--- /dev/null
+/* File: readseq.c
+ * main() program for ureadseq.c, ureadseq.h
+ *
+ * Reads and writes nucleic/protein sequence in various
+ * formats. Data files may have multiple sequences.
+ *
+ * Copyright 1990 by d.g.gilbert
+ * biology dept., indiana university, bloomington, in 47405
+ * e-mail: gilbertd@bio.indiana.edu
+ *
+ * This program may be freely copied and used by anyone.
+ * Developers are encourged to incorporate parts in their
+ * programs, rather than devise their own private sequence
+ * format.
+ *
+ * This should compile and run with any ANSI C compiler.
+ * Please advise me of any bugs, additions or corrections.
+ *
+ */
+
+const char *title
+ = "readSeq (1Feb93), multi-format molbio sequence reader.\n";
+
+ /* History
+ 27 Feb 90. 1st release to public.
+ 4 Mar 90. + Gary Olsen format
+ + case change
+ * minor corrections to NBRF,EMBL,others
+ * output 1 file per sequence for gcg, unknown
+ * define -DNOSTR for c-libraries w/o strstr
+ - readseq.p, pascal version, becomes out-of-date
+ 24 May 90. + Phylip 3.2 output format (no input)
+ 20 Jul 90. + Phylip 3.3 output (no input yet)
+ + interactive output re-direction
+ + verbose progress info
+ * interactive help output
+ * dropped line no.s on NBRF output
+ * patched in HyperGCG XCMD corrections,
+ - except for seq. documentation handling
+ * dropped the IG special nuc codes, as IG has
+ adopted the standard IUB codes (now if only
+ everyone would adopt a standard format !)
+ 11 Oct 90. * corrected bug in reading/writing of EMBL format
+
+ 17 Oct 91. * corrected bug in reading Olsen format
+ (serious-deletion)
+ 10 Nov 91. * corrected bug in reading some GCG format files
+ (serious-last line duplicated)
+ + add format name parsing (-fgb, -ffasta, ...)
+ + Phylip v3.4 output format (== v3.2, sequential)
+ + add checksum output to all forms that have document
+ + skip mail headers in seq file
+ + add pipe for standard input == seq file (with -p)
+ * fold in parts of MacApp Seq object
+ * strengthen format detection
+ * clarify program structure
+ * remove fixed sequence size limit (now dynamic, sizeof memory)
+ * check and fold in accumulated bug reports:
+ * Now ANSI-C fopen(..,"w") & check open failure
+ * Define -DFIXTOUPPER for nonANSI C libraries that mess
+ up toupper/tolower
+ = No command-line changes; callers of readseq main() should be okay
+ - ureadseq.h functions have changed; client programs need to note.
+ + added Unix and VMS Make scripts, including validation tests
+
+ 4 May 92. + added 32 bit CRC checksum as alternative to GCG 6.5bit checksum
+ (-DBIGCHECKSUM)
+ Aug 92 = fixed Olsen format input to handle files w/ more sequences,
+ not to mess up when more than one seq has same identifier,
+ and to convert number masks to symbols.
+ = IG format fix to understand ^L
+
+ 25-30 Dec 92
+ * revised command-line & interactive interface. Suggested form is now
+ readseq infile -format=genbank -output=outfile -item=1,3,4 ...
+ but remains compatible with prior commandlines:
+ readseq infile -f2 -ooutfile -i3 ...
+ + added GCG MSF multi sequence file format
+ + added PIR/CODATA format
+ + added NCBI ASN.1 sequence file format
+ + added Pretty, multi sequence pretty output (only)
+ + added PAUP multi seq format
+ + added degap option
+ + added Gary Williams (GWW, G.Williams@CRC.AC.UK) reverse-complement option.
+ + added support for reading Phylip formats (interleave & sequential)
+ * string fixes, dropped need for compiler flags NOSTR, FIXTOUPPER, NEEDSTRCASECMP
+ * changed 32bit checksum to default, -DSMALLCHECKSUM for GCG version
+
+ 1Feb93
+ = revert GenBank output to a fixed left number width which
+ other software depends on.
+ = fix for MSF input to handle symbols in names
+ = fix bug for possible memory overrun when truncating seqs for
+ Phylip or Paup formats (thanks Anthony Persechini)
+
+ */
+
+
+
+/*
+ Readseq has been tested with:
+ Macintosh MPW C
+ GNU gcc
+ SGI cc
+ VAX-VMS cc
+ Any ANSI C compiler should be able to handle this.
+ Old-style C compilers barf all over the source.
+
+
+How do I build the readseq program if I have an Ansi C compiler?
+#--------------------
+# Unix ANSI C
+# Use the supplied Makefile this way:
+% make CC=name-of-c-compiler
+# OR do this...
