGTCCAAAGAGGTAAG\n+CACAAAGGCGCAGTATGTGATTACTCTATCATTCTTTAGCAAAACCAGGATAGGAGTATA\n+TGTATAAGAAATATGCAACGCCATCATTTAATGCAATAGACACGACATGCCCTTTACATG\n+AGGTGGTACAATGTTTTAATATTGTGTCAGGGCAAGTACATGATAATATCGTTTAAAGAT\n+GATGCTAGAGTAAAAGTATGAAGTGAAAGAAAAGGGCAATTGATTGACTAAGCGGATGTT\n+GTAGGATGATATAGTGGCTCATGATCTGTAAATGATCGGTTGACCGCAGTATTATATAAT\n+AACATCCGTATAAGTACATATACTACCATGTCTGTTCTCTACATTGCTTTTTATTCAAGA\n+TTATTGGTTTTCCTAACCGCCGCGCCGCGCAGGTACCCCGCGCATCTCTTCTTCTCGAAG\n+AAAGCGGAAAAAACAAAAAAAAAAGTATAAATAGTGGAGTCTTTTCCCATTTAACATTTA\n+GAAAAAAATTCGAATGGAAATTTCTTGCCGAACATTTAACCGGAGACCCTTGGCGGCTTT\n+TTCTCAGTTTCGTGGGCTAGTACATTTTACCTAGTATGCTGGGAACTTTTTTTCCGTATT\n+CTATTCTATTCCTTGCCTTACTTTTCTTATCATTTTTTATATAACCAATTTCAAAAATAC\n+TTTTTAACTGTCATAGACGCATTTTGTTTATTACAAATTAAAAGAATCAAATATAATATG\n+TGCAATTAATAACTCCACAAGTAGCGAAAGCAATGGCCGCCATTAGAGACTACAAGACCG\n+CACTAGATCTTACCAAGAGCCTACCAAGACCGGATGGTTTGTCAGTGCAGGAACTGATGG\n+ACTCCAAGATCAGAGGTGGGTTGGCTTATAACGATTTTTTAATCTTACCAGGTTTAGTCG\n+ATTTTGCGTCCTCTGAAGTTAGCCTACAGACCAAGCTAACCAGGAATATTACTTTAAACA\n+TTCCATTAGTATCCTCTCCAATGGACACTGTGACGGAATCTGAAATGGCCACTTTTATGG\n+CTCTGTTGGATGGTATCGGTTTCATTCACCATAACTGTACTCCAGAGGACCAAGCTGACA\n+TGGTCAGAAGAGTCAAGAACTATGAAAATGGGTTTATTAACAACCCTATAGTGATTTCTC\n+CAACTACGACCGTTGGTGAAGCTAAGAGCATGAAGGAAAAGTATGGATTTGCAGGCTTCC\n+CTGTCACGGCAGATGGAAAGAGAAATGCAAAGTTGGTGGGTGCCATCACCTCTCGTGATA\n+TACAATTCGTTGAGGACAACTCTTTACTCGTTCAGGATGTCATGACCAAAAACCCTGTTA\n+CCGGCGCACAAGGTATCACATTATCAGAAGGTAACGAAATTCTAAAGAAAATCAAAAAGG\n+GTAGGCTACTGGTTGTTGATGAAAAGGGTAACTTAGTTTCTATGCTTTCCCGAACTGATT\n+TAATGAAAAATCAGAAGTACCCATTAGCGTCCAAATCTGCCAACACCAAGCAACTGTTAT\n+GGGGTGCTTCTATTGGGACTATGGACGCTGATAAAGAAAGACTAAGATTATTGGTAAAAG\n+CTGGCTTGGATGTCGTCATATTGGATTCCTCTCAAGGTAACTCTATTTTCCAATTGAACA\n+TGATCAAATGGATTAAAGAAACTTTCCCAGATTTGGAAATCATTGCTGGTAACGTTGTCA\n+CCAAGGAACAAGCTGCCAATTTGATTGCTGCCGGTGCGGACGGTTTGAGAATTGGTATGG\n+GAACTGGCTCTATTTGTATTACCCAAAAAGTTATGGCTTGTGGTAGGCCACAAGGTACAG\n+CCGTCTACAACGTGTGTGAATTTGCTAACCAATTCGGTGTTCCATGTATGGCTGATGGTG\n+GTGTTCAAAAACATTGGTCATATTATTACCAAAGCTTTGGCTCTTGGTTCTTCTACTGTT\n+ATGATGGGTGGTATGTTGGCCGGTACTACCGAATCACCAGGTGAATATCTCTATCAAGAT\n+GGTAAAAGATTGAAGGCGTATCGTGGTATGGGCTCCATTGACGCCATGCAAAAGACTGGT\n+ACCAAAGGTAATGCATCTACCTCCCGTTACTTTTCCGAATCAGACAGTGTTTTGGTCGCA\n+CAAGGTGTCTCTGGCGCTGTCGTTGACAAAGGATCCATTAAGAAATTTATTCCGTACTTG\n+TACAATGGATTACAACATTCTTGTCAAGACATCGGCTGTAGGTCGTTAACTTTACTAAAG\n+GAAAATGTCCAAAGCGGTAAAGTTAGATTTGAATTCAGAACCGCTTCTGCTCAACTAGAA\n+GGTGGTGTTAATAACTTACATTCCTACGAAAAACGTTTACATAACTGAATGTTAAATGGG\n+ATCATTAATACAATAGTACTGTACGTATGGCACCTGTACATACTGCGTTATAAATGTACT\n+AATGGAATGATATATTAATATATAGTGTGTTTATACCTTATTATTGATGATTAGTATATA\n+TTTTTATATTTAGGTGATTTTAGTGGAGATTATTTGGTGGTAATTACACTAGTATACATA\n+AAATGGGTAGTGGATATTTGTATAGAAAGGGCATTACGCATGGAGTTAAGAGTATTTACA\n+TGATAATTGGGTTCCGTGATTCATTATAGATAATAAAACGTGGATAATATTGGGTGTTAT\n+AGGTAAATGGGACAGGGTATAGACCGCTGAGGCAAGTGCCGTGTATGGTGATGTGGTATG\n+GTATCGAGTACCGATGGAGTGAGAGATGGCCTTGGTGTAGAGTATTATGGCGGGTAAGTT\n+AGATGATGTATTGTTTACGTTATATTTGTTTAAATTGGATTTGTTTACATTAGATTTGTT\n+TACATTTCAATATATCAATGGAGGGTATGTAGCATTATGGTAAGTAGCACGTGGTAGATG\n+GGGATTGTAGGTGGATGGTAGGATGAGTGGTAGTGAGAGTTGGATAAGATATATTGGGCA\n+GGGGATAGATGGTTGTTGGGGTGTGGTGATGGATAGTGAGTGGATAGTGAGTGGATGGAT\n+GGTGGAGTGGGGGAATGAGACAGGGCATGGGGTGGTGAGGTAAGTGCCGTGGATTGTGAT\n+GATGGAGAGGGAGGGTAGTTGACATGGAGTTAGAATTGGGTCAGTGTTAGTGTTAGTGTT\n+AGTATTAGGGTGTGGTGTGTGGGTGTGGTGTGGGTGTGGGTGTGGGTGTGGGTGTGGGTG\n+TGGGTGTGGTGTGGTGTGTGGGTGTGGTGTGGGTGTGGTGTGTGTGGG\n' |
| b |
| diff -r 000000000000 -r 06dea02a2a39 nupop_0.1/test_nupop_pred_chr1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nupop_0.1/test_nupop_pred_chr1.txt Tue Jun 07 17:41:06 2011 -0400 |
| b |
| b'@@ -0,0 +1,230210 @@\n+Chromosome/Contig = chr1\n+Position P-start Occup N/L Affinity\n+1 0.000 0.000 0 NA\n+2 0.032 0.032 0 NA\n+3 0.840 0.872 1 NA\n+4 0.000 0.872 1 NA\n+5 0.001 0.872 1 NA\n+6 0.000 0.872 1 NA\n+7 0.019 0.891 1 NA\n+8 0.017 0.908 1 NA\n+9 0.003 0.911 1 NA\n+10 0.001 0.912 1 NA\n+11 0.000 0.912 1 NA\n+12 0.000 0.912 1 NA\n+13 0.008 0.920 1 NA\n+14 0.073 0.992 1 NA\n+15 0.000 0.993 1 NA\n+16 0.000 0.993 1 NA\n+17 0.000 0.993 1 NA\n+18 0.004 0.997 1 NA\n+19 0.000 0.997 1 NA\n+20 0.000 0.997 1 NA\n+21 0.000 0.997 1 NA\n+22 0.003 1.000 1 NA\n+23 0.000 1.000 1 NA\n+24 0.000 1.000 1 NA\n+25 0.000 1.000 1 NA\n+26 0.000 1.000 1 NA\n+27 0.000 1.000 1 NA\n+28 0.000 1.000 1 NA\n+29 0.000 1.000 1 NA\n+30 0.000 1.000 1 NA\n+31 0.000 1.000 1 NA\n+32 0.000 1.000 1 NA\n+33 0.000 1.000 1 NA\n+34 0.000 1.000 1 NA\n+35 0.000 1.000 1 NA\n+36 0.000 1.000 1 NA\n+37 0.000 1.000 1 NA\n+38 0.000 1.000 1 NA\n+39 0.000 1.000 1 NA\n+40 0.000 1.000 1 NA\n+41 0.000 1.000 1 NA\n+42 0.000 1.000 1 NA\n+43 0.000 1.000 1 NA\n+44 0.000 1.000 1 NA\n+45 0.000 1.000 1 NA\n+46 0.000 1.000 1 NA\n+47 0.000 1.000 1 NA\n+48 0.000 1.000 1 NA\n+49 0.000 1.000 1 NA\n+50 0.000 1.000 1 NA\n+51 0.000 1.000 1 NA\n+52 0.000 1.000 1 NA\n+53 0.000 1.000 1 NA\n+54 0.000 1.000 1 NA\n+55 0.000 1.000 1 NA\n+56 0.000 1.000 1 NA\n+57 0.000 1.000 1 NA\n+58 0.000 1.000 1 NA\n+59 0.000 1.000 1 NA\n+60 0.000 1.000 1 NA\n+61 0.000 1.000 1 NA\n+62 0.000 1.000 1 NA\n+63 0.000 1.000 1 NA\n+64 0.000 1.000 1 NA\n+65 0.000 1.000 1 NA\n+66 0.000 1.000 1 NA\n+67 0.000 1.000 1 NA\n+68 0.000 1.000 1 NA\n+69 0.000 1.000 1 NA\n+70 0.000 1.000 1 NA\n+71 0.000 1.000 1 NA\n+72 0.000 1.000 1 NA\n+73 0.000 1.000 1 NA\n+74 0.000 1.000 1 2.843\n+75 0.000 1.000 1 2.839\n+76 0.000 1.000 1 2.815\n+77 0.000 1.000 1 2.814\n+78 0.000 1.000 1 2.809\n+79 0.000 1.000 1 2.794\n+80 0.000 1.000 1 2.775\n+81 0.000 1.000 1 2.740\n+82 0.000 1.000 1 2.745\n+83 0.000 1.000 1 2.720\n+84 0.000 1.000 1 2.706\n+85 0.000 1.000 1 2.703\n+86 0.000 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