The gto_fastq_complement replaces the ACGT bases with their complements in a FASTQ file format.
For help type:
./gto_fastq_complement -h
In the following subsections, we explain the input and output paramters.
The gto_fastq_complement 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_complement [options] [[--] args]
or: ./gto_fastq_complement [options]
It replaces the ACGT bases with their complements in a FASTQ file format.
-h, --help Show this help message and exit
Basic options
< input.fastq Input FASTQ file (stdin)
> output.fastq Output FASTQ file (stdout)
Example: ./gto_fastq_complement < 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
GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACCAAGTTACCCTTAACAACTTAAGGGTTTTCAAATAGA
+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
GTTCAGGGATACGACGTTTGTATTTTAAGAATCTGAAGCAGAAGTCGATGATAATACGCGTCGTTTTATCAT
+SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I
The output of the gto_fastq_complement program is the FASTQ file with the ACGT base complements.
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
CCCACTACCGGCGACGGCTACCGCAGTTTAGGGTGGTTCAATGGGAATTGTTGAATTCCCAAAAGTTTATCT
+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
CAAGTCCCTATGCTGCAAACATAAAATTCTTAGACTTCGTCTTCAGCTACTATTATGCGCAGCAAAATAGTA
+SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII6IBIIIIIIIIIIIIIIIIIIIIIIIGII>IIIII-I)8I