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dib-lab / dammit

just annotate it, dammit!
http://dib-lab.github.io/dammit/
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Error in BLAST remap #51

Closed camillescott closed 8 years ago

camillescott commented 8 years ago

[originally from @abshah]

Hi Camille, I just tried running the example datasets and ended up with a slightly different error!

`--- Running annotate!

      Transcriptome file: cdna_nointrons_utrs.fa

      Output directory: /home/abhijeet/dammit_test/cdna_nointrons_utrs.fa.dammit

      [ ] cdna_nointrons_utrs.fa

      [ ] transcriptome_stats:cdna_nointrons_utrs.fa

      [ ] busco:cdna_nointrons_utrs.fa-eukaryota

      [ ] TransDecoder.LongOrfs:cdna_nointrons_utrs.fa

      [ ] hmmscan:longest_orfs.pep.x.Pfam-A.hmm

      [ ] remap_hmmer:longest_orfs.pep.pfam.tbl

      [ ] TransDecoder.Predict:cdna_nointrons_utrs.fa

      [ ] cmscan:cdna_nointrons_utrs.fa.x.Rfam.cm

      [ ] lastal:cdna_nointrons_utrs.fa.x.orthodb.maf

      [ ] sanitize_fasta:pep.fa

      [ ] crb-blast:cdna_nointrons_utrs.fa.x.pep.fa

      [ ] maf_best_hits:cdna_nointrons_utrs.fa.x.orthodb.maf-
      cdna_nointrons_utrs.fa.x.orthodb.maf.best.csv

      [ ] maf-gff3:cdna_nointrons_utrs.fa.x.orthodb.maf.gff3

      [ ] hmmscan-gff3:cdna_nointrons_utrs.fa.pfam.csv.gff3

      [ ] cmscan-gff3:cdna_nointrons_utrs.fa.rfam.tbl.gff3

      [ ] crbb-gff3:cdna_nointrons_utrs.fa.x.pep.fa.crbb.tsv.gff3

Some tasks failed![dammit.annotate:ERROR] TaskError - taskid:crbb-gff3:cdna_nointrons_utrs.fa.x.pep.fa.crbb.tsv.gff3[dammit.annotate:ERROR] PythonAction Error Traceback (most recent call last): File "/home/abhijeet/anaconda2/lib/python2.7/site-packages/doit/action.py", line 383, in execute returned_value = self.py_callable(_self.args, *_kwargs) File "/home/abhijeet/anaconda2/lib/python2.7/site-packages/dammit/tasks.py", line 539, in cmd remap=True): File "/home/abhijeet/anaconda2/lib/python2.7/site-packages/dammit/parsers.py", line 284, in crb_to_df_iter remap_blast(group) File "/home/abhijeet/anaconda2/lib/python2.7/site-packages/dammit/blast.py", line 68, in remap_blast_coords_df df['sstrand'] = coords[coords:,4] IndexError: invalid slice [dammit.annotate:ERROR] Some tasks failed![dammit.annotate:ERROR] UnmetDependency - taskid:gff3-merge:cdna_nointrons_utrs.fa.dammit.gff3[dammit.annotate:ERROR] crbb-gff3:cdna_nointrons_utrs.fa.x.pep.fa.crbb.tsv.gff3 [dammit.annotate:ERROR] Some tasks failed![dammit.annotate:ERROR] UnmetDependency - taskid:fasta-annotate:cdna_nointrons_utrs.fa.dammit.fasta[dammit.annotate:ERROR] gff3-merge:cdna_nointrons_utrs.fa.dammit.gff3 [dammit.annotate:ERROR]`

mpj5142 commented 8 years ago

I'm running this on the test data now (I had the same issue as @abshah), but I think it could be a typo/bug in blast.py:

Line 68 reads df['sstrand'] = coords[coords:,4] But maybe it should be df['sstrand'] = coords[:,4] as the rest of the remapping functions follow that pattern.

I'll report back after re-running the code with the correction...

mpj5142 commented 8 years ago

That fix worked! I'm pretty new to GitHub so I don't want to mess anything up with a pull request...

camillescott commented 8 years ago

Indeed, it is definitely just a typo (and I'm kind of vexed how it got past the acceptance tests) -- I intend to push a new release tomorrow, but I've been very swamped with the end of our quarter :) I really ought to put up some contributor instructions for people to help with fixes like this!

mpj5142 commented 8 years ago

Glad I could help!

abshah commented 8 years ago

Runs fine now! Thanks @camillescott and @mpj5142

camillescott commented 8 years ago

Officially fixed in 0.2.8, thanks all!