From news@ulrik.uio.no Wed Feb 9 04:51:19 1994 Received: from net.bio.net by sunflower.bio.indiana.edu (4.1/9.7jsm) id AA17015; Wed, 9 Feb 94 04:51:13 EST Received: from nac.no by net.bio.net (8.6.5/IG-2.0) with SMTP id BAA24220; Wed, 9 Feb 1994 01:46:36 -0800 Received: from pat.uio.no by nac.no with SMTP (PP) id <23776-0@nac.no>; Wed, 9 Feb 1994 10:44:12 +0100 Received: from ulrik.uio.no by pat.uio.no with local-SMTP (PP) id <22498-0@pat.uio.no>; Wed, 9 Feb 1994 10:43:51 +0100 Received: by hermod.uio.no ; Wed, 9 Feb 1994 10:43:49 +0100 To: bionet-software-sources@nac.no Path: biomaster.uio.no!rodrigol From: rodrigo.lopez@biotek.uio.no (Rodrigo Lopez) Newsgroups: bionet.software.gcg,bionet.software.sources Subject: fastacheck.f Date: 9 Feb 1994 09:43:48 GMT Organization: The Norwegian EMBnet node Lines: 259 Distribution: world Message-Id: <2jab8k$3rn@hermod.uio.no> Nntp-Posting-Host: biomaster.uio.no Status: R Program FastaCheck Implicit None Integer HITLISTSIZE Parameter (HITLISTSIZE = 1000) Character HitList(512,HITLISTSIZE) Character DocLines(512,HITLISTSIZE) Character OutLine(512) Integer InFile, OutFile, ILen Integer IHits, NHits Integer IDoc, NDoc Character InFName(256), OutFName(256) Character Line(512) Integer NSeq, NRes, IWord Character DbName(256), SeqName(256) Real meann, mean1, sdn, sd1 Integer init1, initn, opt Real SDs Real hitpct Integer HitRes Real ScorePct Logical Check1, Checkn Real MinSd1/3./, MinSdn/3./ Logical Accepted /.false./ Integer i Integer AcceptCnt Logical CLNoInteract, CLGetOldFName, CLGetNewFName Logical StrMatch, CLGetReal Integer ReadString, CIStrFind, GetString Logical AcceptScore, CheckSd Call Doc ('eGenRunDoc:fastacheck.txt') Call CLComCheck ('eGenRunDoc:fastacheck.cmd') Check1 = CLGetReal('MINSD1',0., 99., MinSd1) Checkn = CLGetReal('MINSDN',0., 99., MinSdn) If (.not.CLGetOldFName('INfile1', 1, InFName) .and. & .not.CLNoInteract() ) Then Call WriteF ('\n FASTACHECK of what FASTA output file ? ') If (GetString(InFName).eq.0) Stop ' ' End If Call OpenF (InFile, InFName, 'r') Call StrCopy (OutFName, InFName) Call BaseName (OutFName) Call NewFileType (OutFName, '.check') If (.not.CLGetNewFName('OUTfile1', 2, OutFName) .and. & .not.CLNoInteract() ) Then Call WriteF ('\n What should I call the output file'// & ' (* %s *) ? ', OutFName) Call GetString(OutFName) End If Call OpenF (OutFile, OutFName, 'w') Call ReadString(InFile, Line, ILen) If (Ilen .lt. 0) stop ' ' !* read file heading Do While (CIStrFind('(Peptide) ', Line) .eq. 0) Call ReadString(InFile, Line, ILen) If (Ilen .lt. 0) stop ' ' End Do Call SReadF (Line, 'of: %s', SeqName) !* copy to summary line Do While (CIStrFind('Word Size', Line) .eq. 0) Call FWriteF (OutFile, '%s\n', Line) Call ReadString(InFile, Line, ILen) If (Ilen .lt. 0) stop ' ' End Do Call SReadF (Line, 'TO: %s Sequences: %d '// & 'Symbols: %d Word Size: %d', & DbName, NSeq, NRes, IWord) !* get mean scores and standard deviations Do While (CIStrFind('mean init', Line) .eq. 0) Call ReadString(InFile, Line, ILen) If (Ilen .lt. 0) stop ' ' End Do Call SReadF (Line, 'score: %f (%f)', meann, sdn) Call ReadString(InFile, Line, ILen) If (Ilen .lt. 0) stop ' ' Call SReadF (Line, 'score: %f (%f)', mean1, sd1) !