414 lines
16 KiB
FortranFixed
414 lines
16 KiB
FortranFixed
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subroutine formid(seqid,seq,nseq,nmax,used)
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c RESEARCHER: M. ZUKER
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c JUN 1986
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c DS TUDHOPE
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c WRITTEN TO WORK ON VAX-11-750 UNDER VMS4.3 USING STANDARD F-77
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c #### NOTE #### USE OF CARRIAGE CONTROL LINE FEED SUPPRESSION
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c IS USED IN THIS PROGRAM AND IS NOT STANDARD
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c FORTRAN-77
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c SEE '$' IN FORMAT STATEMENT 102
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implicit integer*2 (a-z)
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logical found,endfil,valid,used
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integer*2 sline(500),seqnum(500)
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integer*4 nseq,nmax
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character*8 stype
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character*30 seqids(500)
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character*30 choice,seqid
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character*50 filnam,fmtseq(500)
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character*80 reclin
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character*1 seq(nmax)
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data found/.false./,
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. endfil/.false./,
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. valid/.false./
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c **************************************************************
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c subroutine number FS372, test main driver FP475
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c biomath program catalogued as FS372.FOR named formid.for
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c **************************************************************
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c PURPOSE:
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c subroutine used to extract sequences from various
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c format type files including
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c STANFORD,GENBANK,EMBL,PIR,and,NRC
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c **************************************************************
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c variable list table:
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c * -- sent down from main returned unchanged
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c ** - returned to main from subroutine
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c ***- sent down from main and returned changed
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c INTEGERS:IDCNT -- to keep track of the number of sequence
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c identifiers found in the file
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c I,K -- loop counters
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c LINE -- to point to the record line number of a file
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c N -- counter to extract the correct number of
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c sequence elements
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c * NMAX -- maximum length of sequence expected by user
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c ** NSEQ -- length of the sequence retrieved from file
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c POINTR -- pointer to point to sequence identifier
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c chosen from array of identifiers
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c SEQNUM -- an ARRAY of the length of the sequences
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c for the sequence identifiers found in the
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c NRC-format type files
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c SLINE -- an ARRAY of the record-line numbers where
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c a sequence starts in a file
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c START -- defines what column of a record to start
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c reading the sequence in.
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c CHARACTERS:CHOICE-- character string of length 20 to read in
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c choice for sequence identifier to retrieve
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c FILNAM -- character string of length 50 to read in
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c the filename.
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c FMTSEQ -- an ARRAY of characters, each length 50,
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c describing how the sequence is to be read
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c RECLIN -- a record of a file, length 80 characters
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c ** SEQ -- an ARRAY of characters each length 1 to
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c store the sequence
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c ** SEQID -- retrieved name of the sequence
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c SEQIDS -- an ARRAY of retrieved names of sequences
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c STYPE -- character string of length 8 defining the
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c format type of the file.
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c LOGICALS:FOUND -- logical variable used in looping until
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c something retrieved
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c *** USED -- logical variable used in determining if the
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c subroutine has been previously called
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c VALID -- logical variable used in looping until
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c some input valid
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c
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c
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c if the subroutine has NOT been USED then must
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c input the filename and do error checking on filename
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c else branch to listing the sequences available in this file
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if (.not.used) then
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10 found = .false.
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valid = .false.
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used = .false.
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c initialize for a new file by setting variables back
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c to zero and blanking out old names
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if (nmax.eq.0) nmax = 9999
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nseq = 0
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stype = ' '
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seqid = ' '
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filnam= ' '
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do 500 i = 1,500
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sline(i) = 0
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seqnum(i)= 0
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seqids(i)=' '
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fmtseq(i)=' '
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500 continue
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111 write(6,102) 'Input sequence file name (/ to end) '
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102 format(1x,a37,$)
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read(5,110,end=999,err=111) filnam
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if (filnam(1:1).eq.'/') then
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goto 999
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endif
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110 format(a50)
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c open the file only after a valid filename has been retrieved
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c error in filename results in prompting for the input again
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open(66,file=filnam,status='OLD',err=10)
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c find sequence file format type and the sequence identifiers
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idcnt = 0
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line = 1
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c DO WHILE (.NOT.FOUND)
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600 read(66,120,end = 410,err = 991) reclin
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120 format(a80)
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c STANFORD format, recognized by the ';' in the first column
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c of the record
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if (reclin(1:1).eq.';') then
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c DO WHILE (.NOT.ENDFIL)
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610 line = line + 1
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read(66,120,end = 410,err=991) reclin
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c to find the next sequence identifer scroll through the
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c file until the first character in the line is not ';'
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if (reclin(1:1).ne.';') then
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found = .true.
