Created
January 4, 2017 21:25
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gffutils weird error for inserting transcript on novel feature
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| (outrigger) ➜ outrigger git:(merge_exon_finding_and_junction_adjacencies) ✗ python -m pdb outrigger/commandline.py index --sj-out-tab outrigger/tests/data/tasic2016/unprocessed/sj_out_tab/originals/CAV_LP_Ipsi_tdTpos_cell_1*SJ.out.tab --gtf outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.subset.gtf --output $OUTPUT | |
| > /Users/olga/workspace-git/outrigger/outrigger/commandline.py(3)<module>() | |
| -> import argparse | |
| (Pdb) c | |
| 2017-01-04 12:41:14 Creating folder tasic2016_big_outrigger_output ... | |
| 2017-01-04 12:41:14 Done. | |
| 2017-01-04 12:41:14 Creating folder tasic2016_big_outrigger_output/index ... | |
| 2017-01-04 12:41:14 Done. | |
| 2017-01-04 12:41:14 Creating folder tasic2016_big_outrigger_output/index/gtf ... | |
| 2017-01-04 12:41:14 Done. | |
| 2017-01-04 12:41:14 Creating folder tasic2016_big_outrigger_output/junctions ... | |
| 2017-01-04 12:41:14 Done. | |
| 2017-01-04 12:41:14 Reading SJ.out.files and creating a big splice junction table of reads spanning exon-exon junctions... | |
| 2017-01-04 12:41:16 Writing tasic2016_big_outrigger_output/junctions/reads.csv ... | |
| 2017-01-04 12:41:21 Done. | |
| 2017-01-04 12:41:21 Filtering for only junctions with minimum 10 reads ... | |
| 2017-01-04 12:41:22 75379/108342 junctions remain after filtering out 32963 junctions with < 10 reads. | |
| 2017-01-04 12:41:22 Done. | |
| 2017-01-04 12:41:22 Creating splice junction metadata of merely where junctions start and stop | |
| 2017-01-04 12:41:22 Done. | |
| 2017-01-04 12:41:22 Writing metadata of junctions to tasic2016_big_outrigger_output/junctions/metadata.csv ... | |
| 2017-01-04 12:41:22 Found GTF file in outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.subset.gtf | |
| 2017-01-04 12:41:22 Creating a "gffutils" database tasic2016_big_outrigger_output/index/gtf/gencode.vM10.annotation.subset.gtf.db ... | |
| 2017-01-04 12:41:23,363 - INFO - Committing changes: 0 features | |
| INFO:gffutils.create:Committing changes | |
| 2017-01-04 12:41:23,387 - INFO - Populating features table and first-order relations: 772 features | |
| INFO:gffutils.create:Populating features table and first-order relations: 772 features | |
| 2017-01-04 12:41:23,387 - INFO - Creating relations(parent) index | |
| INFO:gffutils.create:Creating relations(parent) index | |
| 2017-01-04 12:41:23,389 - INFO - Creating relations(child) index | |
| INFO:gffutils.create:Creating relations(child) index | |
| 2017-01-04 12:41:23,390 - INFO - Creating features(featuretype) index | |
| INFO:gffutils.create:Creating features(featuretype) index | |
| 2017-01-04 12:41:23,391 - INFO - Creating features (seqid, start, end) index | |
| INFO:gffutils.create:Creating features (seqid, start, end) index | |
| 2017-01-04 12:41:23,392 - INFO - Creating features (seqid, start, end, strand) index | |
| INFO:gffutils.create:Creating features (seqid, start, end, strand) index | |
| 2017-01-04 12:41:23,393 - INFO - Running ANALYSE features | |
| INFO:gffutils.create:Running ANALYSE features | |
| 2017-01-04 12:41:23 Done. | |
| 2017-01-04 12:41:23 Looking up which exons are already defined ... | |
| 2017-01-04 12:41:23 Done. | |
| 2017-01-04 12:41:23 Detecting de novo exons based on gaps between junctions ... | |
| 2017-01-04 12:41:23 Finding novel exons that are <=100nt between two junctions on chromosome GL456233.1 ... | |
| 2017-01-04 12:41:23 Done. | |
| 2017-01-04 12:41:23 Filtering for only novel exons on chromosome GL456233.1 ... | |
| 2017-01-04 12:41:23 Done. | |
| 2017-01-04 12:41:23 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:23 Done. | |
| 2017-01-04 12:41:23 Updating gffutils database with 4 novel exons on chromosome GL456233.1 ... | |
| 2017-01-04 12:41:23 Done. | |
| 2017-01-04 12:41:23 Finding novel exons that are <=100nt between two junctions on chromosome GL456350.1 ... | |
| 2017-01-04 12:41:23 Done. | |
