Empty archives when created from an assembly

[EricR86]

Original report (archived issue) by Mickaël Mendez (Bitbucket: Mickael Mendez).

The original report had attachments: concatenated_agp_file.agp.gz

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Creating an archive from an assembly results in an almost empty archive.

I tried with the genomedata-load and the four steps commands but the archives are always the same size of 65M.

command used:

genomedata-load -s ./concatenated_agp_file.agp -t my_track=my_signal_file.bg --assembly my_archive

The genomedata exists but it seems that the assembly file could not be parsed properly and the open_chromosome field contains the name of the assembly file instead of the chromosome names:

>>> print g.open_chromosomes
{'concatenated_agp_file': <Chromosome 'concatenated_agp_file', file='genomedata/my_archive/concatenated_agp_file.genomedata'>}

Note: the assembly file (attached) was generated by concatenating the reference agp files from the ncbi ftp, after filtering out the comment lines starting with the character '#'

[EricR86]

Original comment by Mickaël Mendez (Bitbucket: Mickael Mendez).

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@ericr86 I think that this was solved in one of the recent PR, could you confirm that?

[EricR86]

Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

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• changed state from "new" to "resolved"

This should have been resolved in the 1.4.0 release