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input.f90
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2195 lines (1773 loc) · 58.9 KB
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SUBROUTINE Add_DNA(start,finish,reverse,gf)
!
! Adds a block of nucleotides to the growing sequence
!
USE dnaworks_data
USE dnaworks_test
IMPLICIT NONE
INTEGER :: i,j,k,start,finish,first
CHARACTER(LEN=1) :: nt
INTEGER,EXTERNAL :: NT2Int
LOGICAL :: reverse,done,gf
CHARACTER(LEN=9999) :: tempDNAseq
done=.FALSE.
IF (TEST0) PRINT *,"Add_DNA" !TEST0
NumberOfSeq=NumberOfSeq+1
! degenerate sequences are allowed for nucleotides... to a point
DO i=start,finish
DO j=1,LEN_TRIM(InputArrayUC(i))
nt=InputArrayUC(i)(j:j)
IF (nt.eq.'A'.or.nt.eq.'C'.or.nt.eq.'G'.or.nt.eq.'T'.or.nt.eq.'N'.or. &
nt.eq.'M'.or.nt.eq.'R'.or.nt.eq.'W'.or.nt.eq.'S'.or.nt.eq.'Y'.or. &
nt.eq.'K'.or.nt.eq.'B'.or.nt.eq.'D'.or.nt.eq.'H'.or.nt.eq.'V') THEN
DNAlen=DNAlen+1
INITlen=INITlen+1
INIT2Seq(INITlen)=NumberOfSeq
IF (DNAlen.gt.MaxDNAlen) CALL Stop_Program("Too many nucleotides.")
CurrDNA%DNAseq(DNAlen:DNAlen)=nt
INITseq(INITlen:INITlen)=nt
ORIGDNAseq(DNAlen:DNAlen)=nt
CurrDNA%NUMseq(DNAlen)=NT2Int(nt) ! if the nt is degenerate, this is undefined
IF (.not.done) THEN
first = DNAlen
done = .TRUE.
END IF
END IF
IF (nt.eq.'M'.or.nt.eq.'R'.or.nt.eq.'W'.or.nt.eq.'S'.or.nt.eq.'Y'.or. &
nt.eq.'K'.or.nt.eq.'B'.or.nt.eq.'D'.or.nt.eq.'H'.or.nt.eq.'V'.or. &
nt.eq.'N') THEN
IF (.not.gf) CALL Stop_Program("Degenerate sequences must be gapfixed.")
NumDegPos=NumDegPos+1
DegPos(NumDegPos)=DNAlen
CurrDNA%Degen(DNAlen) = .TRUE.
! determine degenerate index and assign it
DO k=1,11
IF (DegenSeq(k)%DegNT.eq.nt) THEN
CurrDNA%DegenNum(DNAlen) = k
END IF
END DO
ELSE
CurrDNA%Degen(DNAlen) = .FALSE.
END IF
END DO
END DO
! reverse the nucleotide sequence if desired
IF (reverse) THEN
SeqReverse(NumberOfSeq)=.TRUE.
CALL RevComplStr(CurrDNA%DNAseq(first:DNAlen))
DO i=first,DNAlen
CurrDNA%NUMseq(i)=NT2Int(CurrDNA%DNAseq(i:i))
END DO
END IF
! assign the GapFix array if the positions need to be in a gap
IF (gf) THEN
SeqGapFix(NumberOfSeq)=.TRUE.
DO i=first,DNAlen
CurrDNA%GapFixPos(i)=.TRUE.
END DO
END IF
END SUBROUTINE Add_DNA
SUBROUTINE Add_Previous
USE dnaworks_data
USE dnaworks_test
IMPLICIT NONE
CHARACTER(LEN=256) :: a1,a2,a3,a4,a5,a6
INTEGER,EXTERNAL :: StrToInt
REAL,EXTERNAL :: StrToReal
LOGICAL,EXTERNAL :: Read_Old_Logfile
INTEGER :: ierr,i,j,k,i1,i2
IF (TEST0) PRINT *,"Add_Previous" !TEST0
! PREVIOUS
! MutantRun
! PrevTrial
prev: DO i=1,InputArrayNum
a1=""
a2=""
a3=""
IF (INDEX(InputArrayUC(i),'PREVIOUS').eq.1) THEN
READ(InputArray(i),*,IOSTAT=ierr) a1,a2,a3 ! are there three lines?
IF (ierr.eq.0) THEN
IF ((LEN_TRIM(a3)).ne.0) oldlogfile=a3
ELSE
READ(InputArrayUC(i),*,IOSTAT=ierr) a1,a2
IF (ierr.ne.0) EXIT prev
END IF
PrevTrial=StrToInt(a2)
IF (PrevTrial.gt.0) THEN
MutantRun=.TRUE.
! try to read the oldlogfile -- if successful, replace all the relevant info
IF (Read_Old_Logfile(PrevTrial)) THEN
FinalScore(1)%Oligo=OligoLen
FinalScore(1)%MeltT=MeltTemp
TotalNumberOfSolutions=1
WRITE(a4,FMT='(i3)') PrevTrial
a4=TRIM(a4)
a4=ADJUSTL(a4)
i2=LEN_TRIM(jobname)
j=LEN_TRIM(OLDjobname)
k=LEN_TRIM(a4)
jobname=jobname(1:i2)//' (using trial '//a4(1:k)//' parameters from previous job '//OLDjobname(1:j)//')'
END IF
ELSE
PrevTrial=0
END IF
EXIT prev
END IF
END DO prev
END SUBROUTINE Add_Previous
SUBROUTINE Add_Protein(start,finish,reverse,gf)
!
! Adds residue to PROTseq, translates protein, fills in growing arrays
!
USE dnaworks_data
USE dnaworks_test
IMPLICIT NONE
INTEGER :: i,j,k,n,x,start,finish,z,first,last,tempDNAlen,tempPROTlen
INTEGER :: pos1,pos2,pos3
REAL :: rand
LOGICAL :: no_codons
LOGICAL :: done
LOGICAL :: reverse,gf
INTEGER,EXTERNAL :: NT2Int
CHARACTER(LEN=3) :: tempCodonSeq
done=.FALSE.
tempDNAlen=0
tempPROTlen=0
IF (TEST0) PRINT *,"Add_Protein" !TEST0
! first get the basic sequence and amino acid type
DO i=start,finish
DO z=1,LEN_TRIM(InputArrayUC(i))
chk1: DO j=1,21
IF (InputArrayUC(i)(z:z).eq.AAT(j)%AA1) THEN
! Add the residue to the protein sequence
PROTlen=PROTlen+1
tempPROTlen=tempPROTlen+1
tempDNAlen=tempDNAlen+3
IF (PROTlen.gt.MaxPROTlen) CALL Stop_Program("Too many protein residues.")
PROTseq(PROTlen:PROTlen)=AAT(j)%AA1
prot2aa(PROTlen)=j
! Build up the initial sequence for logfile output
INITlen=INITlen+1
INITseq(INITlen:INITlen)=AAT(j)%AA1
! Increment NumberOfChains and prot2chain array
IF (.not.done) THEN
NumberOfChains=NumberOfChains+1
NumberOfSeq=NumberOfSeq+1
first = PROTlen
IF (reverse) ChainReverse(NumberOfChains)=.TRUE.
IF (reverse) SeqReverse(NumberOfSeq)=.TRUE.
IF (gf) ChainGapFix(NumberOfChains)=.TRUE.
IF (gf) SeqGapFix(NumberOfSeq)=.TRUE.
SeqIsProt(NumberOfSeq)=.TRUE.
END IF
prot2chain(PROTlen)=NumberOfChains
INIT2Seq(INITlen)=NumberOfSeq
! Next residue, please
done=.TRUE.
EXIT chk1
END IF
END DO chk1
END DO
END DO
last=PROTlen
j=0
! now create the links between DNA sequence and PROT sequence
DO i=first,last
j=j+3
! Either choose the codon with the highest frequency
k = 1
! or choose the codon randomly unless the codon is not allowed
IF (CodonRandom) THEN
CALL RANDOM_NUMBER(rand)
k=(INT(rand*(AAT(prot2aa(i))%NumOfActiveCodons)))+1
END IF
tempCodonSeq=CFT(AAT(prot2aa(i))%Codon(k))%Seq
! Increment mutPROT2prot array
IF (AAT(prot2aa(i))%NumOfActiveCodons.gt.1) THEN
mutPROTnum = mutPROTnum+1
mutPROT2prot(mutPROTnum) = i
END IF
! Fill prot2cod arrays
CurrDNA%prot2cod(i) = AAT(prot2aa(i))%Codon(k)
! If reverse is true, put protein in backward
IF (.not.reverse) THEN
pos1=DNAlen+j-2
pos2=DNAlen+j-1
pos3=DNAlen+j
ELSE
pos1=DNAlen+tempDNAlen-j+1
pos2=DNAlen+tempDNAlen-j+2
pos3=DNAlen+tempDNAlen-j+3
CALL RevComplStr(tempCodonSeq)
END IF
! Fill prot2nt, nt2aa, nt2prot, and prot2nt arrays
nt2aa(pos2) = prot2aa(i)
prot2nt(i) = pos2
nt2prot(pos1) = i
nt2prot(pos2) = i
nt2prot(pos3) = i
! Insert codon into the DNA sequence.