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stype ='STANFORD'
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idcnt = idcnt + 1
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sline(idcnt)= line
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seqids(idcnt) = reclin(1:30)
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line = line + 1
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read(66,120,end = 410,err=991) reclin
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c DO WHILE ((INDEX(RECLIN,'1').EQ.0).AND.
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c . (INDEX(RECLIN,'2').EQ.0))
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c ENDDO
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615 if (index(reclin,'1').eq.0) then
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if (index(reclin,'2').eq.0) then
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line = line + 1
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read(66,120,end = 410,err=991) reclin
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goto 615
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endif
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endif
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c assume at least one line not a sequence identifier occurs
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c after last sequence read in to get around the CTRL-L problem.
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c therefore, after reading in the record containing the end
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c of sequence identifier, read in another record
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line = line + 1
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read(66,120,end = 410,err=991) reclin
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endif
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c ENDDO
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if (.not.endfil) goto 610
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c GENBANK format, recognized by the word LOCUS starting in the
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c first position of the record
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elseif (reclin(1:5).eq.'LOCUS') then
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found = .true.
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stype = 'GENBANK '
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idcnt = 1
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seqids(idcnt) = reclin(13:27)
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c DO WHILE (.NOT.ENDFIL)
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620 line = line + 1
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read(66,120,end = 410,err=991) reclin
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c scrolling through to find the key phrase ORIGIN because
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c the line after this key phrase occurrance is where the sequence
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c occurs in the file;
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c read through the file obtaining other sequences by scrolling
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c through to the '//' which signals the end of sequence
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c Then start looking for another sequence identifier.
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if (reclin(1:6).eq.'ORIGIN') then
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sline(idcnt) = line
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c DO WHILE (RECLIN(1:2).NE.'//')
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625 if (reclin(1:2).ne.'//') then
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line = line + 1
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read(66,120,end = 410,err=991) reclin
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goto 625
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c ENDDO
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endif
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elseif (reclin(1:5).eq.'LOCUS') then
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idcnt = idcnt + 1
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seqids(idcnt) = reclin(13:27)
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endif
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c ENDDO
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if (.not.endfil) goto 620
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c PIR format, recognized by the '>' occurring in column 1 of a
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c record. The sequence itself start 2 lines down from the record
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c containing '>'.
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elseif (reclin(1:1).eq.'>') then
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found = .true.
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stype = 'PIR '
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c DO WHILE (.NOT.ENDFIL)
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630 if (reclin(1:1).eq.'>') then
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idcnt = idcnt + 1
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sline(idcnt) = line + 1
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seqids(idcnt) = reclin(5:25)
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endif
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line = line + 1
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read(66,120,end = 410,err=991) reclin
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c ENDDO
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if (.not.endfil) goto 630
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c EMBL (european) format, recognized by the key phrase ID in the
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c first column of the record.
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elseif (reclin(1:5).eq.'ID ') then
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found = .true.
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stype = 'EMBL '
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c scrolling through to find the key phrase 'SQ Sequence' because
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c the line after this key phrase occurrance is where the sequence
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c occurs in the file;
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c DO WHILE (.NOT.ENDFIL)
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640 if (reclin(1:5).eq.'ID ') then
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idcnt = idcnt + 1
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seqids(idcnt) = reclin(6:index(reclin,' '))
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elseif (reclin(1:13).eq.'SQ Sequence') then
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sline(idcnt) = line
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endif
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line = line + 1
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read(66,120,end = 410,err=991) reclin
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c ENDDO
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if (.not.endfil) goto 640
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c NRC format, recognized by '(' occurring in the first column of
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c a record. The record line following this line holds the number
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c of elements in the sequence and the name of the sequence. The
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c following line signals the beginning of the sequence.
