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annotator's Issues

Error but maybe still worked? 

[ecwheele@tscc-1-37 annotator]$ python annotate.py --input /projects/ps-yeolab3/clip_not_encode/ecwheele/20170614_SRSF2_eirini_all_clip/clipper_intjob_test/EW42_SRSF2_C1-8_diff_IP.merged.r2.peaks.for.kmers.bed --output /projects/ps-yeolab3/clip_not_encode/ecwheele/20170614_SRSF2_eirini_all_clip/clipper_intjob_test/EW42_SRSF2_C1-8_diff_IP.merged.r2.peaks.for.kmers.bed.annotated.bed --gtfdb /projects/ps-yeolab/genomes/hg19/gencode_v19/gencode.v19.annotation.gtf.db


Initializing/creating defs:  14%|#####8                                   | 1/7 [00:00<00:01,  5.46it/s]featuretypes = ['cds', 'selenocysteine', 'utr', 'exon', 'gene', 'start_codon', 'stop_codon', 'transcript']
Adding all CDS boundaries: 100%|##########################################| 7/7 [08:38<00:00, 76.37s/it]Traceback (most recent call last):                                                                      
  File "annotate.py", line 163, in <module>
    main()
  File "annotate.py", line 159, in main
    transcript_priority, gene_priority, species, append_chr, fuzzy
  File "build/bdist.linux-x86_64/egg/annotator/Annotator.py", line 661, in annotate
    interval, unstranded, transcript_priority, gene_priority,
ValueError: need more than 2 values to unpack

But the output looks like this:

chr1    17460   17568   3.5     6.13602943803   -       noncoding_exon  WASH7P  ENSG00000227232.4       
chr1    18350   18366   3.5     -3.47868845335  -       noncoding_exon  WASH7P  ENSG00000227232.4       
chr1    24737   24749   3.5     -3.45734563282  -       noncoding_exon  WASH7P  ENSG00000227232.4       
chr1    135156  135268  3.5     1.27031936123   -       3UTR    AL627309.1      ENSG00000237683.5       
chr1    135160  135268  3.5     -0.387692423984 -       3UTR    AL627309.1      ENSG00000237683.5       
chr1    137793  137852  3.5     0.13758028368   -       3UTR    AL627309.1      ENSG00000237683.5       
chr1    137794  137844  3.5     -2.14554667036  -       3UTR    AL627309.1      ENSG00000237683.5       
chr1    137963  137997  3.5     -3.83516567863  -       3UTR    AL627309.1      ENSG00000237683.5       
chr1    139037  139088  3.5     -0.768221275007 -       CDS     AL627309.1      ENSG00000237683.5

annotator.py error out

Command:
[ecwheele@tscc-login1 ica_testing]$ python /home/bay001/projects/codebase/annotator/annotate.py --input /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/outrigger/EW69_outrigger/outrigger_output/psi/outrigger_psi.bed --output /projects/ps-yeolab3/ecwheele/20170627_srsf2_all_rnaseq_eirini/outrigger/EW69_outrigger/outrigger_output/psi/outrigger_psi.annotated.bed --gtfdb /projects/ps-yeolab/genomes/hg19/gencode_v19/gencode.v19.annotation.gtf.db

Error:
Initializing/creating defs: 14%|###8 | 1/7 [00:00<00:01, 3.33it/s]featuretypes = ['cds', 'selenocysteine', 'utr', 'exon', 'gene', 'start_codon', 'stop_codon', 'transcript']
Building gene ids -> gene names dictionary: 29%|###1 | 2/7 [00:15<00:23, 4.71s/it]Traceback (most recent call last): | 0/25 [00:00<?, ?it/s]
File "/home/bay001/projects/codebase/annotator/annotate.py", line 183, in
main()
File "/home/bay001/projects/codebase/annotator/annotate.py", line 179, in main
transcript_priority, gene_priority, species, append_chr, fuzzy
File "/home/bay001/processing_scripts/codebase/annotator/Annotator.py", line 668, in annotate
annotator = Annotator(db_file, chroms, species, append_chr, fuzzy)
File "/home/bay001/processing_scripts/codebase/annotator/Annotator.py", line 71, in init
self._hash_features(append_chr, fuzzy)
File "/home/bay001/processing_scripts/codebase/annotator/Annotator.py", line 149, in _hash_features
for element in self._db.region(seqid=chrom):
TypeError: region() got an unexpected keyword argument 'seqid'

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