--prefix not used

[webbchen]

Dear developers

I ran:

/path/to/apps/fixchr/bin/fixchr \
-c /path/to/some_comparative_genomics/syri_Hp1_to_pm1.delta.m.coords \
-r /path/to/some_comparative_genomics/assembly_pm1_v1_upper.fasta \
-q /path/to/some_comparative_genomics/Hp1.fasta \
--contig_size 5000 \
--dir /path/to/some_comparative_genomics/ \
--prefix Hp1_to_pm1

but the output had no prefix whatsoever.

ref.filtered.fa
qry.filtered.fa
homologous_strand_corrected.pdf
homologous_strand_corrected_alignments.txt
homologous_alignments.txt
homologous.pdf
input.pdf
input_alignments.txt

Which is harmless, unless you run more than one instance.

Kind regards,

AWebb

[mnshgl0110]

Thanks for pointing this out. It seems that I have not implemented this yet. I will try to add this when I get some time. Pull requests to add this feature are also welcome.

[hyBio]

“
ref.filtered.fa
qry.filtered.fa
homologous_strand_corrected.pdf
homologous_strand_corrected_alignments.txt
homologous_alignments.txt
homologous.pdf
input.pdf
input_alignments.txt
”
Which file is the input file that needs to be used for the syri -c, I found that the files returned by fixchr will have a header line, which will cause the syri to report an error, and I may need to delete them manually, can this be avoided in the code? like this:
$$$ awk '!($1 ~ /^[0-9]+$/) {print}' homologous_strand_corrected_alignments.txt
aStart aEnd bStart bEnd aLen bLen iden aDir bDir aChr bChr cigar

[mnshgl0110]

@hyBio Please check this: #9 (comment)

[hyBio]

I don't think the link you gave me solves my problem. Fixchr cannot be downloaded from bioconda at all. I think it is necessary for you to write a separate tutorial on how to seamlessly connect the results of fixchr to syri. It would be great if that were the case.

[hyBio]

One more thing. If I use fixchr for adjustment, it means I need to adjust the second query fa according to the chromosome of the first fa, and then use the second fa as the new ref to adjust the third one. And so on. This is a very complicated task and I don't know if the accuracy of the alignment can be guaranteed.