Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Problem when simulate a simple graph #72

Open
slbai01 opened this issue Jul 22, 2022 · 0 comments
Open

Problem when simulate a simple graph #72

slbai01 opened this issue Jul 22, 2022 · 0 comments

Comments

@slbai01
Copy link

slbai01 commented Jul 22, 2022

To track the minigraph behaviour, I design a simple graph which contains some INS/DEL and INV.

for x in `seq 1 500000`; do echo $(( ( RANDOM % 4 ) + 1 )); done | sed 's/1/A/g' | sed 's/2/T/g' | sed 's/3/C/g' | sed 's/4/G/g' | tr '\n' ' ' | sed 's/ //g'  > seg1.fa
for x in `seq 1 350000`; do echo $(( ( RANDOM % 4 ) + 1 )); done | sed 's/1/A/g' | sed 's/2/T/g' | sed 's/3/C/g' | sed 's/4/G/g' | tr '\n' ' ' | sed 's/ //g'  > seg2.fa
for x in `seq 1 410000`; do echo $(( ( RANDOM % 4 ) + 1 )); done | sed 's/1/A/g' | sed 's/2/T/g' | sed 's/3/C/g' | sed 's/4/G/g' | tr '\n' ' ' | sed 's/ //g'  > seg3.fa
for x in `seq 1 320000`; do echo $(( ( RANDOM % 4 ) + 1 )); done | sed 's/1/A/g' | sed 's/2/T/g' | sed 's/3/C/g' | sed 's/4/G/g' | tr '\n' ' ' | sed 's/ //g'  > seg4.fa
for x in `seq 1 460000`; do echo $(( ( RANDOM % 4 ) + 1 )); done | sed 's/1/A/g' | sed 's/2/T/g' | sed 's/3/C/g' | sed 's/4/G/g' | tr '\n' ' ' | sed 's/ //g'  > seg5.fa
for x in `seq 1 500000`; do echo $(( ( RANDOM % 4 ) + 1 )); done | sed 's/1/A/g' | sed 's/2/T/g' | sed 's/3/C/g' | sed 's/4/G/g' | tr '\n' ' ' | sed 's/ //g'  > seg6.fa
for x in `seq 1 450000`; do echo $(( ( RANDOM % 4 ) + 1 )); done | sed 's/1/A/g' | sed 's/2/T/g' | sed 's/3/C/g' | sed 's/4/G/g' | tr '\n' ' ' | sed 's/ //g'  > seg7.fa
for x in `seq 1 380000`; do echo $(( ( RANDOM % 4 ) + 1 )); done | sed 's/1/A/g' | sed 's/2/T/g' | sed 's/3/C/g' | sed 's/4/G/g' | tr '\n' ' ' | sed 's/ //g'  > seg8.fa
for x in `seq 1 520000`; do echo $(( ( RANDOM % 4 ) + 1 )); done | sed 's/1/A/g' | sed 's/2/T/g' | sed 's/3/C/g' | sed 's/4/G/g' | tr '\n' ' ' | sed 's/ //g'  > seg9.fa


echo ">seq1" > seq1.fa; cat seg1.fa seg2.fa seg3.fa seg4.fa seg5.fa seg6.fa >> seq1.fa 
echo ">seq2" > seq2.fa; cat seg1.fa seg7.fa seg8.fa seg2.fa seg4.fa seg6.fa >> seq2.fa 
echo ">seq3" > seq3.fa; cat seg1.fa seg9.fa seg3.fa seg5.fa seg4.fa seg6.fa >> seq3.fa

But when I run the command, only one sequence generates, this makes me confused.
I install the software through conda, and I used two version (0.19-r551 and 0.15-r426)

minigraph -cxggs -l10k seq1.fa seq2.fa seq3.fa   > sample.gfa && cut -f 1,2,4- sample.gfa
# S       s1      LN:i:2540000    SN:Z:seq1       SO:i:0  SR:i:0
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant