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link to #3910

link to #3910

Link to #3910

link to #3910

See #3515.

See #3515.

Note that we should also keep inframeP, which has gaps.
See #3515.

Partially revert 806f2180.
See #2645.

We also want to be able to take sequences from NCBI and gap them. See #2645.
Partially revert 806f2180.

This allows to use IMGT sequences even for up and downstream sequences.

The messages are saved and displayed at the end to ease the analysis of those warnings.

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.

Otherwise it creates .1, .2, … files

See #3356.

Between get_updownstream_sequences and get_gene_sequence

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)

See #3362

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

As raised by @magiraud in !182 the parameters are far from being obvious

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)

Make sure that IGHD and IGHD+up orders are identical and that the
IGHD+up looks ok.

See #3148

Not sure that the l flag from should.py could nicely apply here.

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?

chromosome:GRCh38:14:105916826:105916885:-1

See #3009

We are aware that the header is not correct. However this is not new.

See !182

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.

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

See #3009

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

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/

We use this for reorganizing where tests are launched

See #3009.

Closes #3009 ? To be verified.