CurrDNA%DNAseq(pos1:pos3)=tempCodonSeq
! Fill nt2codon arrays
CurrDNA%nt2cod(pos2) = AAT(prot2aa(i))%Codon(k)
! Fill the numerical sequence array
CurrDNA%NUMseq(pos1)=NT2Int(CurrDNA%DNAseq(pos1:pos1))
CurrDNA%NUMseq(pos2)=NT2Int(CurrDNA%DNAseq(pos2:pos2))
CurrDNA%NUMseq(pos3)=NT2Int(CurrDNA%DNAseq(pos3:pos3))
! Fill the GapFixPos array
IF (gf) THEN
CurrDNA%GapFixPos(pos1) = .TRUE.
CurrDNA%GapFixPos(pos2) = .TRUE.
CurrDNA%GapFixPos(pos3) = .TRUE.
END IF
END DO
DNAlen=DNAlen+tempDNAlen
END SUBROUTINE Add_Protein
SUBROUTINE Default_Param
!
USE dnaworks_data
USE dnaworks_test
IMPLICIT NONE
INTEGER :: i,j,k
CHARACTER(LEN=63) :: a,b
CHARACTER(LEN=192) :: c
INTEGER,EXTERNAL :: CurrentTimeSeconds
INTEGER :: values(8)
CHARACTER(LEN=8) :: date
CHARACTER(LEN=10) :: time
CHARACTER(LEN=5) :: zone
INTEGER,EXTERNAL :: NT2Int
IF (TEST0) PRINT *,"Default_Param" !TEST0
a='ACDEFGHIKLMNPQRSTVWXY '
b='AlaCysAspGluPheGlyHisIleLysLeuMetAsnProGlnArgSerThrValTrpEndTyr'
c='TTTTCTTATTGTTTCTCCTACTGCTTATCATAATGATTGTCGTAGTGGCTTCCTCATCGTCTCC&
&CCCACCGCCTACCACAACGACTGCCGCAGCGGATTACTAATAGTATCACCAACAGCATAACAAA&
&AAGAATGACGAAGAGGGTTGCTGATGGTGTCGCCGACGGCGTAGCAGAAGGAGTGGCGGAGGGG'
! Initialize the arrays
DO i=1,9999
nt2aa(i) = 0
CurrDNA%nt2cod(i) = 0
CurrDNA%GapFixPos(i) = .FALSE.
END DO
DO i=1,21
j=((i-1)*3)+1
AAT(i)%AA1=a(i:i) ! Assign One Letter Aa values
AAT(i)%AA3=b(j:j+2) ! Assign Three Letter Aa values
AAT(i)%NumOfCodons=0
AAT(i)%NumOfActiveCodons=0
AAT(i)%NumberSum=0
DO k=1,10
AAT(i)%Codon(k)=0
AAT(i)%Freq(k)=0
END DO
END DO
DO i=1,64
j=((i-1)*3)+1
CFT(i)%Seq=c(j:j+2)
CFT(i)%SeqRC(1:3)=c(j:j+2)
CALL RevComplStr(CFT(i)%SeqRC(1:3))
CFT(i)%Check=.TRUE. ! all are true by default
CFT(i)%AA1=''
CFT(i)%AA3=''
CFT(i)%Freq=0
CFT(i)%Number=0
DO k=1,3
CFT(i)%num(k)=NT2Int(CFT(i)%Seq(k:k))
CFT(i)%numRC(k)=NT2Int(CFT(i)%SeqRC(k:k))
END DO
END DO
DO i=1,99
ChainReverse(i)=.FALSE.
ChainGapFix(i)=.FALSE.
SeqReverse(i)=.FALSE.
SeqGapFix(i)=.FALSE.
SeqIsProt(i)=.FALSE.
