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feschottelab / REPCLASS

This tool facilitates transposable elements consensus classification
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wublast has been made obsolete #1

Open asifzubair opened 8 years ago

asifzubair commented 8 years ago

Hi,

The link for WU-BLAST - http://www.advbiocomp.com/blast.html - claims that wublast has been made obsolete. Instead, it has been replaced with AB-BLAST .

The README for REPCLASS doesn't seem to indicate if this change is supported by REPCLASS. Some documentation on this would be great.

Thanks !

asifzubair commented 8 years ago

Also, using the xdformat command in AB-BLAST is returning this error.

ab-blast $ ./xdformat -n -o db/repbase_all.fasta ~/projects/REPCLASS/1.0.1/repbase/repbase_all.fasta 
XDFORMAT 3.0PE-AB [2009-10-30] [macosx-10.5-x64-I32LPF64 2009-10-30T16:56:42]
Start:  2016-01-30T15:02:12
XDF Output Database:  db/repbase_all.fasta
 Alphabet:  NCBI2na.1
Input: "/Users/asifzubair/projects/REPCLASS/1.0.1/repbase/repbase_all.fasta"
  In sequence "Mariner-N4_NV" (record no. 11074):
    Invalid letter code encountered:  "l" (0x6c hex)
    Invalid letter code encountered:  "e" (0x65 hex)
XDF database removed

FATAL:  Aborted
asifzubair commented 8 years ago

I tried using the sed command in the README.md

sed '/>/! s/[QLSR]/N/g' input.seqs.fa > input.seqs.WBok.fa

but still getting the following error:

ab-blast$ ./xdformat -n -o my_db ~/projects/REPCLASS/1.0.1/repbase/input.seqs.WBok.fa
XDFORMAT 3.0PE-AB [2009-10-30] [macosx-10.5-x64-I32LPF64 2009-10-30T16:56:42]
Start:  2016-01-30T17:50:55
XDF Output Database:  my_db
 Alphabet:  NCBI2na.1
Input: "~/projects/REPCLASS/1.0.1/repbase/input.seqs.WBok.fa"
  In sequence "Mariner-N4_NV" (record no. 11074):
    Invalid letter code encountered:  "l" (0x6c hex)
    Invalid letter code encountered:  "e" (0x65 hex)
XDF database removed

FATAL:  Aborted
feschottelab commented 8 years ago

Hi, Could you try with this sed command? sed '/>/! s/[QLSRle]/N/g' input.seqs.fa > input.seqs.WBok.fa And you can add in the brackets any letter that create an error. Seems like AB-Blast, like Wu-Blast, does not support any unconventional letters in the consensus sequences. Let me know if the rest works with ab-blast instead of wublast!

JosieReinhardt commented 8 years ago

Hi, I'm trying to run REPCLASS as well, using ab-blast in the place of wublast. I found that the homology search was failing (and thus REPCLASS produced no output) because wu-blastall executable does not exist for ab-blast. I made a copy of the ab-blastall executable named wu-blastall and tried to run it again, and it does seem to be working.

On another note, it would be great if REPCLASS could be made compatible with ncbi blast, or if not, then the free version of wublast, which is still available here (http://www.advbiocomp.com/blast/obsolete/). The free version does not come with xdformat so it seems it can't be used with REPCLASS. Thanks!

stomk commented 7 years ago

Hi, I'm also thinking of using REPCLASS and came into the problem that WU-BLAST is unavailable anymore.

It would be great if you make the program compatible with NCBI-BLAST. As I'm a bit in a hurry, I'm thinking of doing it by myself, if you do not reply soon. In that case, I will send a pull request if the replacement works.

Thank you!

feschottelab commented 7 years ago

Could you send an email to 4urelie.k@gmail.com regarding this issue? Thanks!