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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 does not always annotate using Ensembl (and 10X) GTF files
Using ftp://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
annotator does not identify transcripts that do not have a 'gene' annotation (ie. ENST00000606034)
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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