src/hg/encode/validateFiles/validateFiles.c 1.4
1.4 2009/03/13 08:22:13 mikep
fix so comment lines only appear at top of fastq, and added csfasta format
Index: src/hg/encode/validateFiles/validateFiles.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/validateFiles/validateFiles.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/encode/validateFiles/validateFiles.c 13 Mar 2009 04:52:28 -0000 1.3
+++ src/hg/encode/validateFiles/validateFiles.c 13 Mar 2009 08:22:13 -0000 1.4
@@ -17,8 +17,11 @@
struct hash *chrHash = NULL;
char dnaChars[256];
char qualChars[256];
char seqName[256];
+char digits[256];
+char alpha[256];
+char csSeqName[256];
void usage()
/* Explain usage and exit. */
{
@@ -26,9 +29,10 @@
"validateFiles - validate format of different track input files\n"
"usage:\n"
" validateFiles -type=FILE_TYPE file1 [file2 [...]]\n"
"options:\n"
- " -type=(fastq|tagAlign|pairedTagAlign)\n"
+ " -type=(fastq|csfasta|tagAlign|pairedTagAlign)\n"
+ " csfasta = Colorspace fasta (SOLiD platform)\n"
" -chromInfo=file.txt Specify chromInfo file to validate chrom names and sizes\n"
" -maxErrors=N Maximum lines with errors to report in one file before \n"
" stopping (default %d)\n"
" -zeroSizeOk For BED-type positional data, allow rows with start==end\n"
@@ -57,17 +61,18 @@
// seqName: fastq sequence name chars [A-Za-z0-9_.:/-]
{
int i;
for (i=0 ; i < 256 ; ++i)
- dnaChars[i] = qualChars[i] = seqName[i] = 0;
+ dnaChars[i] = qualChars[i] = seqName[i] = csSeqName[i] = digits[i] = alpha[i] = 0;
dnaChars['a'] = dnaChars['c'] = dnaChars['g'] = dnaChars['t'] = dnaChars['n'] = 1;
dnaChars['A'] = dnaChars['C'] = dnaChars['G'] = dnaChars['T'] = dnaChars['N'] = 1;
dnaChars['0'] = dnaChars['1'] = dnaChars['2'] = dnaChars['3'] = 1;
for (i= (int)'A' ; i <= (int)'Z' ; ++i)
- seqName[i] = seqName[i+(int)('a'-'A')] = 1;
+ seqName[i] = seqName[i+(int)('a'-'A')] = alpha[i] = alpha[i+(int)('a'-'A')] = 1;
for (i= (int)'0' ; i <= (int)'9' ; ++i)
- seqName[i] = 1;
+ seqName[i] = digits[i] = csSeqName[i] = 1;
seqName['_'] = seqName['.'] = seqName[':'] = seqName['/'] = seqName['-'] = 1;
+csSeqName[','] = csSeqName['.'] = csSeqName['-'] = csSeqName['#'] = 1;
for (i= (int)'!' ; i <= (int)'~' ; ++i)
qualChars[i] = 1;
}
@@ -178,8 +183,71 @@
}
return TRUE;
}
+char *getDigits(char *s)
+// Consume 1 or more digits from s, return pointer to next non-digit
+// Return NULL if no digits consumed
+{
+char *s0 = s;
+while (digits[(int) *s])
+ ++s;
+if (s > s0)
+ return s;
+else
+ return NULL;
+}
+
+boolean checkTrailingCsSeqName(char *s)
+// Return true if all chars in s (if any) are csSeqName chars
+// Return false otherwise
+{
+while (csSeqName[(int) *s])
+ ++s;
+if (*s == 0)
+ return TRUE;
+else
+ return FALSE;
+}
+
+// >461_19_209_F3
+// T022213002230311203200200322000
+// >920_22_656_F3,1.-152654094.1.35.35.0###,19.43558664.1.35.35.0###
+// T01301010111200210102321210100112312
+
+boolean checkCsSeqName(char *file, int line, char *s)
+// Return TRUE if string has non-zero length, matches CS name pattern contains only csSeqName[] chars
+// Othewise print warning that seqName is empty and return FALSE