| 2017-01-04 12:41:23 Filtering for only novel exons on chromosome GL456350.1 ... | |
| 2017-01-04 12:41:23 Done. | |
| 2017-01-04 12:41:23 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:23 Done. | |
| 2017-01-04 12:41:23 Updating gffutils database with 1 novel exons on chromosome GL456350.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Finding novel exons that are <=100nt between two junctions on chromosome GL456370.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Filtering for only novel exons on chromosome GL456370.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Updating gffutils database with 0 novel exons on chromosome GL456370.1 ... | |
| 2017-01-04 12:41:24 No novel exons found on chromosome GL456370.1 | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Finding novel exons that are <=100nt between two junctions on chromosome JH584293.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Filtering for only novel exons on chromosome JH584293.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Updating gffutils database with 3 novel exons on chromosome JH584293.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Finding novel exons that are <=100nt between two junctions on chromosome JH584294.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Filtering for only novel exons on chromosome JH584294.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Updating gffutils database with 2 novel exons on chromosome JH584294.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Finding novel exons that are <=100nt between two junctions on chromosome JH584304.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Filtering for only novel exons on chromosome JH584304.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Updating gffutils database with 0 novel exons on chromosome JH584304.1 ... | |
| 2017-01-04 12:41:24 No novel exons found on chromosome JH584304.1 | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Finding novel exons that are <=100nt between two junctions on chromosome JH792828.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Filtering for only novel exons on chromosome JH792828.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Updating gffutils database with 0 novel exons on chromosome JH792828.1 ... | |
| 2017-01-04 12:41:24 No novel exons found on chromosome JH792828.1 | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Finding novel exons that are <=100nt between two junctions on chromosome JH792830.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Filtering for only novel exons on chromosome JH792830.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Updating gffutils database with 1 novel exons on chromosome JH792830.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Finding novel exons that are <=100nt between two junctions on chromosome KB469738.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Filtering for only novel exons on chromosome KB469738.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Updating gffutils database with 2 novel exons on chromosome KB469738.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Finding novel exons that are <=100nt between two junctions on chromosome KB469740.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Filtering for only novel exons on chromosome KB469740.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Updating gffutils database with 3 novel exons on chromosome KB469740.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Finding novel exons that are <=100nt between two junctions on chromosome KB469741.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Filtering for only novel exons on chromosome KB469741.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Updating gffutils database with 1 novel exons on chromosome KB469741.1 ... | |
| 2017-01-04 12:41:24 Done. | |
| 2017-01-04 12:41:24 Finding novel exons that are <=100nt between two junctions on chromosome chr1 ... | |
| 2017-01-04 12:41:35 Done. | |
| 2017-01-04 12:41:35 Filtering for only novel exons on chromosome chr1 ... | |
| 2017-01-04 12:41:35 Done. | |