END DO
! Degenerate sequences
DegenSeq(1)%DegNT = 'K'
DegenSeq(1)%NumOfNT = 2
DegenSeq(1)%Seq(1) = 'G'
DegenSeq(1)%NumSeq(1) = NT2Int(DegenSeq(1)%Seq(1))
DegenSeq(1)%Seq(2) = 'T'
DegenSeq(1)%NumSeq(2) = NT2Int(DegenSeq(1)%Seq(2))
DegenSeq(2)%DegNT = 'M'
DegenSeq(2)%NumOfNT = 2
DegenSeq(2)%Seq(1) = 'A'
DegenSeq(2)%NumSeq(1) = NT2Int(DegenSeq(2)%Seq(1))
DegenSeq(2)%Seq(2) = 'C'
DegenSeq(2)%NumSeq(2) = NT2Int(DegenSeq(2)%Seq(2))
DegenSeq(3)%DegNT = 'R'
DegenSeq(3)%NumOfNT = 2
DegenSeq(3)%Seq(1) = 'A'
DegenSeq(3)%NumSeq(1) = NT2Int(DegenSeq(3)%Seq(1))
DegenSeq(3)%Seq(2) = 'G'
DegenSeq(3)%NumSeq(2) = NT2Int(DegenSeq(3)%Seq(2))
DegenSeq(4)%DegNT = 'S'
DegenSeq(4)%NumOfNT = 2
DegenSeq(4)%Seq(1) = 'C'
DegenSeq(4)%NumSeq(1) = NT2Int(DegenSeq(4)%Seq(1))
DegenSeq(4)%Seq(2) = 'G'
DegenSeq(4)%NumSeq(2) = NT2Int(DegenSeq(4)%Seq(2))
DegenSeq(5)%DegNT = 'W'
DegenSeq(5)%NumOfNT = 2
DegenSeq(5)%Seq(1) = 'A'
DegenSeq(5)%NumSeq(1) = NT2Int(DegenSeq(5)%Seq(1))
DegenSeq(5)%Seq(2) = 'T'
DegenSeq(5)%NumSeq(2) = NT2Int(DegenSeq(5)%Seq(2))
DegenSeq(6)%DegNT = 'Y'
DegenSeq(6)%NumOfNT = 2
DegenSeq(6)%Seq(1) = 'C'
DegenSeq(6)%NumSeq(1) = NT2Int(DegenSeq(6)%Seq(1))
DegenSeq(6)%Seq(2) = 'T'
DegenSeq(6)%NumSeq(2) = NT2Int(DegenSeq(6)%Seq(2))
DegenSeq(7)%DegNT = 'B'
DegenSeq(7)%NumOfNT = 3
DegenSeq(7)%Seq(1) = 'C'
DegenSeq(7)%NumSeq(1) = NT2Int(DegenSeq(7)%Seq(1))
DegenSeq(7)%Seq(2) = 'G'
DegenSeq(7)%NumSeq(2) = NT2Int(DegenSeq(7)%Seq(2))
DegenSeq(7)%Seq(3) = 'T'
DegenSeq(7)%NumSeq(3) = NT2Int(DegenSeq(7)%Seq(3))
DegenSeq(8)%DegNT = 'D'
DegenSeq(8)%NumOfNT = 3
DegenSeq(8)%Seq(1) = 'A'
DegenSeq(8)%NumSeq(1) = NT2Int(DegenSeq(8)%Seq(1))
DegenSeq(8)%Seq(2) = 'C'
DegenSeq(8)%NumSeq(2) = NT2Int(DegenSeq(8)%Seq(2))
DegenSeq(8)%Seq(3) = 'T'
DegenSeq(8)%NumSeq(3) = NT2Int(DegenSeq(8)%Seq(3))
DegenSeq(9)%DegNT = 'H'
DegenSeq(9)%NumOfNT = 3
DegenSeq(9)%Seq(1) = 'A'
DegenSeq(9)%NumSeq(1) = NT2Int(DegenSeq(9)%Seq(1))
DegenSeq(9)%Seq(2) = 'C'
DegenSeq(9)%NumSeq(2) = NT2Int(DegenSeq(9)%Seq(2))
DegenSeq(9)%Seq(3) = 'T'
DegenSeq(9)%NumSeq(3) = NT2Int(DegenSeq(9)%Seq(3))
DegenSeq(10)%DegNT = 'V'
DegenSeq(10)%NumOfNT = 3
DegenSeq(10)%Seq(1) = 'A'
DegenSeq(10)%NumSeq(1) = NT2Int(DegenSeq(10)%Seq(1))
DegenSeq(10)%Seq(2) = 'C'
DegenSeq(10)%NumSeq(2) = NT2Int(DegenSeq(10)%Seq(2))
DegenSeq(10)%Seq(3) = 'G'
DegenSeq(10)%NumSeq(3) = NT2Int(DegenSeq(10)%Seq(3))
DegenSeq(11)%DegNT = 'N'
DegenSeq(11)%NumOfNT = 4
DegenSeq(11)%Seq(1) = 'A'
DegenSeq(11)%NumSeq(1) = NT2Int(DegenSeq(11)%Seq(1))
DegenSeq(11)%Seq(2) = 'C'
DegenSeq(11)%NumSeq(2) = NT2Int(DegenSeq(11)%Seq(2))
DegenSeq(11)%Seq(3) = 'G'
DegenSeq(11)%NumSeq(3) = NT2Int(DegenSeq(11)%Seq(3))
DegenSeq(11)%Seq(4) = 'T'
DegenSeq(11)%NumSeq(4) = NT2Int(DegenSeq(11)%Seq(4))
END SUBROUTINE Default_Param
SUBROUTINE Fix_Codons
!
! Determines if 64 codons are present, sorts frequencies, and assigns check
!
