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immcantation / changeo

Changeo-O is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). Change-O provides tools for processing the output of V(D)J alignment tools, assigning clonal clusters, and reconstructing germline sequences.
https://changeo.readthedocs.io
GNU Affero General Public License v3.0
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IMGT/V-QUEST #72

Closed ssnn-airr closed 8 years ago

ssnn-airr commented 8 years ago

Original report by Robert Amezquita (Bitbucket: [Robert A. Amezquita](https://bitbucket.org/Robert A. Amezquita), ).

Error with using IMGT/V-QUEST (not the HighV-QUEST) output. The resulting output (selecting C. Excel File, with outputs 1, 2, 3, 6 selected) seems to be missing a column for SEQUENCE. Might just be something that can be munged and added as an "aligner" option..?

[ra364@localhost changeo]$ MakeDb.py imgt -i ../imgt/ko_vquest.zip -s ../sequences/ko_seqs.fasta START> MakeDb ALIGNER> IMGT ALIGN_RESULTS> ../imgt/ko_vquest.zip SEQ_FILE> ko_seqs.fasta NO_PARSE> False SCORE_FIELDS> False REGION_FIELDS> False

Traceback (most recent call last): File "/home/ra364/.local/bin/MakeDb.py", line 1020, in args.func(**args_dict) File "/home/ra364/.local/bin/MakeDb.py", line 886, in parseIMGT score_fields=score_fields, region_fields=region_fields, out_args=out_args) File "/home/ra364/.local/bin/MakeDb.py", line 728, in writeDb for record in db_gen: File "/home/ra364/.local/bin/MakeDb.py", line 538, in readIMGT 'SEQUENCE_INPUT': sm['Sequence']} KeyError: 'Sequence'

ssnn-airr commented 8 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

So, it does indeed look like the field is missing in both "normal" V-QUEST and "indel" V-QUEST mode. I think the thing to do is just note in the docs that MakeDb-imgt only works with HighV-QUEST. I don't think maintaining separate V-QUEST support is worth it, especially if IMGT is going to continue to change the output.

ssnn-airr commented 8 years ago

Original comment by Namita Gupta (Bitbucket: namita1025, GitHub: namita1025).

Updated documentation to reflect V-QUEST is not supported in 6075a17913f7