+% gcc readseq.c ureadseq.c -o readseq
+
+#--------------------
+$!VAX-VMS cc
+$! Use the supplied Make.Com this way:
+$ @make
+$! OR, do this:
+$ cc readseq, ureadseq
+$ link readseq, ureadseq, sys$library:vaxcrtl/lib
+$ readseq :== $ MyDisk:[myacct]readseq
+
+#--------------------
+# Macintosh Simple Input/Output Window application
+# requires MPW-C and SIOW library (from APDA)
+# also uses files macinit.c, macinit.r, readseqSIOW.make
+#
+Buildprogram readseqSIOW
+
+#--------------------
+#MPW-C v3 tool
+C ureadseq.c
+C readseq.c
+link -w -o readseq -t MPST -c 'MPS ' ¶
+ readseq.c.o Ureadseq.c.o ¶
+ "{Libraries}"Interface.o ¶
+ "{Libraries}"ToolLibs.o ¶
+ "{Libraries}"Runtime.o ¶
+ "{CLibraries}"StdClib.o
+readseq -i1 ig.seq
+
+# MPW-C with NCBI tools
+
+set NCBI "{Boot}@molbio:ncbi:"; EXPORT NCBI
+set NCBILIB1 "{NCBI}"lib:libncbi.o; export NCBILIB1
+set NCBILIB2 "{NCBI}"lib:libncbiobj.o; export NCBILIB2
+set NCBILIB3 "{NCBI}"lib:libncbicdr.o; export NCBILIB3
+set NCBILIB4 "{NCBI}"lib:libvibrant.o; export NCBILIB4
+
+C ureadseq.c
+C -d NCBI -i "{NCBI}"include: ureadasn.c
+C -d NCBI -i "{NCBI}"include: readseq.c
+link -w -o readseq -t MPST -c 'MPS ' ¶
+ ureadseq.c.o ureadasn.c.o readseq.c.o ¶
+ {NCBILIB4} {NCBILIB2} {NCBILIB1} ¶
+ "{Libraries}"Interface.o ¶
+ "{Libraries}"ToolLibs.o ¶
+ "{Libraries}"Runtime.o ¶
+ "{CLibraries}"CSANELib.o ¶
+ "{CLibraries}"Math.o ¶
+ "{CLibraries}"StdClib.o
+
+===========================================================*/
+
+
+
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+
+#include "ureadseq.h"
+
+#pragma segment readseq
+
+
+
+static char inputfilestore[256], *inputfile = inputfilestore;
+
+const char *formats[kMaxFormat+1] = {
+ " 1. IG/Stanford",
+ " 2. GenBank/GB",
+ " 3. NBRF",
+ " 4. EMBL",
+ " 5. GCG",
+ " 6. DNAStrider",
+ " 7. Fitch",
+ " 8. Pearson/Fasta",
+ " 9. Zuker (in-only)",
+ "10. Olsen (in-only)",
+ "11. Phylip3.2",
+ "12. Phylip",
+ "13. Plain/Raw",
+ "14. PIR/CODATA",
+ "15. MSF",
+ "16. ASN.1",
+ "17. PAUP/NEXUS",
+ "18. Pretty (out-only)",
+ "" };
+
+#define kFormCount 30
+#define kMaxFormName 15
+
+const struct formatTable {
+ char *name;
+ short num;
+ } formname[] = {
+ {"ig", kIG},
+ {"stanford", kIG},
+ {"genbank", kGenBank},
+ {"gb", kGenBank},
+ {"nbrf", kNBRF},
+ {"embl", kEMBL},
+ {"gcg", kGCG},
+ {"uwgcg", kGCG},
+ {"dnastrider", kStrider},
+ {"strider", kStrider},
+ {"fitch", kFitch},
+ {"pearson", kPearson},
+ {"fasta", kPearson},
+ {"zuker", kZuker},
+ {"olsen", kOlsen},
+ {"phylip", kPhylip},
+ {"phylip3.2", kPhylip2},
+ {"phylip3.3", kPhylip3},
+ {"phylip3.4", kPhylip4},
+ {"phylip-interleaved", kPhylip4},
+ {"phylip-sequential", kPhylip2},
+ {"plain", kPlain},
+ {"raw", kPlain},
+ {"pir", kPIR},
+ {"codata", kPIR},
+ {"asn.1", kASN1},
+ {"msf", kMSF},
+ {"paup", kPAUP},
+ {"nexus", kPAUP},
+ {"pretty", kPretty},
+ };
+
+const char *kASN1headline = "Bioseq-set ::= {\nseq-set {\n";
+
+/* GWW table for getting the complement of a nucleotide (IUB codes) */
+/* ! "#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[ \]^_`abcdefghijklmnopqrstuvwxyz{|}~ */
+const char compl[] = " !\"#$%&'()*+,-./0123456789:;<=>?@TVGHNNCDNNMNKNNYRYSAABWNRN[\\]^_`tvghnncdnnmnknnyrysaabwnrn{|}~";
+
+
+
+char *formatstr( short format)
+{
+ if (format < 1 || format > kMaxFormat) {
+ switch (format) {
+ case kASNseqentry :
+ case kASNseqset : return formats[kASN1-1];
+ case kPhylipInterleave:
+ case kPhylipSequential: return formats[kPhylip-1];
+ default: return "(unknown)";
+ }
+ }
+ else return formats[format-1];
+}
+
+int parseformat( char *name)
+{
+#define kDupmatch -2
+ int namelen, maxlen, i, match, matchat;
+ char lname[kMaxFormName+1];
+
+ skipwhitespace(name);
+ namelen = strlen(name);
+ if (namelen == 0)
+ return kNoformat;
+ else if (isdigit(*name)) {
+ i = atol( name);
+ if (i < kMinFormat | i > kMaxFormat) return kNoformat;
+ else return i;
+ }
+
