optimized-insilico

Dependencies:

• pysam
• itertools

Installation

git clone https://github.com/TaoZhou2021/optimized-insilico.git or git clone [email protected]:TaoZhou2021/optimized-insilico.git

There are three scripts in the optimized-insilico/bin/

• sam2fq.py ------------- select the mate-pairs and also filtered mate-pairs(optional)
• simulate.py ------------- simulate the ancient DNA reads using one strand of paired-end reads
• summary.py ------------- summary the results of mate-pairs aligned to the reference(select mate-pairs or filtered mate-pairs)

Getting Started

select mate-pairs without output their align results
(1) only select mate-pairs:

python3 sam2fq.py -s 500 -dev 0.2 -length 100 -in 500-mp.sam -ss select-500-mp.sam -out1 select-500-mp.R1.fq -out2 select-500-mp.R2.fq  

(2) select mate-pairs and also output of filtered mate-pairs without their align results:

python3 sam2fq.py -s 500 -dev 0.2 -length 100 -in 500-mp.sam -ss select-500-mp.sam -out1 select-500-mp.R1.fq -out2 select-500-mp.R2.fq -fs filter-500-mp.sam -f1 filter-500-mp.R1.fq -f2 filter-500-mp.R2.fq

select mate-paris with output their align results

(1) only select mate-pairs and its summary file:

python3 sam2fq.py -s 500 -dev 0.2 -length 100 -in 500-mp.sam -ss select-500-mp.sam -out1 select-500-mp.R1.fq -out2 select-500-mp.R2.fq -as align_select-500-mp.txt

(2) select mate-pairs, output of filtered mate-pairs with their align results:

python3 sam2fq.py -s 500 -dev 0.2 -length 100 -in 500-mp.sam -ss select-500-mp.sam -out1 select-500-mp.R1.fq -out2 select-500-mp.R2.fq -as align_select-500-mp.txt -fs filter-500-mp.sam -f1 filter-500-mp.R1.fq -f2 filter-500-mp.R2.fq -af algin_filter-500-mp.txt

simulate ancient DNA reads

(1) simulate ancient DNA reads (80 to 100 bp long)

python3 simulate.py -s 80 -e 100 -in my.fastq -out simulate-aDNA.fq.gz

summary the align results of mate-pairs

(1) summary the align results of selected mate-pairs

python3 summary.py -s 500 -in align_select-500-mp.txt -out summary-select-500-mp.txt

(2) summary the align results of filtered mate-pairs

python3 summary.py -s 500 -in align_filter-500-mp.txt -out summary-filter-500-mp.txt