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c The sequence itself is read in by using variable format
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c described by the '(' record line. This format statement on the
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c record containing '(' ,must also be retrieved.
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elseif (reclin(1:1).eq.'(') then
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found = .true.
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stype = 'NRC '
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c DO WHILE (.NOT.ENDFIL)
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650 if (reclin(1:1).eq.'(') then
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idcnt = idcnt + 1
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fmtseq(idcnt) = reclin(1:index(reclin,')'))
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line = line + 1
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read(66,140,end = 410,err = 991)
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. seqnum(idcnt),seqids(idcnt)
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sline(idcnt) = line
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endif
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line = line + 1
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read(66,120,end = 410,err=991) reclin
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c ENDDO
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140 format(i4,5x,a30)
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if (.not.endfil) goto 650
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endif
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c keep scrolling through the file until a key phrase signalling
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c a format type is recognized or the end of file is found
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line = line + 1
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c ENDDO
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if (.not.found) goto 600
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c if a format type has not been found then this cannot be a
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c sequence file and return to main.
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410 if (.not.found) then
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write(6,105) ' No sequence identifiers found in this file '
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105 format(a50)
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return
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endif
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c if this is a valid format type proceed
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used = .true.
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endif
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c IF USED this call before start at listing identifiers
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c listing the sequence identifiers
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c allow the user to input the number requested
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c or control d to finish here and return to
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c entering a new filename
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valid = .false.
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c keep outputting the list of sequence identifiers
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c while NOT VALID choice of sequence identifier is inputted
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c DO WHILE (.NOT.VALID)
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660 write(6,150) 'Available sequences in ',filnam
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150 format(/,1x,a23,a50)
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do 525 k = 1,idcnt,2
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if (sline(k).ne.0) then
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if (k .eq. idcnt) then
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write (6,151) k,'.',seqids(k)
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else
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write (6,191) k,'.',seqids(k),k+1,'.',seqids(k+1)
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endif
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151 format(1x,i3,a1,1x,a30)
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191 format(1x,i3,a1,1x,a30,3x,i3,a1,1x,a30)
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endif
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525 continue
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choice = ' '
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seqid = ' '
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pointr = 0
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write(6,152)
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. 'Choose sequence by number or name , or ? for relist; '
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write(6,152)
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. ' <return> defaults to the first one, / for new file.'
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152 format(1x,a60)
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read(5,153,end=10) choice
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153 format(a30)
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c error checking of the inputted CHOICE and determining
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c if this input is a number, a default value, a relist command
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c or the name of the sequence identifier
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i = 1
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do while (choice(i:i).eq.' '.and.i.lt.6)
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i = i + 1
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enddo
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if ((choice(i:i).ge.'1').and.(choice(i:i).le.'9')) then
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c using COLLATING sequence to convert character to number value
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pointr = ichar(choice(i:i)) - ichar('0')
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if (choice(i+1:i+1).ne.' ') then
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pointr = ichar(choice(i+1:i+1)) - ichar('0') + 10 * pointr
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endif
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if (choice(i+2:i+2).ne.' ') then
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pointr = ichar(choice(i+2:i+2)) - ichar('0') + 10 * pointr
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endif
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if (pointr.gt.idcnt) then
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write(6,154) ' NUMBER CHOICE BETWEEN 1 AND ',idcnt
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154 format(a30,i2)
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else
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seqid = seqids(pointr)
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valid = .true.
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endif
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elseif (ichar(choice(6:6)).eq.32) then
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pointr = 1
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seqid = seqids(1)
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valid = .true.
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elseif (choice(1:1).eq.'?') then
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continue
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else
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c find out if the inputted choice is in the list of seq identifiers.
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pointr = 0
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do 535 k = 1,idcnt
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if (seqids(k).eq.choice) then
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seqid = seqids(k)
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pointr = k
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valid = .true.