+ /* else match character name */
+ maxlen = min( kMaxFormName, namelen);
+ for (i=0; i<maxlen; i++) lname[i] = to_lower(name[i]);
+ lname[maxlen]=0;
+ matchat = kNoformat;
+
+ for (i=0; i<kFormCount; i++) {
+ match = strncmp( lname, formname[i].name, maxlen);
+ if (match == 0) {
+ if (strlen(formname[i].name) == namelen) return (formname[i].num);
+ else if (matchat == kNoformat) matchat = i;
+ else matchat = kDupmatch; /* 2 or more partial matches */
+ }
+ }
+ if (matchat == kNoformat || matchat == kDupmatch)
+ return kNoformat;
+ else
+ return formname[matchat].num;
+}
+
+
+
+static void dumpSeqList(char *list, short format)
+{
+ long i, l, listlen;
+ char s[256];
+
+ listlen = strlen(list);
+ printf("Sequences in %s (format is %s)\n", inputfile, formatstr(format));
+ for (i=0, l=0; i < listlen; i++) {
+ if (list[i] == (char)NEWLINE) {
+ s[l] = '\0'; l = 0;
+ puts(s);
+ }
+ else if (l < 255)
+ s[l++] = list[i];
+ }
+ putchar('\n');
+}
+
+
+
+void usage()
+{
+ short i, midi;
+
+ fprintf(stderr,title);
+ fprintf(stderr,
+ "usage: readseq [-options] in.seq > out.seq\n");
+ fprintf(stderr," options\n");
+/* ? add -d[igits] to allow digits in sequence data, &/or option to specify seq charset !? */
+ fprintf(stderr, " -a[ll] select All sequences\n");
+ fprintf(stderr, " -c[aselower] change to lower case\n");
+ fprintf(stderr, " -C[ASEUPPER] change to UPPER CASE\n");
+ fprintf(stderr, " -degap[=-] remove gap symbols\n");
+ fprintf(stderr, " -i[tem=2,3,4] select Item number(s) from several\n");
+ fprintf(stderr, " -l[ist] List sequences only\n");
+ fprintf(stderr, " -o[utput=]out.seq redirect Output\n");
+ fprintf(stderr, " -p[ipe] Pipe (command line, <stdin, >stdout)\n");
+ fprintf(stderr, " -r[everse] change to Reverse-complement\n");
+ fprintf(stderr, " -v[erbose] Verbose progress\n");
+ fprintf(stderr, " -f[ormat=]# Format number for output, or\n");
+ fprintf(stderr, " -f[ormat=]Name Format name for output:\n");
+ midi = (kMaxFormat+1) / 2;
+ for (i = kMinFormat-1; i < midi; i++)
+ fprintf( stderr, " %-20s %-20s\n",
+ formats[i], formats[midi+i]);
+
+ /* new output format options, esp. for pretty format: */
+ fprintf(stderr, " \n");
+ fprintf(stderr, " Pretty format options: \n");
+ fprintf(stderr, " -wid[th]=# sequence line width\n");
+ fprintf(stderr, " -tab=# left indent\n");
+ fprintf(stderr, " -col[space]=# column space within sequence line on output\n");
+ fprintf(stderr, " -gap[count] count gap chars in sequence numbers\n");
+ fprintf(stderr, " -nameleft, -nameright[=#] name on left/right side [=max width]\n");
+ fprintf(stderr, " -nametop name at top/bottom\n");
+ fprintf(stderr, " -numleft, -numright seq index on left/right side\n");
+ fprintf(stderr, " -numtop, -numbot index on top/bottom\n");
+ fprintf(stderr, " -match[=.] use match base for 2..n species\n");
+ fprintf(stderr, " -inter[line=#] blank line(s) between sequence blocks\n");
+
+ /****** not ready yet
+ fprintf(stderr, " -code=none,rtf,postscript,ps code syntax\n");
+ fprintf(stderr, " -namefont=, -numfont=, -seqfont=font font choice\n");
+ fprintf(stderr, " font suggestions include times,courier,helvetica\n");
+ fprintf(stderr, " -namefontsize=, -numfontsize=, -seqfontsize=#\n");
+ fprintf(stderr, " fontsize suggestions include 9,10,12,14\n");
+ fprintf(stderr, " -namefontstyle=, -numfontstyle=, -seqfontstyle= style fontstyle for names\n");
+ fprintf(stderr, " fontstyle options are plain,italic,bold,bold-italic\n");
+ ******/
+}
+
+void erralert(short err)
+{
+ switch (err) {
+ case 0 :
+ break;
+ case eFileNotFound: fprintf(stderr, "File not found: %s\n", inputfile);
+ break;
+ case eFileCreate: fprintf(stderr, "Can't open output file.\n");
+ break;
+ case eASNerr: fprintf(stderr, "Error in ASN.1 sequence routines.\n");
+ break;
+ case eNoData: fprintf(stderr, "No data in file.\n");
+ break;
+ case eItemNotFound: fprintf(stderr, "Specified item not in file.\n");
