discosnp contig extension on test dataset

Question

[rob.lanfear]

Hi,

I have been trying to replicate the test analyses in the discosnp manual, but I am running into trouble with the extending the central sequence with contigs and unitigs.

Specifically, using v2.0.0 I get identical output (i.e. a .fa file with central sequences only, pasted below) when I run these three commands:

./run_discoSnp++.sh -r "data_sample/reads_sequence1.fasta.gz data_sample/reads_sequence2.fasta.gz" -p test
./run_discoSnp++.sh -r "data_sample/reads_sequence1.fasta.gz data_sample/reads_sequence2.fasta.gz" -p test -T
./run_discoSnp++.sh -r "data_sample/reads_sequence1.fasta.gz data_sample/reads_sequence2.fasta.gz" -p test -t

I have checked that it's nothing to do with passing the arguments through the script: it makes no difference to the output if I change the default in the script instead of passing the argument via the command line, i.e. changing

extend=""to extend="-T" or extend="-t" and running the script without passing additional options still produces the same .fa file as pasted below. (Note, I delete the file after each run, just to make sure..., and the script finishes successfully each time).

Any tips? Am I doing something wrong?

Thanks,

Rob

Output from all commands in this file:

test_k_31_c_4_D_0_P_1_b_0_coherent.fa

>SNP_higher_path_3|high|nb_pol_1|C1_0|C2_134|rank_1.00000
CAAGTGCACTTCCACAGAGCGCGGTAGAGAGTCATCCACCCGGCAGCTCTGTAATAGGGAC
>SNP_lower_path_3|high|nb_pol_1|C1_124|C2_0|rank_1.00000
CAAGTGCACTTCCACAGAGCGCGGTAGAGACTCATCCACCCGGCAGCTCTGTAATAGGGAC
>SNP_higher_path_2|high|nb_pol_1|C1_0|C2_86|rank_1.00000
ACTAATAGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCGGTCCAT
>SNP_lower_path_2|high|nb_pol_1|C1_74|C2_0|rank_1.00000
ACTAATAGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCGGTCCAT
>SNP_higher_path_1|high|nb_pol_1|C1_110|C2_0|rank_1.00000
GCAGCGCAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCAGTTCTA
>SNP_lower_path_1|high|nb_pol_1|C1_0|C2_114|rank_1.00000
GCAGCGCAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCAGTTCTA

Answer 1

[pierre.peterlongo]

Hi again Rob

Indeed, we have a problem with the command line parser. We fix this problem, hopefully that day.

Pierre

[pierre.peterlongo]

Hello there,

The bug about parameter parsing was fixed today. The new discoSnp++ release (2.0.1) works well with option -t and -T (and -l that was also affected).

Download here: https://colibread.inria.fr/files/2013/10/DiscoSNPpp-2.0.1-Source.zip

(for Rob: the display problem remains on OSX, it should be fixed soon)

Pierre

[rob.lanfear]

Thanks! This is awesome. I know what a pain it is spending time on fixing bugs with different OS's (rather than developing the actual methods), so I'm super grateful.

[rob.lanfear]

Just to confirm: I downloaded, recompiled, and reran the tests. This time I get the expected behaviour with -T and -t.

Thanks,

Rob