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dnanexus-archive / viral-ngs

viral-ngs
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updated DNAnexus wrapper to account for changes to fasta-fetching command interface #5

Closed tomkinsc closed 8 years ago

tomkinsc commented 8 years ago

There is a change to the broadinstitute/viral-ngs interface for fetching fastas, feature tables, and full GenBank records. Consequently, the DNAnexus wrapper script needs to be updated.

We can check which commands are present and call them as appropriate. Since argparse returns an error code if a command is missing, and exits zero if a command is present (even if arguments are missing), we can use exit codes to determine the correct functions to call.

tomkinsc commented 8 years ago

The interface change is currently present in the branch broadinstitute/viral-ngs/ct-multialign-dev2, and will be merged to ct-multialign if this wrapper change pull request is accepted. The changes will be in master sometime after then.

tomkinsc commented 8 years ago

Closing this pull request due to #6.