+ break;
+ case eUnequalSize: fprintf(stderr,
+ "This format requires equal length sequences.\nSequence truncated or padded to fit.\n");
+ break;
+ case eUnknownFormat: fprintf(stderr, "Error: this format is unknown to me.\n");
+ break;
+ case eOneFormat: fprintf(stderr,
+ "Warning: This format permits only 1 sequence per file.\n");
+ break;
+ case eMemFull: fprintf(stderr, "Out of storage memory. Sequence truncated.\n");
+ break;
+ default: fprintf(stderr, "readSeq error = %d\n", err);
+ break;
+ }
+} /* erralert */
+
+
+int chooseFormat( boolean quietly)
+{
+ char sform[128];
+ int midi, i, outform;
+
+ if (quietly)
+ return kPearson; /* default */
+ else {
+ midi = (kMaxFormat+1) / 2;
+ for (i = kMinFormat-1; i < midi; i++)
+ fprintf( stderr, " %-20s %-20s\n",
+ formats[i], formats[midi+i]);
+ fprintf(stderr,"\nChoose an output format (name or #): \n");
+ gets(sform);
+ outform = parseformat(sform);
+ if (outform == kNoformat) outform = kPearson;
+ return outform;
+ }
+}
+
+
+
+/* read paramater(s) */
+
+boolean checkopt( boolean casesense, char *sopt, const char *smatch, short minword)
+{
+ long lenopt, lenmatch;
+ boolean result;
+ short minmaxw;
+
+ lenopt = strlen(sopt);
+ lenmatch= strlen(smatch);
+ minmaxw= max(minword, min(lenopt, lenmatch));
+
+ if (casesense)
+ result= (!strncmp( sopt, smatch, minmaxw));
+ else
+ result= (!Strncasecmp( sopt, smatch, minmaxw ));
+ /* if (result) { */
+ /* fprintf(stderr,"true checkopt(opt=%s,match=%s,param=%s)\n", sopt, smatch, *sparam); */
+ /* } */
+ return result;
+}
+
+
+#define kMaxwhichlist 50
+
+/* global for readopt(), main() */
+boolean chooseall = false, quietly = false, gotinputfile = false,
+ listonly = false, closeout = false, verbose = false,
+ manyout = false, dolower = false, doupper = false, doreverse= false,
+ askout = true, dopipe= false, interleaved = false;
+short nfile = 0, iwhichlist=0, nwhichlist = 0;
+short whichlist[kMaxwhichlist+1];
+long whichSeq = 0, outform = kNoformat;
+char onamestore[128], *oname = onamestore;
+FILE *foo = NULL;
+
+void resetGlobals()
+/* need this when used from SIOW, as these globals are not reinited automatically
+between calls to local main() */
+{
+ chooseall = false; quietly = false; gotinputfile = false;
+ listonly = false; closeout = false; verbose = false;
+ manyout = false; dolower = false; doupper = false; doreverse= false;
+ askout = true; dopipe= false; interleaved = false;
+ nfile = 0; iwhichlist=0; nwhichlist = 0;
+ whichSeq = 0; outform = kNoformat;
+ oname = onamestore;
+ foo = NULL;
+
+ gPrettyInit(gPretty);
+}
+
+
+#define kOptOkay 1
+#define kOptNone 0
+
+int readopt( char *sopt)
+{
+ char sparamstore[256], *sparam= sparamstore;
+ short n, slen= strlen(sopt);
+
+ /* fprintf(stderr,"readopt( %s) == ", sopt); */
+
+ if (*sopt == '?') {
+ usage();
+ return kOptNone; /*? eOptionBad or kOptNone */
+ }
+
+ else if (*sopt == '-') {
+
+ char *cp= strchr(sopt,'=');
+ *sparam= '\0';
+ if (cp) {
+ strcpy(sparam, cp+1);
+ *cp= 0;
+ }
+
+ if (checkopt( false, sopt, "-help", 2)) {
+ usage();
+ return kOptNone;
+ }
+
+ if (checkopt( false, sopt, "-all", 2)) {
+ whichSeq= 1; chooseall= true;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-colspace", 4)) { /* test before -c[ase] */
+ n= atoi( sparam);
+ gPretty.spacer = n;
+ return kOptOkay;
+ }
+
+ if (checkopt( true, sopt, "-caselower", 2)) {
+ dolower= true;
+ return kOptOkay;
+ }
+ if (checkopt( true, sopt, "-CASEUPPER", 2)) {
+ doupper= true;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-pipe", 2)) {
+ dopipe= true; askout= false;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-list", 2)) {
+ listonly = true; askout = false;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-reverse", 2)) {
+ doreverse = true;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-verbose", 2)) {
+ verbose = true;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-match", 5)) {
