adds synteny info to GSTF prep tool #148
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nsoranzo
reviewed
Jun 9, 2021
nsoranzo
reviewed
Jun 10, 2021
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
nsoranzo
reviewed
Jun 10, 2021
| cur.execute('SELECT gene_id FROM gene where species=? AND seq_region_name=? ORDER BY seq_region_start ASC', | ||
| (genome, ref, )) | ||
|
|
||
| return cur.fetchall() |
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That's probably a bit too far :D
I'd take lines 542-549 and make a function with them (you could re-use populate_synteny as a name) and merge the other 4 functions (fetch_genomes, fetch_seq_region_names, fetch_genes_by_order, populate_synteny) in it.
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
nsoranzo
reviewed
Jun 11, 2021
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
nsoranzo
reviewed
Jun 14, 2021
nsoranzo
reviewed
Jun 14, 2021
…f_preparation/gstf_preparation.py Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
…on.py Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
…o fetch gene_id in tools/gstf_preparation/gstf_preparation.py Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
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