add sequence read in for 10x json #619
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grst
reviewed
Jun 7, 2025
| @@ -130,6 +130,9 @@ def _read_10x_vdj_json( | |||
| chain["productive"] = contig["productive"] | |||
| chain["is_cell"] = contig["is_cell"] | |||
| chain["high_confidence"] = contig["high_confidence"] | |||
| chain["sequence"] = contig["sequence"] | |||
| chain["aa_sequence"] = contig["aa_sequence"] | |||
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The AIRR field should be sequence_aa, no?
https://docs.airr-community.org/en/latest/datarep/rearrangements.html#fields
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you are correct. I can also look into adding support for csv load on this PR.
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Previously, full nt or aa tcr sequences from 10x contigs are not being read in by
read_10x_vdj. This PR adds those attributes when read from 10x json output.