Changeset: 6ac8a891a8d4 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=6ac8a891a8d4
Modified Files:
clients/mapiclient/mclient.c
Branch: DVframework_bam
Log Message:
Extended mclient with a renderer for the FASTQ format. This renderer expects
five string columns: qname, seq1, qual1, seq2, qual2.
To use the fastq renderer, the following command can be entered inside mclient:
\f fastq[/path/to/file1, /path/to/file2]
The renderer will then write output to these files and will ignore the
toConsole variable on writing the query result.
diffs (185 lines):
diff --git a/clients/mapiclient/mclient.c b/clients/mapiclient/mclient.c
--- a/clients/mapiclient/mclient.c
+++ b/clients/mapiclient/mclient.c
@@ -115,12 +115,15 @@ enum formatters {
CSVformatter,
XMLformatter,
TESTformatter,
- CLEANformatter
+ CLEANformatter,
+ FASTQformatter
};
static enum formatters formatter = NOformatter;
char *output = NULL; /* output format as string */
char *separator = NULL; /* column separator for CSV/TAB format
*/
int csvheader = 0; /* include header line in CSV format */
+char *fastq_filepath1 = NULL;
+char *fastq_filepath2 = NULL;
#define DEFWIDTH 80
@@ -715,6 +718,50 @@ CSVrenderer(MapiHdl hdl)
}
static void
+FASTQrenderer(MapiHdl hdl)
+{
+ int fields;
+ char *qname, *seq1, *qual1, *seq2, *qual2;
+ FILE *file1 = fopen(fastq_filepath1, "w"), *file2 =
fopen(fastq_filepath2, "w");
+
+ if(file1 == NULL || file2 == NULL) {
+ mnstr_printf(toConsole, "Couldn't open FASTQ file for writing.");
+ return;
+ }
+
+ while (!mnstr_errnr(toConsole) && (fields = fetch_row(hdl)) != 0) {
+ qname = mapi_fetch_field(hdl, 0);
+ seq1 = mapi_fetch_field(hdl, 1);
+ qual1 = mapi_fetch_field(hdl, 2);
+ seq2 = mapi_fetch_field(hdl, 3);
+ qual2 = mapi_fetch_field(hdl, 4);
+
+ if (qname == NULL || seq1 == NULL || qual1 == NULL || seq2 ==
NULL || qual2 == NULL) {
+ mnstr_printf(toConsole, "Attributes couldn't be fetched
from query result");
+ return;
+ }
+ fputc('@' , file1);
+ fputs(qname , file1);
+ fputc('\n' , file1);
+ fputs(seq1 , file1);
+ fputs("\n+\n", file1);
+ fputs(qual1 , file1);
+ fputc('\n' , file1);
+
+ fputc('@' , file2);
+ fputs(qname , file2);
+ fputc('\n' , file2);
+ fputs(seq2 , file2);
+ fputs("\n+\n", file2);
+ fputs(qual2 , file2);
+ fputc('\n' , file2);
+ }
+
+ fclose(file1);
+ fclose(file2);
+}
+
+static void
SQLseparator(int *len, int fields, char sep)
{
int i, j;
@@ -1325,6 +1372,40 @@ SQLrenderer(MapiHdl hdl, char singleinst
free(numeric);
}
+static int
+readFilenameAndOpenFile(char **s, char file[], char endsymbol) {
+ int index = 0;
+ FILE *testfile;
+ while(index < 255 && **s != '\0' && **s != endsymbol) {
+ file[index++] = **s;
+ (*s)++;
+ }
+ file[index] = '\0';
+ if(index == 255) {
+ mnstr_printf(toConsole, "Filename of file %s too long. Only 255
characters are allowed.\n", file);
+ return 0;
+ }
+ if(**s == '\0') {
+ mnstr_printf(toConsole, "Parse error: End of string character found
before '%c' character.\n", endsymbol);
+ return 0;
+ }
+
+ /* to prevent a FASTQ result to be calculated but being unable to write to
file, test the actual creation */
+ testfile = fopen(file, "w");