+{
+char *s0;
+if (s[0] == 0)
+ {
+ warn("Error [file=%s, line=%d]: sequence name empty [%s]", file, line, s);
+ return FALSE;
+ }
+else if (s[0] != '>')
+ {
+ warn("Error [file=%s, line=%d]: sequence name first char invalid (got '%c', wanted '>') [%s]",
+ file, line, s[0], s);
+ return FALSE;
+ }
+if ( (s0 = getDigits(s+1))
+ && (*(s0++) == '_')
+ && (s0 = getDigits(s0)) && (*(s0++) == '_')
+ && (s0 = getDigits(s0)) && (*(s0++) == '_')
+ && alpha[(int) *(s0++)] && digits[(int) *(s0++)]
+ && checkTrailingCsSeqName(s0) )
+ {
+ verbose(2,"[%s %3d] OK [%s] file(%s) line=%d\n", __func__, __LINE__, s, file, line);
+ return TRUE;
+ }
+else
+ {
+ warn("Error [file=%s, line=%d]: invalid sequence name [%s]", file, line, s);
+ return FALSE;
+ }
+}
+
boolean checkQual(char *file, int line, char *s)
// Return TRUE if string has non-zero length and contains only qualChars[] chars
// Othewise print warning that quality is empty and return FALSE
{
@@ -345,18 +413,24 @@
char *qName = NULL;
char *qual = NULL;
int line = 0;
int errs = 0;
+boolean startOfFile = TRUE;
FILE *f = mustOpen(file, "rb");
verbose(2,"[%s %3d] file(%s)\n", __func__, __LINE__, file);
while ( (seqName = readLine(f)) )
{
++line;
+ if (startOfFile)
+ {
if (*seqName == '#')
{
freez(&seqName);
continue;
}
+ else
+ startOfFile = FALSE;
+ }
if (checkSeqName(file, line, seqName, '@', "sequence name")
&& (seq = readLine(f))
&& checkSeq(file, ++line, seq, seq, "sequence")
&& (qName = readLine(f))
@@ -382,8 +456,57 @@
carefulClose(&f);
return errs;
}
+// CS Fasta:
+// >461_19_209_F3
+// T022213002230311203200200322000
+// >920_22_656_F3,1.-152654094.1.35.35.0###,19.43558664.1.35.35.0###
+// T01301010111200210102321210100112312
+
+int validateCsfasta(char *file)
+{
+char *seqName = NULL;
+char *seq = NULL;
+int line = 0;
+int errs = 0;
+boolean startOfFile = TRUE;
+FILE *f = mustOpen(file, "rb");
+verbose(2,"[%s %3d] file(%s)\n", __func__, __LINE__, file);
+while ( (seqName = readLine(f)) )
+ {
+ ++line;
+ if (startOfFile)
+ {
+ if (*seqName == '#')
+ {
+ freez(&seqName);
+ continue;
+ }
+ else
+ startOfFile = FALSE;
+ }
+ if (checkCsSeqName(file, line, seqName)
+ && (seq = readLine(f))
+ && checkSeq(file, ++line, seq, seq, "sequence") )
+ {
+ if (printOkLines)
+ printf("%s\n%s\n", seqName, seq);
+ }
+ else
+ {
+ if (printFailLines)
+ printf("%s\n%s\n", seqName, seq);
+ if (++errs >= maxErrors)
+ errAbort("Aborting .. found %d errors\n", errs);
+ }
+ freez(&seqName);
+ freez(&seq);
+ }
+carefulClose(&f);
+return errs;
+}
+
void validateFiles(int (*validate)(char *file), int numFiles, char *files[])
/* validateFile - validate format of different track input files. */
{
int i;
@@ -432,8 +555,9 @@
// Setup the function hash keyed by type
hashAdd(funcs, "tagAlign", &validateTagAlign);
hashAdd(funcs, "pairedTagAlign", &validatePairedTagAlign);
hashAdd(funcs, "fastq", &validateFastq);
+hashAdd(funcs, "csfasta", &validateCsfasta);
if (!(func = hashFindVal(funcs, type)))
errAbort("Cannot validate %s type files\n", type);
validateFiles(func, argc, argv);
return 0;