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endif
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535 continue
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if (pointr.eq.0) then
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write(6,105) 'Does not match any in given list'
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endif
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endif
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c ENDDO
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if (.not.valid) goto 660
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c having obtained a valid sequence choice or default of
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c one available sequence, rewind the file and retrieve the
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c sequence
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rewind(66,err = 992)
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c having retrieved the line number in the file where this
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c identifier occurs from SLINE(POINTR) scroll through the
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c file until this line is reached
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c
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c SUN WARNING: brancd into block.
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do 550 i = 1,sline(pointr)
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read(66,120,end = 410,err=991) reclin
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550 continue
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c if nrc type then read sequence according to format type
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if (stype.eq.'NRC ') then
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nseq = seqnum(pointr)
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c if the number in the NRC sequence is greater than
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c the maximum number sent down from main, then
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c truncate to NMAX and output a message to the user.
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if (nseq.gt.nmax) then
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write(6,160) ' Sequence truncated to ',nseq
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160 format(1x,a30,i5)
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nseq = nmax
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|
endif
|
||
|
|
read(66,fmtseq(pointr),end = 420,err=991)
|
||
|
|
. (seq(k),k=1,seqnum(pointr))
|
||
|
|
c Else if not type NRC then find the sequence by taking
|
||
|
|
c each letter of the next records until end-of-sequence
|
||
|
|
c indicator found or number in the sequence NMAX is reached
|
||
|
|
else
|
||
|
|
n = 1
|
||
|
|
found = .false.
|
||
|
|
c DO WHILE (.NOT.FOUND)
|
||
|
|
670 read(66,120,end = 420,err=991) reclin
|
||
|
|
c there is a need for the two positions to start reading the
|
||
|
|
c sequence; to accommodate the GENBANK format and the STANFORD
|
||
|
|
c end-of-sequence checks.
|
||
|
|
if (stype.eq.'GENBANK ') then
|
||
|
|
start = 10
|
||
|
|
else
|
||
|
|
start = 1
|
||
|
|
endif
|
||
|
|
do 565 i = start,80
|
||
|
|
c if the number in the sequence is less than the desired
|
||
|
|
c number, NMAX sent down from main, then retrieve sequence
|
||
|
|
if (n.le.nmax) then
|
||
|
|
if (.not.found) then
|
||
|
|
seq(n) = reclin(i:i)
|
||
|
|
c check if an early end of sequence
|
||
|
|
if ((seq(n).eq.'1').or.(seq(n).eq.'2').or.
|
||
|
|
. (reclin(1:1).eq.'/').or.(seq(n).eq.'*')) then
|
||
|
|
seq(n) = ' '
|
||
|
|
nseq = n - 1
|
||
|
|
found = .true.
|
||
|
|
c if not an end-of-sequence character but have gone far
|
||
|
|
c enough, then truncate to NMAX
|
||
|
|
elseif (n.eq.nmax) then
|
||
|
|
nseq = nmax
|
||
|
|
found = .true.
|
||
|
|
write(6,160) ' Sequence truncated to ',nseq
|
||
|
|
c if not a end-of-sequence character, check to see if it is
|
||
|
|
c not a blank character. Blank characters will not be added
|
||
|
|
c to the sequence.
|
||
|
|
elseif (seq(n).ne.' ') then
|
||
|
|
n = n + 1
|
||
|
|
endif
|
||
|
|
endif
|
||
|
|
c if the number of sequence characters found is Greater than
|
||
|
|
c NMAX then all of the sequence has been found.
|
||
|
|
else
|
||
|
|
found = .true.
|
||
|
|
nseq = n
|
||
|
|
write(6,160)
|
||
|
|
. ' Sequence truncated to ',nseq
|
||
|
|
endif
|
||
|
|
565 continue
|
||
|
|
c ENDDO
|
||
|
|
if (.not.found) goto 670
|
||
|
|
endif
|
||
|
|
420 return
|
||
|
|
c 991 stop ' ERROR IN READING FILE '
|
||
|
|
c 992 stop ' ERROR IN REWINDING FILE'
|
||
|
|
c 999 stop ' END of SESSION...GOOD BYE'
|
||
|
|
991 call exit(1)
|
||
|
|
992 call exit(1)
|
||
|
|
999 call exit(1)
|
||
|
|
end
|