| 2017-01-04 12:41:35 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:36 Done. | |
| 2017-01-04 12:41:36 Updating gffutils database with 1277 novel exons on chromosome chr1 ... | |
| 2017-01-04 12:41:36 Done. | |
| 2017-01-04 12:41:36 Finding novel exons that are <=100nt between two junctions on chromosome chr10 ... | |
| 2017-01-04 12:41:45 Done. | |
| 2017-01-04 12:41:45 Filtering for only novel exons on chromosome chr10 ... | |
| 2017-01-04 12:41:45 Done. | |
| 2017-01-04 12:41:45 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:41:45 Done. | |
| 2017-01-04 12:41:45 Updating gffutils database with 1000 novel exons on chromosome chr10 ... | |
| 2017-01-04 12:41:46 Done. | |
| 2017-01-04 12:41:46 Finding novel exons that are <=100nt between two junctions on chromosome chr11 ... | |
| 2017-01-04 12:42:03 Done. | |
| 2017-01-04 12:42:03 Filtering for only novel exons on chromosome chr11 ... | |
| 2017-01-04 12:42:03 Done. | |
| 2017-01-04 12:42:03 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:42:03 Done. | |
| 2017-01-04 12:42:03 Updating gffutils database with 1663 novel exons on chromosome chr11 ... | |
| 2017-01-04 12:42:04 Done. | |
| 2017-01-04 12:42:04 Finding novel exons that are <=100nt between two junctions on chromosome chr12 ... | |
| 2017-01-04 12:42:11 Done. | |
| 2017-01-04 12:42:11 Filtering for only novel exons on chromosome chr12 ... | |
| 2017-01-04 12:42:11 Done. | |
| 2017-01-04 12:42:11 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:42:11 Done. | |
| 2017-01-04 12:42:11 Updating gffutils database with 1026 novel exons on chromosome chr12 ... | |
| 2017-01-04 12:42:12 Done. | |
| 2017-01-04 12:42:12 Finding novel exons that are <=100nt between two junctions on chromosome chr13 ... | |
| 2017-01-04 12:42:18 Done. | |
| 2017-01-04 12:42:18 Filtering for only novel exons on chromosome chr13 ... | |
| 2017-01-04 12:42:19 Done. | |
| 2017-01-04 12:42:19 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:42:19 Done. | |
| 2017-01-04 12:42:19 Updating gffutils database with 860 novel exons on chromosome chr13 ... | |
| 2017-01-04 12:42:19 Done. | |
| 2017-01-04 12:42:19 Finding novel exons that are <=100nt between two junctions on chromosome chr14 ... | |
| 2017-01-04 12:42:26 Done. | |
| 2017-01-04 12:42:26 Filtering for only novel exons on chromosome chr14 ... | |
| 2017-01-04 12:42:26 Done. | |
| 2017-01-04 12:42:26 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:42:26 Done. | |
| 2017-01-04 12:42:26 Updating gffutils database with 848 novel exons on chromosome chr14 ... | |
| 2017-01-04 12:42:26 Done. | |
| 2017-01-04 12:42:26 Finding novel exons that are <=100nt between two junctions on chromosome chr15 ... | |
| 2017-01-04 12:42:33 Done. | |
| 2017-01-04 12:42:33 Filtering for only novel exons on chromosome chr15 ... | |
| 2017-01-04 12:42:33 Done. | |
| 2017-01-04 12:42:33 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:42:33 Done. | |
| 2017-01-04 12:42:33 Updating gffutils database with 794 novel exons on chromosome chr15 ... | |
| 2017-01-04 12:42:33 Done. | |
| 2017-01-04 12:42:33 Finding novel exons that are <=100nt between two junctions on chromosome chr16 ... | |
| 2017-01-04 12:42:40 Done. | |
| 2017-01-04 12:42:40 Filtering for only novel exons on chromosome chr16 ... | |
| 2017-01-04 12:42:40 Done. | |
| 2017-01-04 12:42:40 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:42:40 Done. | |
| 2017-01-04 12:42:40 Updating gffutils database with 784 novel exons on chromosome chr16 ... | |
| 2017-01-04 12:42:40 Done. | |
| 2017-01-04 12:42:40 Finding novel exons that are <=100nt between two junctions on chromosome chr17 ... | |
| 2017-01-04 12:42:48 Done. | |
| 2017-01-04 12:42:48 Filtering for only novel exons on chromosome chr17 ... | |
| 2017-01-04 12:42:48 Done. | |
| 2017-01-04 12:42:48 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:42:48 Done. | |
| 2017-01-04 12:42:48 Updating gffutils database with 934 novel exons on chromosome chr17 ... | |
| 2017-01-04 12:42:49 Done. | |