+ gPretty.domatch= true;
+ if (*sparam >= ' ') gPretty.matchchar= *sparam;
+ return kOptOkay;
+ }
+ if (checkopt( false, sopt, "-degap", 4)) {
+ gPretty.degap= true;
+ if (*sparam >= ' ') gPretty.gapchar= *sparam;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-interline", 4)) {
+ gPretty.interline= atoi( sparam);
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-item", 2)) {
+ char *cp = sparam;
+ nwhichlist= 0;
+ whichlist[0]= 0;
+ if (*cp == 0) cp= sopt+2; /* compatible w/ old way */
+ do {
+ while (*cp!=0 && !isdigit(*cp)) cp++;
+ if (*cp!=0) {
+ n = atoi( cp);
+ whichlist[nwhichlist++]= n;
+ while (*cp!=0 && isdigit(*cp)) cp++;
+ }
+ } while (*cp!=0 && n>0 && nwhichlist<kMaxwhichlist);
+ whichlist[nwhichlist++]= 0; /* 0 == stopsign for loop */
+ whichSeq= max(1,whichlist[0]); iwhichlist= 1;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-format", 5)) {/* -format=phylip, -f2, -form=phylip */
+ if (*sparam==0) { for (sparam= sopt+2; isalpha(*sparam); sparam++) ; }
+ outform = parseformat( sparam);
+ return kOptOkay;
+ }
+ if (checkopt( false, sopt, "-f", 2)) { /* compatible w/ -fphylip prior version */
+ if (*sparam==0) sparam= sopt+2;
+ outform = parseformat( sparam);
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-output", 3)) {/* -output=myseq */
+ if (*sparam==0) { for (sparam= sopt+3; isalpha(*sparam); sparam++) ; }
+ strcpy( oname, sparam);
+ foo = fopen( oname, "w");
+ if (!foo) { erralert(eFileCreate); return eFileCreate; }
+ closeout = true;
+ askout = false;
+ return kOptOkay;
+ }
+ if (checkopt( false, sopt, "-o", 2)) { /* compatible w/ -omyseq prior version */
+ if (*sparam==0) sparam= sopt+2;
+ strcpy( oname, sparam);
+ foo = fopen( oname, "w");
+ if (!foo) { erralert(eFileCreate); return eFileCreate; }
+ closeout = true;
+ askout = false;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-width", 2)) {
+ if (*sparam==0) { for (sparam= sopt+2; !isdigit(*sparam) && *sparam!=0; sparam++) ; }
+ n= atoi( sparam);
+ if (n>0) gPretty.seqwidth = n;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-tab", 4)) {
+ if (*sparam==0) { for (sparam= sopt+2; !isdigit(*sparam) && *sparam!=0; sparam++) ; }
+ n= atoi( sparam);
+ gPretty.tab = n;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-gapcount", 4)) {
+ gPretty.baseonlynum = false;
+ /* if (*sparam >= ' ') gPretty.gapchar= *sparam; */
+ return kOptOkay;
+ }
+ if (checkopt( false, sopt, "-nointerleave", 8)) {
+ gPretty.noleaves = true;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-nameleft", 7)) {
+ if (*sparam==0) { for (sparam= sopt+2; !isdigit(*sparam) && *sparam!=0; sparam++) ; }
+ n= atoi( sparam);
+ if (n>0 && n<50) gPretty.namewidth = n;
+ gPretty.nameleft= true;
+ return kOptOkay;
+ }
+ if (checkopt( false, sopt, "-nameright", 7)) {
+ if (*sparam==0) { for (sparam= sopt+2; !isdigit(*sparam) && *sparam!=0; sparam++) ; }
+ n= atoi( sparam);
+ if (n>0 && n<50) gPretty.namewidth = n;
+ gPretty.nameright= true;
+ return kOptOkay;
+ }
+ if (checkopt( false, sopt, "-nametop", 6)) {
+ gPretty.nametop= true;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-numleft", 6)) {
+ if (*sparam==0) { for (sparam= sopt+2; !isdigit(*sparam) && *sparam!=0; sparam++) ; }
+ n= atoi( sparam);
+ if (n>0 && n<50) gPretty.numwidth = n;
+ gPretty.numleft= true;
+ return kOptOkay;
+ }
+ if (checkopt( false, sopt, "-numright", 6)) {
+ if (*sparam==0) { for (sparam= sopt+2; !isdigit(*sparam) && *sparam!=0; sparam++) ; }
+ n= atoi( sparam);
+ if (n>0 && n<50) gPretty.numwidth = n;
+ gPretty.numright= true;
+ return kOptOkay;
+ }
+
+ if (checkopt( false, sopt, "-numtop", 6)) {
+ gPretty.numtop= true;
+ return kOptOkay;
+ }
+ if (checkopt( false, sopt, "-numbottom", 6)) {
+ gPretty.numbot= true;
+ return kOptOkay;
+ }
+
+ else {
+ usage();
+ return eOptionBad;
+ }
+ }
+
+ else {
+ strcpy( inputfile, sopt);
