[Biopython] SeqIO.parse for imgt

Liu, Chang cliu32 at wustl.edu
Fri Nov 4 15:30:12 UTC 2016


Hi, everyone,
I am new to this mail list, so please bear with my ignorance.
I am using SeqIO to parse the hla.dat file from the IMGT/HLA database (https://github.com/ANHIG/IMGTHLA/tree/3160):
Handle='hla.dat'
records=SeqIO.parse(handle, 'imgt')
The code only works for files up to version 3.16.0, but not any data files after that. The following was raised:
ValueError: Did not recognise the ID line layout:
ID   HLA00001; SV 1; standard; DNA; HUM; 3503 BP.
Apparently the format has changed in the data file, which looks like this for the ID line before 3.16.0:
ID   HLA00001   standard; DNA; HUM; 3503 BP.
Could someone tell me how the module can be updated to parse current and future data files. Thank you so much!!
Chang


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