- 23 May, 2019 4 commits
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Mathieu Giraud authored
link to #3910
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Thonier Florian authored
link to #3910
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Thonier Florian authored
Link to #3910
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Thonier Florian authored
link to #3910
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- 06 Dec, 2018 3 commits
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Mathieu Giraud authored
See #3515.
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Mathieu Giraud authored
See #3515.
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Mathieu Giraud authored
Note that we should also keep inframeP, which has gaps. See #3515.
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- 13 Jul, 2018 8 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
Partially revert 806f2180. See #2645.
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Mathieu Giraud authored
We also want to be able to take sequences from NCBI and gap them. See #2645. Partially revert 806f2180.
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Mikaël Salson authored
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Mikaël Salson authored
This allows to use IMGT sequences even for up and downstream sequences.
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Mikaël Salson authored
The messages are saved and displayed at the end to ease the analysis of those warnings.
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Mikaël Salson authored
We need to ignore case as well as dots that can be introduced by gapped sequences as well as comments that may be introduced by missing Phe.
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Mikaël Salson authored
Otherwise it creates .1, .2, … files
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- 12 Jul, 2018 6 commits
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Mikaël Salson authored
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Mikaël Salson authored
See #3356.
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Mikaël Salson authored
Between get_updownstream_sequences and get_gene_sequence
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Mikaël Salson authored
When the J gene is too deleted we may not have enough signal. This should help recognizing more J recombinations. See #3008. (edited by @magiraud following 928c7390)
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Mikaël Salson authored
See #3362
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Mikaël Salson authored
Changes in IMGT: - Addition of 8 IGHV genes and alleles (8 F):IGHV1-8*03, IGHV1-69*15, IGHV1-69*16, IGHV2-26*02, IGHV2-26*03, IGHV2-70*15, IGHV2-70*16, IGHV2-70*17. - Update of reference sequences of IGHV1-45*03 and IGHV2-70*04 (partial sequences were replaced with complete V-REGION). - TRAJ13*02 reference sequence is AB258131. See http://www.imgt.org/IMGTgenedbdoc/dataupdates.html Other changes in MD5 should be due to changes in headers but this is not always true. - IGKV2D-26*02 has gained 2 nucleotides at its end - TRGV2*03 has appeared We note that the new IGHV genes allow to diminish the number of ambiguous k-mers on S22 dataset
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- 11 Jul, 2018 5 commits
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Mikaël Salson authored
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Mikaël Salson authored
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Mikaël Salson authored
As raised by @magiraud in !182 the parameters are far from being obvious
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Mikaël Salson authored
Having a key for upstream and downstream data is not adapted to our current needs. Different sequences may share a common accession number which then leads to a problem when outputting sequences (see #3148). Followed @magiraud suggestion: #3148 (comment 104665)
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Mikaël Salson authored
Make sure that IGHD and IGHD+up orders are identical and that the IGHD+up looks ok. See #3148
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- 10 Jul, 2018 14 commits
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Mikaël Salson authored
Not sure that the l flag from should.py could nicely apply here.
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Mikaël Salson authored
In the XML output the coordinates are 0-based: “returns the chromosomal position of that gene in 0-based coordinates” https://www.ncbi.nlm.nih.gov/books/NBK179288/ Are you serious guys?
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Mikaël Salson authored
chromosome:GRCh38:14:105916826:105916885:-1 See #3009
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Mikaël Salson authored
We are aware that the header is not correct. However this is not new. See !182
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Mikaël Salson authored
I'm not sure what the case should be as some sequences are uppercase while others are lowercase. Thus the regex should ignore case to be more robust.
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Mikaël Salson authored
If a genome position is available we get the upstream and downstream sequences and paste it to the existing allele sequence. Therefore now we always have to recover the allele sequence, which was not the case before. See #3009
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Mikaël Salson authored
See #3009
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Mikaël Salson authored
Used for #3009. We just want to get the upstream or the downstream raw sequence to be able to paste it before the allele sequence by itself. We need to take care on the sequence orientation. fixup ncbi.py updown
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Mikaël Salson authored
Allow to reach up to 10 rq/sec instead of 3. See here for having one : https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
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Mikaël Salson authored
We use this for reorganizing where tests are launched
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Mathieu Giraud authored
See #3009.
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
Closes #3009 ? To be verified.
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