+ gotinputfile = (*inputfile != 0);
+ nfile++;
+ return kOptOkay;
+ }
+
+ /* return kOptNone; -- never here */
+}
+
+
+
+
+/* this program suffers some as it tries to be a quiet translator pipe
+ _and_ a noisy user interactor
+*/
+
+/* return is best for SIOW, okay for others */
+#ifdef SIOW
+#define Exit(a) return(a)
+siow_main( int argc, char *argv[])
+
+#else
+#define Exit(a) exit(a)
+
+main( int argc, char *argv[])
+#endif
+{
+boolean closein = false;
+short ifile, nseq, atseq, format, err = 0, seqtype = kDNA,
+ nlines, seqout = 0, phylvers = 2;
+long i, skiplines, seqlen, seqlen0;
+unsigned long checksum= 0, checkall= 0;
+char *seq, *cp, *firstseq = NULL, *seqlist, *progname, tempname[256];
+char seqid[256], *seqidptr = seqid;
+char stempstore[256], *stemp = stempstore;
+FILE *ftmp, *fin, *fout;
+long outindexmax= 0, noutindex= 0, *outindex = NULL;
+
+#define exit_main(err) { \
+ if (closeout) fclose(fout); \
+ if (closein) fclose(fin); \
+ if (*tempname!=0) remove(tempname);\
+ Exit(err); }
+
+#define indexout() if (interleaved) {\
+ if (noutindex>=outindexmax) {\
+ outindexmax= noutindex + 20;\
+ outindex= (long*) realloc(outindex, sizeof(long)*outindexmax);\
+ if (outindex==NULL) { err= eMemFull; erralert(err); exit_main(err); }\
+ }\
+ outindex[noutindex++]= ftell(fout);\
+ }
+
+
+ resetGlobals();
+ foo = stdout;
+ progname = argv[0];
+ *oname = 0;
+ *tempname = 0;
+ /* initialize gPretty ?? -- done in header */
+
+ for (i=1; i < argc; i++) {
+ err= readopt( argv[i]);
+ if (err <= 0) exit_main(err);
+ }
+
+ /* pipe input from stdin !? */
+ if (dopipe && !gotinputfile) {
+ int c;
+ tmpnam(tempname);
+ inputfile = tempname;
+ ftmp = fopen( inputfile, "w");
+ if (!ftmp) { erralert(eFileCreate); exit_main(eFileCreate); }
+ while ((c = getc(stdin)) != EOF) fputc(c, ftmp);
+ fclose(ftmp);
+ gotinputfile= true;
+ }
+
+ quietly = (dopipe || (gotinputfile && (listonly || whichSeq != 0)));
+
+ if (verbose || (!quietly && !gotinputfile)) fprintf( stderr, title);
+ ifile = 1;
+
+ /* UI: Choose output */
+ if (askout && !closeout && !quietly) {
+ askout = false;
+ fprintf(stderr,"\nName of output file (?=help, defaults to display): \n");
+ gets(oname= onamestore);
+ skipwhitespace(oname);
+ if (*oname == '?') { usage(); exit_main(0); }
+ else if (*oname != 0) {
+ closeout = true;
+ foo = fopen( oname, "w");
+ if (!foo) { erralert(eFileCreate); exit_main(eFileCreate); }
+ }
+ }
+
+ fout = foo;
+ if (outform == kNoformat) outform = chooseFormat(quietly);
+
+ /* set up formats ... */
+ switch (outform) {
+ case kPhylip2:
+ interleaved= false;
+ phylvers = 2;
+ outform = kPhylip;
+ break;
+
+ case kPhylip4:
+ interleaved= true;
+ phylvers = 4;
+ outform = kPhylip;
+ break;
+
+ case kMSF:
+ case kPAUP:
+ interleaved= true;
+ break;
+
+ case kPretty:
+ gPretty.isactive= true;
+ interleaved= true;
+ break;
+
+ }
+
+ if (gPretty.isactive && gPretty.noleaves) interleaved= false;
+ if (interleaved) {
+ fout = ftmp = tmpfile();
+ outindexmax= 30; noutindex= 0;
+ outindex = (long*) malloc(outindexmax*sizeof(long));
+ if (outindex==NULL) { err= eMemFull; erralert(err); exit_main(err); }
+ }
+
+ /* big loop over all input files */
+ do {
+ /* select next input file */
+ gotinputfile = (*tempname != 0);
+ while ((ifile < argc) && (!gotinputfile)) {
+ if (*argv[ifile] != '-') {
+ strcpy( inputfile, argv[ifile]);
+ gotinputfile = (*inputfile != 0);
+ --nfile;
+ }
+ ifile++;
+ }
+
+ while (!gotinputfile) {
+ fprintf(stderr,"\nName an input sequence or -option: \n");
+ inputfile= inputfilestore;
+
+ gets(stemp= stempstore);
+ if (*stemp==0) goto fini; /* !! need this to finish work during interactive use */
+ stemp= strtok(stempstore, " \n\r\t");
+ while (stemp) {
+ err= readopt( stemp); /* will read inputfile if it exists */
+ if (err<0) exit_main(err);
+ stemp= strtok( NULL, " \n\r\t");
+ }
+ }
+ /* thanks to AJB@UK.AC.DARESBURY.DLVH for this PHYLIP3 fix: */