USE dnaworks_data
USE dnaworks_test
IMPLICIT NONE
INTEGER :: i,j,k,n
REAL :: x,y
IF (TEST0) PRINT *,"Fix_Codons" !TEST0
! Stop if not enough codons are read in
j=0
DO i=1,64
IF (CFT(i)%Freq.ne.0) j=j+1
END DO
IF (j.ne.64) CALL Stop_Program("There are too few codons.")
! Sort the frequencies from highest to lowest for each AA
! (i.e., AAT(i)%Freq(1) = highest, AAT(i)%Freq(..NumOfCodons) = lowest
! This is a change --
! To sort from lowest to highest, switch lt to gt in comparison 7/27/05
DO i=1,21
IF (AAT(i)%NumOfCodons.gt.1) THEN
j=AAT(i)%NumOfCodons-1
DO n=j,1,-1
DO k=1,n
IF (AAT(i)%Freq(k).lt.AAT(i)%Freq(k+1)) THEN
CALL RealSwap(AAT(i)%Freq(k),AAT(i)%Freq(k+1))
CALL IntSwap(AAT(i)%Codon(k),AAT(i)%Codon(k+1))
END IF
END DO
END DO
END IF
END DO
! Assign CFT%Check values according to SeqOptimTol
DO i=1,21
DO j=1,AAT(i)%NumOfCodons
! If the SeqOptimToler is higher than the particular codon frequency for that
! amino acid, deactivate that codon
! Unless SeqOptimToler equals 100, which allows scoring and all codons to
! be used.
x=AAT(i)%Freq(j)*100
y=REAL(SeqOptimToler)
IF (SeqOptimToler.lt.100) THEN
IF (AAT(i)%Freq(j)*100.lt.SeqOptimToler) THEN
CFT(AAT(i)%Codon(j))%Check=.FALSE.
END IF
END IF
END DO
! However, keep the two highest frequency codons available for generating DNA
CFT(AAT(i)%Codon(1))%Check=.TRUE.
IF (AAT(i)%NumofCodons.gt.1.and.(.not.CodonStrict)) THEN
CFT(AAT(i)%Codon(2))%Check=.TRUE.
END IF
END DO
! Assign NumOfActiveCodons
DO i=1,21
DO j=1,AAT(i)%NumOfCodons
IF (CFT(AAT(i)%Codon(j))%Check) THEN
AAT(i)%NumOfActiveCodons=AAT(i)%NumOfActiveCodons+1
END IF
END DO
END DO
END SUBROUTINE Fix_Codons
SUBROUTINE Read_Codon_Line(AA3,codon,y,x)
!
! This subroutine reads in a single line of codon frequency file (GCG format).
USE dnaworks_data
USE dnaworks_test
IMPLICIT NONE
INTEGER :: i,j,k
REAL :: freq,number
CHARACTER(LEN=5) :: AA3
CHARACTER(LEN=5) :: codon
CHARACTER(LEN=5) :: x
CHARACTER(LEN=12) :: y
REAL,EXTERNAL :: StrToReal
IF (TEST1) PRINT *,"Read_Codon_Line"
IF (AA3.ne.''.and.codon.ne.''.and.x.ne.'') THEN
! fix the input
AA3=ADJUSTL(AA3)
codon=ADJUSTL(codon)
freq=StrToReal(x)
number=StrToReal(y)
IF (AA3(1:3).eq."Stp") AA3(1:3) = "End"
IF (AA3(1:3).eq."Sto") AA3(1:3) = "End"
IF (AA3(1:3).eq."STO") AA3(1:3) = "End"
! Load the temporary variables into program input variables
loop2: DO j=1,64
IF (codon(1:3).eq.CFT(j)%Seq) THEN
loop3: DO k=1,21
IF (AA3(1:3).eq.AAT(k)%AA3) THEN
AAT(k)%NumOfCodons=AAT(k)%NumOfCodons+1
AAT(k)%Codon(AAT(k)%NumOfCodons)=j
AAT(k)%Freq(AAT(k)%NumOfCodons)=freq
AAT(k)%NumberSum=AAT(k)%NumberSum+number
CFT(j)%AA3 = AA3(1:3)
CFT(j)%AA1 = AAT(k)%AA1
CFT(j)%Freq = freq
CFT(j)%Number = number
EXIT loop3
