Program gto_fastq_cut

The gto_fastq_cut cuts read sequences in a FASTQ file. It requires that the initial and end positions for the cut.

For help type:


			  			./gto_fastq_cut -h

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

Input parameters

The gto_fastq_cut 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_cut [options] [[--] args]
or: ./gto_fastq_cut [options]

It cuts read sequences in a FASTQ file.

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

Basic options
-i, --initial=   Starting position to the cut
-e, --end=       Ending position to the cut
< input.fastq         Input FASTQ file format (stdin)
> output.fastq        Output FASTQ file format (stdout)

Example: ./gto_fastq_cut -i  -e  < 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

Output

The output of the gto_fastq_cut program is a FASTQ file cut.

Using the initial value as 10 and the end value as 30, an example for this input, is:


			  			@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72
CGCTGCCGATGGCGTCAAATC
+
IIIIIIIIIIIIIIIIIIII9
@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72
ACGACGTTTGTATTTTAAGAA
+
IIIIIIIIIIIIIIIIIIIII