+ /* head for end (interleave if needed) */
+ if (*inputfile == 0) break;
+
+ format = seqFileFormat( inputfile, &skiplines, &err);
+
+ if (err == 0) {
+#ifdef NCBI
+ if (format == kASNseqentry || format == kASNseqset)
+ seqlist = listASNSeqs( inputfile, skiplines, format, &nseq, &err);
+ else
+#endif
+ seqlist = listSeqs( inputfile, skiplines, format, &nseq, &err);
+ }
+
+ if (err != 0)
+ erralert(err);
+
+ else if (listonly) {
+ dumpSeqList(seqlist,format);
+ free( seqlist);
+ }
+
+ else {
+ /* choose whichSeq if needed */
+ if (nseq == 1 || chooseall || (quietly && whichSeq == 0)) {
+ chooseall= true;
+ whichSeq = 1;
+ quietly = true; /* no loop */
+ }
+ else if (whichSeq > nseq && quietly) {
+ erralert(eItemNotFound);
+ err= eItemNotFound;
+ }
+ else if (whichSeq > nseq || !quietly) {
+ dumpSeqList(seqlist, format);
+ fprintf(stderr,"\nChoose a sequence (# or All): \n");
+ gets(stemp= stempstore);
+ skipwhitespace(stemp);
+ if (to_lower(*stemp) == 'a') {
+ chooseall= true;
+ whichSeq = 1;
+ quietly = true; /* !? this means we don't ask for another file
+ as well as no more whichSeqs... */
+ }
+ else if (isdigit(*stemp)) whichSeq= atol(stemp);
+ else whichSeq= 1; /* default */
+ }
+ free( seqlist);
+
+ if (false /*chooseall*/) { /* this isn't debugged yet...*/
+ fin = fopen(inputfile, "r");
+ closein= true;
+ }
+
+ while (whichSeq > 0 && whichSeq <= nseq) {
+ /* need to open multiple output files ? */
+ manyout = ((chooseall || nwhichlist>1) && nseq > 1
+ && (outform == kPlain || outform == kGCG));
+ if (manyout) {
+ if ( whichSeq == 1 ) erralert(eOneFormat);
+ else if (closeout) {
+ sprintf( stemp,"%s_%d", oname, whichSeq);
+ freopen( stemp, "w", fout);
+ fprintf( stderr,"Writing sequence %d to file %s\n", whichSeq, stemp);
+ }
+ }
+
+ if (closein) {
+ /* !! this fails... skips most seqs... */
+ /* !! in sequential read, must count seqs already read from whichSeq ... */
+ /* need major revision of ureadseq before we can do this */
+ atseq= whichSeq-1;
+ seqidptr= seqid;
+ seq = readSeqFp( whichSeq, fin, skiplines, format,
+ &seqlen, &atseq, &err, seqidptr);
+ skiplines= 0;
+ }
+ else {
+ atseq= 0;
+ seqidptr= seqid;
+#ifdef NCBI
+ if (format == kASNseqentry || format == kASNseqset) {
+ seqidptr= NULL;
+ seq = readASNSeq( whichSeq, inputfile, skiplines, format,
+ &seqlen, &atseq, &err, &seqidptr);
+ }
+ else
+#endif
+ seq = readSeq( whichSeq, inputfile, skiplines, format,
+ &seqlen, &atseq, &err, seqidptr);
+ }
+
+
+ if (gPretty.degap) {
+ char *newseq;
+ long newlen;
+ newseq= compressSeq( gPretty.gapchar, seq, seqlen, &newlen);
+ if (newseq) {
+ free(seq); seq= newseq; seqlen= newlen;
+ }
+ }
+
+ if (outform == kMSF) checksum= GCGchecksum(seq, seqlen, &checkall);
+ else if (verbose) checksum= seqchecksum(seq, seqlen, &checkall);
+ if (verbose)
+ fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n",
+ whichSeq, seqlen, checksum, formatstr(format), seqidptr);
+
+ if (err != 0) erralert(err);
+ else {
+ /* format fixes that writeseq doesn't do */
+ switch (outform) {
+ case kPIR:
+ if (seqout == 0) fprintf( foo,"\\\\\\\n");
+ break;
+ case kASN1:
+ if (seqout == 0) fprintf( foo, kASN1headline);
+ break;
+
+ case kPhylip:
+ if (seqout == 0) {
+ if (!interleaved) { /* bug, nseq is for 1st infile only */
+ if (chooseall) i= nseq; else i=1;
+ if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen);
+ else fprintf(foo," %d %d YF\n", i, seqlen);
+ }
+ seqlen0 = seqlen;
+ }
+ else if (seqlen != seqlen0) {
+ erralert(eUnequalSize);
+ if (seqlen < seqlen0) seq = (char *)realloc(seq, seqlen0);
+ for (i=seqlen; i<seqlen0; i++) seq[i]= gPretty.gapchar;
+ seqlen = seqlen0;
+ seq[seqlen] = 0;
+ }
+ break;
+
+ case kPAUP:
+ if (seqout == 0) {
+ seqtype= getseqtype(seq, seqlen);
+ seqlen0 = seqlen;
+ }
+ else if (seqlen != seqlen0) {
+ erralert(eUnequalSize);
+ if (seqlen < seqlen0) seq = (char *)realloc(seq, seqlen0);