| 2017-01-04 12:42:49 Finding novel exons that are <=100nt between two junctions on chromosome chr18 ... | |
| 2017-01-04 12:42:54 Done. | |
| 2017-01-04 12:42:54 Filtering for only novel exons on chromosome chr18 ... | |
| 2017-01-04 12:42:54 Done. | |
| 2017-01-04 12:42:54 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:42:54 Done. | |
| 2017-01-04 12:42:54 Updating gffutils database with 657 novel exons on chromosome chr18 ... | |
| 2017-01-04 12:42:54 Done. | |
| 2017-01-04 12:42:54 Finding novel exons that are <=100nt between two junctions on chromosome chr19 ... | |
| 2017-01-04 12:43:00 Done. | |
| 2017-01-04 12:43:00 Filtering for only novel exons on chromosome chr19 ... | |
| 2017-01-04 12:43:00 Done. | |
| 2017-01-04 12:43:00 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:43:00 Done. | |
| 2017-01-04 12:43:00 Updating gffutils database with 660 novel exons on chromosome chr19 ... | |
| 2017-01-04 12:43:00 Done. | |
| 2017-01-04 12:43:00 Finding novel exons that are <=100nt between two junctions on chromosome chr2 ... | |
| 2017-01-04 12:43:16 Done. | |
| 2017-01-04 12:43:16 Filtering for only novel exons on chromosome chr2 ... | |
| 2017-01-04 12:43:16 Done. | |
| 2017-01-04 12:43:16 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:43:16 Done. | |
| 2017-01-04 12:43:16 Updating gffutils database with 1903 novel exons on chromosome chr2 ... | |
| 2017-01-04 12:43:17 Done. | |
| 2017-01-04 12:43:17 Finding novel exons that are <=100nt between two junctions on chromosome chr3 ... | |
| 2017-01-04 12:43:25 Done. | |
| 2017-01-04 12:43:25 Filtering for only novel exons on chromosome chr3 ... | |
| 2017-01-04 12:43:25 Done. | |
| 2017-01-04 12:43:25 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:43:25 Done. | |
| 2017-01-04 12:43:25 Updating gffutils database with 980 novel exons on chromosome chr3 ... | |
| 2017-01-04 12:43:27 Done. | |
| 2017-01-04 12:43:27 Finding novel exons that are <=100nt between two junctions on chromosome chr4 ... | |
| 2017-01-04 12:43:38 Done. | |
| 2017-01-04 12:43:38 Filtering for only novel exons on chromosome chr4 ... | |
| 2017-01-04 12:43:38 Done. | |
| 2017-01-04 12:43:38 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-01-04 12:43:38 Done. | |
| 2017-01-04 12:43:38 Updating gffutils database with 1300 novel exons on chromosome chr4 ... | |
| Traceback (most recent call last): | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py", line 991, in _update_relations | |
| self._insert(f, c) | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py", line 520, in _insert | |
| cursor.execute(constants._INSERT, feature.astuple()) | |
| sqlite3.IntegrityError: UNIQUE constraint failed: features.id | |
| During handling of the above exception, another exception occurred: | |
| Traceback (most recent call last): | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/pdb.py", line 1661, in main | |
| pdb._runscript(mainpyfile) | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/pdb.py", line 1542, in _runscript | |
| self.run(statement) | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/bdb.py", line 431, in run | |
| exec(cmd, globals, locals) | |
| File "<string>", line 1, in <module> | |
| File "/Users/olga/workspace-git/outrigger/outrigger/commandline.py", line 3, in <module> | |
| import argparse | |
| File "/Users/olga/workspace-git/outrigger/outrigger/commandline.py", line 1057, in main | |
| cl = CommandLine(sys.argv[1:]) | |
| File "/Users/olga/workspace-git/outrigger/outrigger/commandline.py", line 343, in __init__ | |
| self.args.func() | |
| File "/Users/olga/workspace-git/outrigger/outrigger/commandline.py", line 347, in index | |
| index.execute() | |
| File "/Users/olga/workspace-git/outrigger/outrigger/commandline.py", line 754, in execute | |
| metadata, db) | |
| File "/Users/olga/workspace-git/outrigger/outrigger/commandline.py", line 618, in make_exon_junction_adjacencies | |
| exon_junction_adjacencies.detect_exons_from_junctions() | |
| File "/Users/olga/workspace-git/outrigger/outrigger/index/adjacencies.py", line 324, in detect_exons_from_junctions | |