END IF
END DO loop3
EXIT loop2
END IF
END DO loop2
END IF
END SUBROUTINE Read_Codon_Line
SUBROUTINE Read_Codons
USE dnaworks_data
USE dnaworks_test
IMPLICIT NONE
CHARACTER(LEN=256) :: a1,a2,a3,a4,a5,a6 ! throw away strings
INTEGER,EXTERNAL :: StrToInt
REAL,EXTERNAL :: StrToReal
INTEGER :: ierr,length,i,j,k,n,start,finish
INTEGER :: i1,i2,i3,i4,i5,i6 ! throw away integers
IF (TEST0) PRINT *,"Read_Codons" !TEST0
main: DO k=1,InputArrayNum
! read an individual line, trim it, and change to upper case
a1=""
a2=""
a3=""
a4=""
a5=""
! CODON frequency table
a1=InputArrayUC(k)
IF (INDEX(a1,'CODON').eq.1) THEN
IF ((INDEX(a1,'ECOLI2')).gt.0) THEN
CALL Read_Organism_CFT('ecoli2')
ELSE IF ((INDEX(a1,'COLI')).gt.0.or.(INDEX(a1,'ESCHER')).gt.0) THEN
CALL Read_Organism_CFT('ecoli ')
ELSE IF ((INDEX(a1,'ELEGAN')).gt.0.or.(INDEX(a1,'CAENOR')).gt.0) THEN
CALL Read_Organism_CFT('celega')
ELSE IF ((INDEX(a1,'MELANO')).gt.0.or.(INDEX(a1,'DROSOP')).gt.0) THEN
CALL Read_Organism_CFT('drosop')
ELSE IF ((INDEX(a1,'SAPIEN')).gt.0.or.(INDEX(a1,'HOMO S')).gt.0) THEN
CALL Read_Organism_CFT('homosa')
ELSE IF ((INDEX(a1,'MUSCUL')).gt.0.or.(INDEX(a1,'MUS MU')).gt.0) THEN
CALL Read_Organism_CFT('musmus')
ELSE IF ((INDEX(a1,'PASTOR')).gt.0.or.(INDEX(a1,'PICHIA')).gt.0) THEN
CALL Read_Organism_CFT('pastor')
ELSE IF ((INDEX(a1,'NORVEG')).gt.0.or.(INDEX(a1,'RATTUS')).gt.0) THEN
CALL Read_Organism_CFT('rattus')
ELSE IF ((INDEX(a1,'CEREVE')).gt.0.or.(INDEX(a1,'SACCHA')).gt.0) THEN
CALL Read_Organism_CFT('saccho')
ELSE IF ((INDEX(a1,'LAEVIS')).gt.0.or.(INDEX(a1,'XENOPU')).gt.0) THEN
CALL Read_Organism_CFT('xenopu')
ELSE
Organism="USER INPUT"
! Find end of codon block
start=k+1
seek: DO j=k,InputArrayNum
IF (INDEX(InputArrayUC(j),'//').gt.0) THEN
finish=j-1
EXIT seek ! end of codon block
END IF
END DO seek
codo: DO j=start,finish
READ(InputArray(j),*,IOSTAT=ierr) a1,a2,a3,a4,a5
IF (ierr.ne.0) CYCLE codo
CALL Read_Codon_Line(a1,a2,a3,a5)
END DO codo
END IF
EXIT main
END IF
END DO main
! Make sure frequencies are set
k=0
DO i=1,64
IF (CFT(i)%Freq.eq.0) THEN
k=k+1
END IF
END DO
IF (k.eq.64) THEN
DO i=1,21
DO j=1,AAT(i)%NumOfCodons
AAT(i)%Freq(j)=CFT(AAT(i)%Codon(j))%Number/AAT(i)%NumberSum
CFT(AAT(i)%Codon(j))%Freq=CFT(AAT(i)%Codon(j))%Number/AAT(i)%NumberSum
END DO
END DO
END IF
! Make sure the input makes sense
k=0
DO i=1,21
k=k+AAT(i)%NumOfCodons
END DO
! Default CFT is E. coli Class II
IF (k.ne.64) THEN
DO i=1,21
AAT(i)%NumOfCodons=0
AAT(i)%NumOfActiveCodons=0
END DO
CALL Read_Organism_CFT('ecoli2')
END IF
CALL Fix_Codons
END SUBROUTINE Read_Codons
SUBROUTINE Read_Input
USE dnaworks_data
USE dnaworks_test
IMPLICIT NONE
! Here are the things needed for input:
!