+ for (i=seqlen; i<seqlen0; i++) seq[i]= gPretty.gapchar;
+ seqlen = seqlen0;
+ seq[seqlen] = 0;
+ }
+ break;
+
+ }
+
+ if (doupper)
+ for (i = 0; i<seqlen; i++) seq[i] = to_upper(seq[i]);
+ else if (dolower)
+ for (i = 0; i<seqlen; i++) seq[i] = to_lower(seq[i]);
+
+ if (doreverse) {
+ long j, k;
+ char ctemp;
+ for (j=0, k=seqlen-1; j <= k; j++, k--) {
+ ctemp = compl[seq[j] - ' '];
+ seq[j] = compl[seq[k] - ' '];
+ seq[k] = ctemp;
+ }
+ }
+
+ if ((gPretty.isactive || outform==kPAUP) && gPretty.domatch && firstseq != NULL) {
+ for (i=0; i<seqlen; i++)
+ if (seq[i]==firstseq[i]) seq[i]= gPretty.matchchar;
+ }
+
+
+ if (gPretty.isactive && gPretty.numtop && seqout == 0) {
+ gPretty.numline = 1;
+ indexout();
+ (void) writeSeq( fout, seq, seqlen, outform, seqidptr);
+ gPretty.numline = 2;
+ indexout();
+ (void) writeSeq( fout, seq, seqlen, outform, seqidptr);
+ gPretty.numline = 0;
+ }
+
+ indexout();
+ nlines = writeSeq( fout, seq, seqlen, outform, seqidptr);
+ seqout++;
+ }
+
+ if ((gPretty.isactive || outform==kPAUP) && gPretty.domatch && firstseq == NULL) {
+ firstseq= seq;
+ seq = NULL;
+ }
+ else if (seq!=NULL) { free(seq); seq = NULL; }
+
+#ifdef NCBI
+ if ( (format == kASNseqentry || format == kASNseqset)
+ && seqidptr && seqidptr!= seqid)
+ free(seqidptr);
+#endif
+ if (chooseall) whichSeq++;
+ else if (iwhichlist<nwhichlist) whichSeq= whichlist[iwhichlist++];
+ else whichSeq= 0;
+ }
+ if (closein) { fclose(fin); closein= false; }
+ }
+ whichSeq = 0;
+ } while (nfile > 0 || !quietly);
+
+
+fini:
+ if (firstseq) { free(firstseq); firstseq= NULL; }
+ if (err || listonly) exit_main(err);
+
+ if (gPretty.isactive && gPretty.numbot) {
+ gPretty.numline = 2;
+ indexout();
+ (void) writeSeq( fout, seq, seqlen, outform, seqidptr);
+ gPretty.numline = 1;
+ indexout();
+ (void) writeSeq( fout, seq, seqlen, outform, seqidptr);
+ gPretty.numline = 0;
+ }
+
+ if (outform == kMSF) {
+ if (*oname) cp= oname; else cp= inputfile;
+ fprintf(foo,"\n %s MSF: %d Type: N January 01, 1776 12:00 Check: %d ..\n\n",
+ cp, seqlen, checkall);
+ }
+
+ if (outform == kPAUP) {
+ fprintf(foo,"#NEXUS\n");
+ if (*oname) cp= oname; else cp= inputfile;
+ fprintf(foo,"[%s -- data title]\n\n", cp);
+ /* ! now have header lines for each sequence... put them before "begin data;... */
+ }
+
+ if (outform==kPhylip && interleaved) {
+ if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen);
+ else fprintf(foo," %d %d YF\n", seqout, seqlen);
+ }
+
+ if (interleaved) {
+ /* interleave species lines in true output */
+ /* nlines is # lines / sequence */
+ short iline, j, leaf, iseq;
+ char *s = stempstore;
+
+ indexout(); noutindex--; /* mark eof */
+
+ for (leaf=0; leaf<nlines; leaf++) {
+ if (outform == kMSF && leaf == 1) {
+ fputs("//\n\n", foo);
+ }
+ if (outform == kPAUP && leaf==1) {
+ switch (seqtype) {
+ case kDNA : cp= "dna"; break;
+ case kRNA : cp= "rna"; break;
+ case kNucleic : cp= "dna"; break;
+ case kAmino : cp= "protein"; break;
+ case kOtherSeq: cp= "dna"; break;
+ }
+ fprintf(foo,"\nbegin data;\n");
+ fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, seqlen);
+ fprintf(foo," format datatype=%s interleave missing=%c", cp, gPretty.gapchar);
+ if (gPretty.domatch) fprintf(foo," matchchar=%c", gPretty.matchchar);
+ fprintf(foo,";\n matrix\n");
+ }
+
+ for (iseq=0; iseq<noutindex; iseq++) {
+ fseek(ftmp, outindex[iseq], 0);
+ for (iline=0; iline<=leaf; iline++)
+ if (!fgets(s, 256, ftmp)) *s= 0;
+ if (ftell(ftmp) <= outindex[iseq+1])
+ fputs( s, foo);
+ }
+
+ for (j=0; j<gPretty.interline; j++)
+ fputs( "\n", foo); /* some want spacer line */
+ }
+ fclose(ftmp); /* tmp disappears */
+ fout= foo;
+ }
+
+ if (outform == kASN1) fprintf( foo, "} }\n");
+ if (outform == kPAUP) fprintf( foo,";\n end;\n");
+
+ if (outindex != NULL) free(outindex);
+ exit_main(0);
+}
+
+
git://source.jalview.org / jpred.git / blobdiff