rapid_join.pl

[Rhia15]

Hi, I recently managed to convert my agp file from pretextview to a tpf and chrs.csv file, however, when I use the rapid_join.pl script to convert these into a fasta file, i get a file with rows of '>' (in image )

When I run the perl script, I get no errors. I have ran this perl script on a previous assembly in the same environment and had no problems producing the fasta file, it seems to be this particular assembly. I have also checked the tpf and csv file produced and they seem to be fine? So I was just wondering if you have previously encountered this?

Thank you very much. Any advice would be greatly appreciated.

I have attached the tpf (txt format), and csv file used to run the script if that helps :)
chrs.csv
out.txt

[additive3]

Hi @Rhia15

Never seen that before. I'll take a look more tomorrow.
Would you be able to provide the AGP and initial assembly file?

[Rhia15]

Hi, Thank you for the quick response! I have attached the agp file in text format, but it won't let me upload the fasta file because it's too large. Can I send this to you via an email address?

pyhap2.2_gap_telomere.pretext.agp.txt

[additive3]

Email limit likely 20Mb attachement size, can you share over sftp, google drive or other? [email protected]