A GNU-make plug-in for the #Illumina FASTQs.
Building a plug-in for the Illumina FASTQs.
Illumina FASTQ files use the following naming scheme:
<sample name>_<barcode sequence>_L<lane (0-padded to 3 digits)>_R<read number>_<set number (0-padded to 3 digits>.fastq.gz
For example, the following is a valid FASTQ file name:
NA10831_ATCACG_L002_R1_001.fastq.gz
Here I'm writing a set of new functions for makefile to extract the different parts (sample, lane...) of a fastq file-name:
First a struct
holding the parts of the file is created:
enum E_IlluminaComponent
{
E_sampleName,
E_barcodeSequence,
E_lane,
E_readNumber,
E_setNumber
};
typedef struct illumina_scheme_t
{
char* filename;
char* components[NUM_ILLUMINA_COMPONENTS];
} IlluminaScheme,*IlluminaSchemePtr ;
and a function parsing the filenames is created:
IlluminaSchemePtr IlluminaSchemeNew(const char* filename)
{
...
}
when the plugin llumina
is loaded as a dynamic C library, the method llumina_gmk_setup
is called,
and we tell make about the new functions with gmk_add_function(name,callback,min_args,max_args,no_expand_content)
:
int illumina_gmk_setup ()
{
gmk_add_function ("illumina_sample",illumina_sample, 1, 1, 0);
gmk_add_function ("illumina_lane",illumina_lane, 1, 1, 0);
(...)
}
A function registered with make must match the gmk_func_ptr
type.
It will be invoked with three parameters: name (the name of the function), argc (the number of arguments to the function), and argv (an array of pointers to arguments to the function). The last pointer (that is, argv[argc]) will be null (0).
The return value of the function is the result of expanding the function.
char* illumina_sample(const char *function_name, unsigned int argc, char **argv)
{
/** extract the filename(s), build and return a string containing the samples */
}
Compiling
the plugin must be compiled as a dynamic C library.
Note: The manual says this step can also be generated in the final 'Makefile' (via load ./illumina.so
) but I was not able to compile a missing library (illumina.so cannot open shared object file: No such file or directory
)
so I compiled it by hand:
gcc -Wall -I/path/to/sources/make-4.0 -shared -fPIC -o illumina.so illumina.c
Test
here is the makefile:
SAMPLES= NA10831_ATCACG_L002_R1_001.fastq.gz \
hello \
NA10832_ATCACG_L002_R1_001.fastq.gz \
NA10831_ATCACG_L002_R2_001.fastq.gz \
NA10832_ATCACG_L002_R2_001.fastq.gz \
NA10833_ATCAGG_L003_R1_003.fastq.gz \
NA10833_ATCAGG_L003_R1_003.fastq.gz \
ERROR_ATCAGG_x003_R3_0z3.fastq.gz \
false
all:
@echo "SAMPLES: " $(illumina_sample ${SAMPLES} )
@echo "BARCODES: " $(illumina_barcode ${SAMPLES} )
@echo "LANE: " $(illumina_lane ${SAMPLES} )
@echo "READ: " $(illumina_read ${SAMPLES} )
@echo "SET: " $(illumina_set ${SAMPLES} )
output:
$ make SAMPLES: NA10831 NA10832 NA10833 BARCODES: ATCACG ATCAGG LANE: L002 L003 READ: R1 R2 SET: 001 003
That's it,
Pierre
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