Program gto_fastq_rand_extra_chars

The gto_fastq_rand_extra_chars substitues in the FASTQ files, the DNA sequence the outside ACGT chars by random ACGT symbols.

For help type:


			  			./gto_fastq_rand_extra_chars -h

In the following subsections, we explain the input and output paramters.

Input parameters

The gto_fastq_rand_extra_chars program needs two streams for the computation, namely the input and output standard. The input stream is a FASTQ file.

The attribution is given according to:


			  			Usage: ./gto_fastq_rand_extra_chars [options] [[--] args]
or: ./gto_fastq_rand_extra_chars [options]

It substitues in the FASTQ files, the DNA sequence the outside ACGT chars by random ACGT symbols.

-h, --help            show this help message and exit

Basic options
< input.fastq         Input FASTQ file format (stdin)
> output.fastq        Output FASTQ file format (stdout)

Example: ./gto_fastq_rand_extra_chars < input.fastq > output.fastq

An example of such an input file is:


			  			@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72
GNNTGATGGCCGCTGCCGATGGCGNANAATCCCACCAANATACCCTTAACAACTTAAGGGTTNTCAAATAGA
+SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
NTTCAGGGATACGACGNTTGTATTTTAAGAATCTGNAGCAGAAGTCGATGATAATACGCGNCGTTTTATCAN
+SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I

Output

The output of the gto_fastq_rand_extra_chars program is a FASTQ file.

Using the input above, an output example for this is the following:


			  			@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72
GTGTGATGGCCGCTGCCGATGGCGCATAATCCCACCAACATACCCTTAACAACTTAAGGGTTTTCAAATAGA
+SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9ICIIIIIIIIIIIIIIIIIIIIDIIIIIII>IIIIII/
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
GTTCAGGGATACGACGATTGTATTTTAAGAATCTGCAGCAGAAGTCGATGATAATACGCGCCGTTTTATCAG
+SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I