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#include "piler2.h"
// GFF fields are:
// <seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes] [comments]
// 0 1 2 3 4 5 6 7 8 9
int GFFLineNr;
// Destructive read -- pokes nuls onto FS
int GetFields(char *Line, char **Fields, int MaxFields, char FS)
{
char *p = Line;
for (int FieldIndex = 0; FieldIndex < MaxFields; ++FieldIndex)
{
Fields[FieldIndex] = p;
char *Tab = strchr(p, FS);
char *End = Tab;
if (0 == End)
End = strchr(p, '\0');
size_t FieldLength = End - p;
if (FieldLength > MAX_GFF_FEATURE_LENGTH)
Quit("Max GFF field length exceeded, field is %d chars, max=%d, line %d",
FieldLength, MAX_GFF_FEATURE_LENGTH, GFFLineNr);
if (0 == Tab)
return FieldIndex + 1;
*Tab = 0;
p = Tab + 1;
}
return MaxFields;
}
bool GetNextGFFRecord(FILE *f, GFFRecord &Rec)
{
for (;;)
{
++GFFLineNr;
const char TAB = '\t';
char Line[MAX_GFF_LINE+1];
char *Ok = fgets(Line, sizeof(Line), f);
if (NULL == Ok)
{
if (feof(f))
return false;
Quit("Error reading GFF file, line=%d feof=%d ftell=%d ferror=%d errno=%d",
GFFLineNr, feof(f), ftell(f), ferror(f), errno);
}
if ('#' == Line[0])
continue;
size_t n = strlen(Line);
if (0 == n)
Quit("fgets returned zero-length line");
if (Line[n-1] != '\n' && !feof(f))
Quit("Max line length in GFF file exceeded, line %d is %d chars long, max=%d",
GFFLineNr, n - 1, MAX_GFF_LINE);
Line[n-1] = 0; // delete newline
char *Fields[9];
int FieldCount = GetFields(Line, Fields, 9, '\t');
if (FieldCount < 8)
Quit("GFF record has < 8 fields, line %d", GFFLineNr);
const char *SeqName = Fields[0];
const char *Source = Fields[1];
const char *Feature = Fields[2];
const char *Start = Fields[3];
const char *End = Fields[4];
const char *Score = Fields[5];
const char *Strand = Fields[6];
const char *Frame = Fields[7];
const char *Attrs = "";
if (FieldCount > 8)
{
// Truncate attrs if comment found
Attrs = Fields[8];
// char *Pound = strchr(Attrs, '#');
// if (0 != Pound)
// *Pound = 0;
}
strcpy(Rec.SeqName, SeqName);
strcpy(Rec.Source, Source);
strcpy(Rec.Feature, Feature);
Rec.Start = atoi(Start);
Rec.End = atoi(End);
Rec.Score = (float) atof(Score);
Rec.Strand = Strand[0];
Rec.Frame = Frame[0] == '.' ? -1 : atoi(Frame);
strcpy(Rec.Attrs, Attrs);
return true;
}
}
// GFF fields are:
// <seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes] [comments]
// 0 1 2 3 4 5 6 7 8 9
void WriteGFFRecord(FILE *f, const GFFRecord &Rec)
{
fprintf(f, "%s\t%s\t%s\t%d\t%d\t%.3g\t%c",
// 0 1 2 3 4 5 6 7 8
Rec.SeqName, // 0
Rec.Source, // 1
Rec.Feature, // 2
Rec.Start, // 3
Rec.End, // 4
Rec.Score, // 5
Rec.Strand); // 6
if (-1 == Rec.Frame)
fprintf(f, "\t.");
else
fprintf(f, "\t%d", Rec.Frame);
fprintf(f, "\t%s\n", Rec.Attrs);
}
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