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immcantation / presto

pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
https://presto.readthedocs.io
GNU Affero General Public License v3.0
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Add barcode length parameter for MaskPrimers #94

Open ggabernet opened 3 weeks ago

ggabernet commented 59 minutes ago

@javh sorry for bothering about pRESTO, but I really could not find the reason why the new unit test I created is failing and I thought maybe you have some ideas.

I tried implementing a barcode_length parameter to be able to extract specific positions as UMI barcodes with MaskPrimers.

It seems to be working fine but the new test I generated is failing though with :

FAIL: test_maskSeq (tests.test_MaskPrimers.TestMaskPrimers.test_maskSeq)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/__w/presto/presto/tests/test_MaskPrimers.py", line 238, in test_maskSeq
    self.assertEqual(self.mask_seq_cut_barcodelen.id, result.id)
AssertionError: 'SEQ|PRIMER=A|BARCODE=CA' != '|PRIMER=A|BARCODE=CA'
- SEQ|PRIMER=A|BARCODE=CA
? ---
+ |PRIMER=A|BARCODE=CA

And I can't figure out why it is not parsing the SEQ as well for this test as I defined it the same way as the other tests.