* read one-line descriptions from best scores list Do While (CIStrFind('The best scores are', Line) .eq. 0) Call ReadString(InFile, Line, ILen) If (Ilen .lt. 0) stop ' ' End Do Call ReadString(InFile, Line, ILen) If (Ilen .lt. 0) stop ' ' Do While (ReadString(InFile, Line, ILen) .gt. 0) NHits = NHits + 1 Call StrCopy (HitList(1,NHits), Line) End Do IHits = 0 Do While (ReadString(InFile, Line, ILen) .ge. 0) Do While (.not.StrMatch(SeqName, Line)) If (CIStrFind('CPU time:',Line) .ne. 0) GoTo 999 If (Accepted) Call FWriteF (OutFile, '%s\n', Line) Call ReadString(InFile, Line, ILen) If (Ilen .lt. 0) stop ' ' End Do NDoc = 0 IHits = IHits + 1 Call ReadString(InFile, Line, ILen) If (Ilen .lt. 0) stop ' ' Do While (CIStrFind('SCORES ', Line) .eq. 0) NDoc = NDoc + 1 Call StrCopy (DocLines(1,NDoc),Line) Call ReadString(InFile, Line, ILen) If (Ilen .lt. 0) stop ' ' End Do !* read scoring details Call SReadF (Line, 'Init1: %d Initn: %d Opt: %d', & init1, initn, opt) Call ReadString(InFile, Line, ILen) If (Ilen .lt. 0) stop ' ' Call SReadF (Line, '%f identity in %d aa overlap', & hitpct, hitres) !* check for acceptability OutLine(1) = Char(0) Accepted = .false. If (AcceptScore (HitPct, HitRes, ScorePct)) Then Call SWriteF (OutLine,'Minimum identity: %.1f%%', & ScorePct) Accepted = .true. End If If (Check1 .and. CheckSD(mean1, sd1, init1, & minsd1, sds)) Then If (Accepted) Call SWriteF (OutLine, '~, ') Call SWriteF (OutLine, '~Init1 SDs: +%.1f', sds) Accepted = .true. End If If (Checkn .and. CheckSD(meann, sdn, initn, & minsdn, sds)) Then If (Accepted) Call SWriteF (OutLine, '~, ') Call SWriteF (OutLine, '~Initn SDs: +%.1f', sds) Accepted = .true. End If If (Accepted) Then Call FWriteF (OutFile, '(%d) %s\n', & IHits, HitList(1,IHits)) i = 3 Do While (i .le. NDoc) Call FWriteF (OutFile, '%s\n', DocLines(1,i)) i = i + 1 End Do Call FWriteF (OutFile, '\nSCORES Init1: %d '// & 'Initn: %d Opt: %d\n', Init1, Initn, Opt) Call FWriteF (OutFile, ' %.2f%% identity '// & 'in %d aa overlap\n', HitPct, HitRes) Call FWriteF (OutFile, ' %s\n\n', OutLine) AcceptCnt = AcceptCnt + 1 End If End Do 999 Call CloseF (InFile) Call CloseF (OutFile) Call WriteF ('\n\n Hits checked: %d\n Accepted: %d\n'// & ' Rejected: %d\n\n', & NHits, AcceptCnt, NHits-AcceptCnt) Call Account ('FastaCheck') Stop ' ' End !***** AcceptScore ************************************************************ !* !****************************************************************************** Logical Function AcceptScore (PctId, Length, ScorePct) Implicit None Real PctId Integer Length Real ScorePct Real Factor /290.15/ Real Exponent /-0.56158/ Integer MinLen /10/ Integer MaxLen /80/ Real MaxPct /25.0/ Logical FirstCall /.true./ If (FirstCall) Then Call CLGetReal('FACTor', -1E10, 1E10, Factor) Call CLGetReal('EXPonent', -1E10, 1E10, Exponent) Call CLGetInt('MINLen', 0, 1000, MinLen) Call CLGetInt('MAXLen', MinLen, 10000, MaxLen) MaxPct = Factor*(Float(MaxLen)**exponent) Call CLGetReal('MAXPct', 0.0, 100.0, MaxPct) End If AcceptScore = .false. If (Length .lt. MinLen) Return If (Length .ge. MaxLen) Then If (PctId .lt. MaxPct) Return ScorePct = MaxPct AcceptScore = .true. Return End If ScorePct = Factor*(Float(Length)**exponent) If (PctId .lt. ScorePct) Return AcceptScore = .true. Return End Logical Function CheckSD (MeanScore, Sd, IScore, MinSd, Sds) Implicit None Real MeanScore, Sd Integer IScore Real MinSd, Sds Real Score Score = Float(IScore) CheckSD = .false. Sds = (Score-MeanScore)/Sd If (Sds .ge. MinSd) CheckSD = .true. Return End -- *************************************************************************** * RODRIGO LOPEZ SERRANO rodrigol@biomed.uio.no - rodrigol@biotek.uio.no * * Norwegian EMBnet node Tel:xx-47-22958756 Fax:xx-47-22694130 * ***************************************************************************