PWMTrain problem accepting FASTA files?

[Rayka Yokoo]

Hello EPD,

I am trying to upload my own sequences for PWMTrain but it doesn't seem to recognize that there are any input sequences.

As a control, I tried:

-- uploading the FASTA file, SRR3402432.fasta from the Sequence Read Archive. 

-- ‎running the 'Select available data sets' option, then downloading the filtered sequences (there is no link provided for input reads), and taking the resulting file, SRR3402432_all.seq, and uploading it.

Both with a sequence length of 30. 

Each time, PWMTrain indicates there are 0 reads in the Input file. When I download the link for the Input reads when I've uploaded SRR3402432.fasta, it appears to return the fasta file as it's been uploaded. When I download the link for the Filtered reads, I get an empty file.

Can you help me figure out what the problem is?

Thank you,

Rayka Yokoo

[CCG EPFL]

Thank you for reporting this issue. This is bug, we are aware of the problem and hope to be able to fix it in due time. Give us a week or so.

Philipp 

[CCG EPFL]

I think I have fixed the bug, You may try a new version at

https://epd.expasy.org/pwmtools/test/pwmtrain.php

and let us know whether it works for you or not.

Philipp