A tarball of compressed mitogenomes can be downloaded here: link (488k).
These are compressed, and may be extracted using: mtdna_uncompress_v3.py.
Then, the full mitogenome dataset may be extracted into a single multisample fasta file, using: Mitogenomes maybe accessed in the following way:
(i) For the full dataset:
zcat v50.0_MT_v1.gz | python mtdna_uncompress_v3.py
(ii) Or: a subset of samples may be pulled using a comma separated list, eg:
zcat v50.0_MT_v1.gz | python mtdna_uncompress_v3.py --id=I0026,I0018
(iii) Or: a subset of samples may be pulled using a file of ids, eg:
zcat v50.0_MT_v1.gz | python mtdna_uncompress_v3.py --file=my.id.file
You may check to see if ids exist using the --check option, eg:
zcat v50.0_MT_v1.gz | python mtdna_uncompress_v3.py --file=my.id.file --check
(a) python 2.7 is used.
(b) 'zcat' is used, expecting:
(i) that the dataset is not automatically uncompressed by your browser, and,
(ii) that 'zcat' operates directly on gzipped files (which is the norm for linux systems, but not on some macs).
If (i) is not true, then your browser may decompress the file to v50.0_MT_v1. In this case use 'cat' instead of 'zcat'.
If (ii) does not work, one solution might be to directly uncompress v50.0_MT_v1.gz on your local system using: 'gunzip v50.0_MT_v1.gz' and then using 'cat' instead of 'zcat'.
Please let us know if there are any changes that may be useful.
[2021_10_16]: repo built