| transform=transform) | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/interface.py", line 853, in update | |
| db._update_relations() | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py", line 993, in _update_relations | |
| fixed, final_strategy = self._do_merge(f, 'merge') | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py", line 288, in _do_merge | |
| self._add_duplicate(orig_id, uniqued_feature.id) | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py", line 360, in _add_duplicate | |
| (idspecid, newid)) | |
| sqlite3.IntegrityError: UNIQUE constraint failed: duplicates.newid | |
| Uncaught exception. Entering post mortem debugging | |
| Running 'cont' or 'step' will restart the program | |
| > /Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py(360)_add_duplicate() | |
| -> (idspecid, newid)) | |
| (Pdb) dir() | |
| ['c', 'idspecid', 'newid', 'self'] | |
| (Pdb) print(c) | |
| <sqlite3.Cursor object at 0x118d46030> | |
| (Pdb) idspecid | |
| 'transcript_1' | |
| (Pdb) newid | |
| 'transcript_1_1' | |
| (Pdb) u | |
| > /Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py(288)_do_merge() | |
| -> self._add_duplicate(orig_id, uniqued_feature.id) | |
| (Pdb) dir() | |
| ['_gffkeys_to_check', 'add_duplicate', 'existing_feature', 'f', 'features_to_merge', 'k', 'merge_strategy', 'orig_id', 'other_attributes_same', 'self', 'uniqued_feature'] | |
| (Pdb) orig_id | |
| 'transcript_1' | |
| (Pdb) existing_feaure | |
| *** NameError: name 'existing_feaure' is not defined | |
| (Pdb) existing_feature | |
| <Feature transcript (chr5:125385965-125390014[-]) at 0x11b433630> | |
| (Pdb) features_to_merge | |
| [] | |
| (Pdb) print(k) | |
| end | |
| (Pdb) print(f) | |
| chr5 gffutils_derived transcript 125387659 125389186 . - . transcript_id=ENSMUST00000108707.2;gene_id=ENSMUSG00000008348.9 | |
| (Pdb) print(uniqued_feature) | |
| chr5 gffutils_derived transcript 125387659 125389186 . - . transcript_id=ENSMUST00000108707.2;gene_id=ENSMUSG00000008348.9 | |
| (Pdb) print(existing_feature) | |
| chr5 gffutils_derived transcript 125385965 125390014 . - . transcript_id "ENSMUST00000136312.1"; gene_id "ENSMUSG00000008348.9"; | |
| (Pdb) existing_feature.id | |
| 'transcript_1' | |
| (Pdb) u | |
| > /Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py(993)_update_relations() | |
| -> fixed, final_strategy = self._do_merge(f, 'merge') | |
| (Pdb) u | |
| > /Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/interface.py(853)update() | |
| -> db._update_relations() | |
| (Pdb) u | |
| > /Users/olga/workspace-git/outrigger/outrigger/index/adjacencies.py(324)detect_exons_from_junctions() | |
| -> transform=transform) | |
| (Pdb) u | |
| > /Users/olga/workspace-git/outrigger/outrigger/commandline.py(618)make_exon_junction_adjacencies() | |
| -> exon_junction_adjacencies.detect_exons_from_junctions() | |
| (Pdb) d | |
| > /Users/olga/workspace-git/outrigger/outrigger/index/adjacencies.py(324)detect_exons_from_junctions() | |
| -> transform=transform) | |
| (Pdb) exon_features | |
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| (Pdb) chr5_features = [x for x in exon_features if x.chrom == 'chr5'] | |
| (Pdb) chr5_features | |
| [] | |
| (Pdb) print(x.chrom) | |
| *** NameError: name 'x' is not defined | |
| (Pdb) exon = exon_features[0] | |
| (Pdb) exon.chrom | |
| 'chr4' | |
| (Pdb) exon.id | |
| 'novel_exon:chr4:132544657-132544751:+' | |
| (Pdb) exon.attributes | |
| <gffutils.attributes.Attributes object at 0x11e9cd9e8> | |
| (Pdb) exon.attributes.items() | |
| [('location_id', ['novel_exon:chr4:132544657-132544751:+'])] | |
| (Pdb) list(exon.attributes.items()) | |
| *** Error in argument: '(exon.attributes.items())' | |
| (Pdb) exon.attributes.items() | |
| [('location_id', ['novel_exon:chr4:132544657-132544751:+'])] | |
| (Pdb) overlapping = [x for x in exon_features if (x.start > 125385965) and (x.stop < 125390014)] | |
| (Pdb) overlapping | |
| [] | |
| (Pdb) ^Z | |
| [3] + 15456 suspended python -m pdb outrigger/commandline.py index --sj-out-tab --gtf --output |
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