+ if(testfile == NULL) {
+ mnstr_printf(toConsole, "File %s couldn't be opened for writing.\n",
file);
+ return 0;
+ }
+
+ /* creation worked, now close the file and even remove it,
+ since we don't want any unneccesary files hanging around */
+ fclose(testfile);
+ remove(file);
+
+ (*s)++;
+ return 1;
+}
+
static void
setFormatter(char *s)
{
@@ -1362,7 +1443,22 @@ setFormatter(char *s)
_set_output_format(_TWO_DIGIT_EXPONENT);
#endif
formatter = TESTformatter;
- } else {
+ } else if (strncmp(s, "fastq[", 6) == 0) {
+ char *s2 = s + 6;
+ char file1[256];
+ char file2[256];
+ if(readFilenameAndOpenFile(&s2, file1, ',') &&
readFilenameAndOpenFile(&s2, file2, ']')) {
+ mnstr_printf(toConsole, "Query results will be written to FASTQ
files '%s' and '%s'.\n", file1, file2);
+ fastq_filepath1 = strdup(file1);
+ fastq_filepath2 = strdup(file2);
+ formatter = FASTQformatter;
+ }
+ }
+ else if (strcmp(s, "fastq") == 0) {
+ mnstr_printf(toConsole, "The fastq renderer needs two filepaths to
write to."
+ " Expected form: \\f fastq[path/to/file1,path/to/file2]\n:");
+ }
+ else {
mnstr_printf(toConsole, "unsupported formatter\n");
}
}
@@ -1577,6 +1673,9 @@ format_result(Mapi mid, MapiHdl hdl, cha
break;
}
break;
+ case FASTQformatter:
+ FASTQrenderer(hdl);
+ break;
default:
RAWrenderer(hdl);
break;
@@ -1789,7 +1888,7 @@ showCommands(void)
mnstr_printf(toConsole, "\\a - disable auto commit\n");
}
mnstr_printf(toConsole, "\\e - echo the query in sql formatting
mode\n");
- mnstr_printf(toConsole, "\\f - format using a built-in renderer
{csv,tab,raw,sql,xml}\n");
+ mnstr_printf(toConsole, "\\f - format using a built-in renderer
{csv,tab,raw,sql,xml,fastq}\n");
mnstr_printf(toConsole, "\\w# - set maximal page width
(-1=unlimited, 0=terminal width, >0=limit to num)\n");
mnstr_printf(toConsole, "\\r# - set maximum rows per page
(-1=raw)\n");
mnstr_printf(toConsole, "\\L file - save client/server interaction\n");
@@ -2472,6 +2571,8 @@ doFile(Mapi mid, const char *file, int u
case XMLformatter:
mnstr_printf(toConsole,
"xml\n");
break;
+ case FASTQformatter:
+ mnstr_printf(toConsole,
"fastq\n");
default:
mnstr_printf(toConsole,
"none\n");
break;
@@ -2605,7 +2706,7 @@ usage(const char *prog, int xit)
#ifdef HAVE_ICONV
fprintf(stderr, " -E charset | --encoding=charset specify encoding
(character set) of the terminal\n");
#endif
- fprintf(stderr, " -f kind | --format=kind specify output
format {csv,tab,raw,sql,xml}\n");
+ fprintf(stderr, " -f kind | --format=kind specify output
format {csv,tab,raw,sql,xml,fastq}\n");
fprintf(stderr, " -H | --history load/save cmdline
history (default off)\n");
fprintf(stderr, " -i | --interactive[=tm] interpret \\
commands on stdin, use time formatting {ms,s,m}\n");
fprintf(stderr, " -l language | --language=lang {sql,mal}\n");
@@ -3079,5 +3180,11 @@ main(int argc, char **argv)
mapi_destroy(mid);
mnstr_destroy(stdout_stream);
mnstr_destroy(stderr_stream);
+ if(fastq_filepath1 != NULL) {
+ free(fastq_filepath1);
+ }
+ if(fastq_filepath2 != NULL) {
+ free(fastq_filepath2);
+ }
return c;
}
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