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Added test for splitted sequence - #9

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r-mllr:added_test_for_splitted_sequence
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Added test for splitted sequence#9
r-mllr wants to merge 3 commits into
jlab:masterfrom
r-mllr:added_test_for_splitted_sequence

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@r-mllr

@r-mllr r-mllr commented Nov 26, 2020

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Added simple tests, which guarantees different md5 checksums for non-identical sequences, which are identical after concatination.

Raphael Müller added 2 commits November 26, 2020 14:51
This test setup checks if the md5 checksum is different if
one entry of the fasta file is split into two
@sjanssen2

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Hi @r-mllr thanks for your PR. I am not sure if I understand exactly what you expect the method to do. Frank brought up the example of two files:

>Seq1
ACGT
>Seq2
ACGT

and

>Seq3
ACGTACGT

which would get the same md5 sum assigned. This is exactly what I want, since I think of fasta files as results of assemblies. The file above would represent an older assembly with two contigs / scaffolds, the lower file is a revision in which people found a way how to resolve the gap between Seq1 and Seq2. The genomic content itself remains unchanged - therefore it is intended that the md5sum also does not change.

@r-mllr

r-mllr commented Nov 26, 2020

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Ah, then, I misunderstood the consept. I thought the checksums should not be equal.

Then, you should change

self.assertNotEqual
to
self.assertEqual

The tests should fail, then

@sjanssen2

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If this method is of general interest, we could add a parameter to control the behaviour.

@r-mllr
r-mllr marked this pull request as draft November 26, 2020 14:38
@r-mllr

r-mllr commented Nov 26, 2020

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not sure. I convert the pull request to a draft pull request for the case it comes up in the future

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2 participants