Closed mschilli87 closed 8 years ago
@@ new_tests #64 diff @@
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There are two issues:
unit_test.py
still returns 0
, resulting in a positive build status.I'll investigate the first in more detail & opened #65 for the latter.
thanks mschilli, it could very well be that the problem is in the list itself (don't remember how and when i derived it). i'll write a small function extracting them directly from the annotation file.
quick and dirty: how about using these one-liners to create new files? when i'll have more time i'll write them in python. -- extract_single_utr_genes.sh zcat test_data/Homo_sapiens.GRCh38.84_chr9.gtf.gz | awk '$3 == "three_prime_utr" {print $18}' | sort | uniq -c | awk '$1 == 1 {print $2}' | cut -c2- | sed 's/..$//' -- extract_genes_with_pAi.sh awk '{print $4}' test_data/output/pAi_gene.bed | uniq | sort | uniq -- extract all single UTR genes WITHOUT pAi comm -23 <(extract_single_utr_genes.sh) <(extract_genes_with_pAi.sh)
I tried to set this up & it might work but this will require building test_data/output/pAi_gene.bed
for every unit test which will also need the corresponding FASTA file first.
Do we really want to go there or just update the list manually once now & keep it in the repo for the time being?
no no no! we don't want to go there! my motivation was that you inspect the one-liners and if you find them ok just update the list manually and add it to the repo :)
Once https://github.com/rajewsky-lab/polyA/pull/69/commits/663a9baf81e0f36f86c4f74947ab8b94c99d5b5d is merged to master
, I'll merge it into here & proceed with updating test_data/single_utr_no_pAi_genes.txt
as suggested.
cool. i merged the bugfix into the master, everything should be fine now.
I merged in https://github.com/rajewsky-lab/polyA/pull/72/commits/021f7ec694bde85f079d90796888206348d6b8b9 and all tests passed now!
Thus, pulling this into master
will finally fix #60.
perfect :) should i test and merge or yo uhave more to commit?
I labeled 'test & merge to master' & assigned you. ;)
haha ok i missed the "being assigned" part. will do asap
Working on issue #60:
Adding unit tests to ensure that genes listed as single UTR no internal poly(A) sites have
edit:
As the single UTR test above failed, I'll add additional tests to figure out what is going on.
These test will ensure that genes listed as single UTR no internal poly(A) sites have