! OligoLenHi user input oligo size (upper limit)
! OligoLenLo user input oligo size (lower limit)
! MeltTempHi Ideal melting temperature (upper limit)
! MeltTempLo Ideal melting temperature (lower limit)
! MeltTol Tolerance for melting temperature deviation
! SeqOptimToler Lowest allowed codon frequency
! NumberOfSolutions
! OligoConcTemp in nM
! SodiumConc in mM
! MgConc in mM
! TBIOSwitch off or on
! RepLen determines the size of repeats to minimize
! MPLn length of misprimes
! MaxNonId maximum number of non-identical nts in misprime
! MPTip identical tip of the misprime, in nts
! PrevTrial number of previous run
CHARACTER(LEN=256) :: line
CHARACTER(LEN=256) :: a1,a2,a3,a4,a5,a6 ! throw away strings
CHARACTER(LEN=3) :: temp
INTEGER,EXTERNAL :: StrToInt
REAL,EXTERNAL :: StrToReal
LOGICAL,EXTERNAL :: Read_Old_Logfile
LOGICAL :: reverse
LOGICAL :: gf
LOGICAL :: skipdquote,skipsquote
INTEGER :: ierr,length,i,j,k,n,start,finish
INTEGER :: i1,i2,i3,i4,i5,i6 ! throw away integers
IF (TEST0) PRINT *,"Read_Input" !TEST0
OPEN (UNIT=inputnum,FILE=inputfile,STATUS='old',IOSTAT=ierr)
IF (ierr.ne.0) THEN
WRITE(UNIT=console,FMT="('')")
WRITE(UNIT=console,FMT="('Where is the inputfile ""',a,'""?')") inputfile(1:LEN_TRIM(inputfile))
PRINT *,""
PRINT *,"Usage: dnaworks [ inputfile ] [ -help ]"
PRINT *,""
STOP
END IF
! Read the input file into the InputArray array
i1=0
reading: DO
READ(UNIT=inputnum,FMT='(a)',IOSTAT=ierr) line
IF (ierr.ne.0) EXIT reading ! dump out if end of file reached
i1=i1+1
! Take out comments
IF ((INDEX(line,'!')).gt.0) line(INDEX(line,'!'):256)=''
IF ((INDEX(line,'#')).gt.0) line(INDEX(line,'#'):256)=''
InputArray(i1) = line
! Take out quoted strings and create uppercase array as well
skipsquote=.FALSE.
skipdquote=.FALSE.
DO i=1,LEN_TRIM(line)
IF (skipsquote) THEN
IF (line(i:i).eq."'") THEN
line(i:i)=' '
skipsquote=.FALSE.
ELSE
line(i:i)=' '
END IF
ELSE
IF (line(i:i).eq."'") THEN
line(i:i)=' '
skipsquote=.TRUE.
END IF
END IF
IF (skipdquote) THEN
IF (line(i:i).eq.'"') THEN
line(i:i)=' '
skipdquote=.FALSE.
ELSE
line(i:i)=' '
END IF
ELSE
IF (line(i:i).eq.'"') THEN
line(i:i)=' '
skipdquote=.TRUE.
END IF
END IF
END DO
InputArrayUC(i1) = line
CALL ToUpperCase(InputArrayUC(i1))
END DO reading
CLOSE (UNIT=inputnum)
InputArrayNum=i1
! It is very important to read these in order...
CALL Read_Parameters
CALL Read_Codons
CALL Read_Patterns
! step through the input
main: DO i=1,InputArrayNum
! NUCLEOTIDE
IF (INDEX(InputArrayUC(i),'NUCLEOTIDE').eq.1) THEN
reverse=.FALSE.
gf=.FALSE.
IF (INDEX(InputArrayUC(i),'REVERSE').gt.0) reverse=.TRUE.
IF (INDEX(InputArrayUC(i),'GAPFIX').gt.0) gf=.TRUE.
IF (INDEX(InputArrayUC(i),'GAPFIX').gt.0) GapFix=.TRUE.
start=i+1
seek1: DO j=i,InputArrayNum
IF (INDEX(InputArray(j),'//').gt.0) THEN
finish=j
EXIT seek1
END IF
END DO seek1
CALL Add_DNA(start,finish,reverse,gf)
END IF
! PROTEIN
IF (INDEX(InputArrayUC(i),'PROTEIN').eq.1) THEN
reverse=.FALSE.
gf=.FALSE.
IF (INDEX(InputArrayUC(i),'REVERSE').gt.0) reverse=.TRUE.
IF (INDEX(InputArrayUC(i),'GAPFIX').gt.0) gf=.TRUE.
IF (INDEX(InputArrayUC(i),'GAPFIX').gt.0) GapFix=.TRUE.
start=i+1
seek2: DO j=i,InputArrayNum
IF (INDEX(InputArrayUC(j),'//').gt.0) THEN
finish=j
EXIT seek2
END IF
END DO seek2
CALL Add_Protein(start,finish,reverse,gf)
END IF
END DO main
! After reading in everything else, find if prev trial is set
CALL Add_Previous
! Don't forget to create OligoCorr and SaltCorr!
CALL TmCorrect
END SUBROUTINE Read_Input
SUBROUTINE Read_Old_Codons
USE dnaworks_data
USE dnaworks_test
IMPLICIT NONE
INTEGER :: ierr,i,j,k,m,z
CHARACTER(LEN=100) :: line
INTEGER,EXTERNAL :: StrToInt
REAL,EXTERNAL :: StrToReal
TYPE(KnownCodon) :: tempCFT(64) ! Codon Frequency Table
TYPE(KnownAA) :: tempAAT(21) ! Amino Acid Table
CHARACTER(LEN=10) :: a1(4),a2(4)
REAL :: r1(4),r2(4)
INTEGER :: i1(4),i2(4)
LOGICAL :: oldCodons=.FALSE. ! are old codons present?
IF (TEST0) PRINT *,'Read_Old_Codons'
OPEN (UNIT=oldlognum,FILE=oldlogfile,STATUS='old',IOSTAT=ierr)
! -- CODON FREQUENCY TABLE --
main: DO
READ(UNIT=oldlognum,FMT='(A100)',IOSTAT=ierr) line
IF (ierr.ne.0) EXIT main
IF (INDEX(line,'CODON FREQUENCY TABLE').gt.0) THEN
! PRINT *,'codon input'
oldCodons=.TRUE.
Organism=line((LogfileOffset+36):(LogfileOffset+65))
m=0
codon: DO z=1,22
READ(UNIT=oldlognum,FMT='(A100)',IOSTAT=ierr) line
IF (ierr.ne.0) EXIT main
READ(line,*,IOSTAT=ierr) a1(1),a2(1),r1(1),a1(2),a2(2),r1(2),a1(3),a2(3),r1(3),a1(4),a2(4),r1(4)
IF (ierr.ne.0) CYCLE codon
IF (m.eq.64) EXIT codon
DO i=1,4
m=m+1
tempCFT(m)%Seq=a1(i)(1:3)
tempCFT(m)%AA1=a2(i)(1:1)
IF (r1(i).le.0) r1(i)=0.001
tempCFT(m)%Freq=r1(i)
! PRINT *,m,tempCFT(m)%Seq,tempCFT(m)%Freq
END DO
END DO codon
END IF
! pull out other AAT and CFT information
! -- ACTIVE CODONS --
IF (INDEX(line,'ACTIVE CODONS').gt.0) THEN
! PRINT *,'active codons'
m=0
amino: DO i=1,31
READ(UNIT=oldlognum,FMT='(A100)',IOSTAT=ierr) line
IF (ierr.ne.0) EXIT main
READ(line,*,IOSTAT=ierr) a1(1),a2(1),i1(1),i2(1),r1(1),r2(1)
IF (ierr.ne.0) CYCLE amino
m=m+1
tempAAT(m)%AA1=a1(1)(1:1)
tempAAT(m)%AA3=a2(1)(1:3)
! PRINT *,m,tempAAT(m)%AA1
END DO amino
END IF
END DO main
CLOSE (UNIT=oldlognum)
! PRINT *,'old log closed'
! stupid: if previous run was DNA only, set CFT to E. coli Class II
IF (.not.oldCodons) THEN
DO i=1,21
AAT(i)%NumOfCodons=0
AAT(i)%NumOfActiveCodons=0
END DO
CALL Read_Organism_CFT('ecoli2')
ELSE
! regenerate CFT and AAT information
DO i=1,21
AAT(i)=tempAAT(i)
AAT(i)%NumOfCodons=0
AAT(i)%NumOfActiveCodons=0
END DO
DO i=1,64
CFT(i)=tempCFT(i)
CFT(i)%SeqRC(1:3)=CFT(i)%Seq(1:3)
CALL RevComplStr(CFT(i)%SeqRC(1:3))
inner: DO j=1,21
IF (CFT(i)%AA1.eq.AAT(j)%AA1) THEN
AAT(j)%NumOfCodons=AAT(j)%NumOfCodons+1
AAT(j)%Codon(AAT(j)%NumOfCodons)=i
CFT(i)%AA3=AAT(j)%AA3
AAT(j)%Freq(AAT(j)%NumOfCodons)=CFT(i)%Freq
! PRINT *,i,j,AAT(j)%AA1,CFT(i)%seq,CFT(i)%Freq
EXIT inner
END IF
END DO inner
END DO
! assign numerical values to codon sequence
DO i=1,64
DO k=1,3
SELECT CASE(CFT(i)%Seq(k:k))
CASE('A')
CFT(i)%num(k)=-1
CASE('T')
CFT(i)%num(k)=1
CASE('C')
CFT(i)%num(k)=-3
CASE('G')
CFT(i)%num(k)=3
END SELECT
END DO
END DO
END IF
CALL Fix_Codons
END SUBROUTINE Read_Old_Codons
SUBROUTINE Read_Old_DNA(str)
USE dnaworks_data
USE dnaworks_test
IMPLICIT NONE
INTEGER :: ierr,begin,tempDNAlen,i,j,ne,ns,nlines
CHARACTER(LEN=100) :: line
CHARACTER(LEN=22) :: str
CHARACTER(LEN=9999) :: tempDNAseq