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ecopcr: now accepting taxonomy from a different DMS than the reference

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This commit is contained in:
mercierc
2021-08-05 11:28:57 +12:00
parent 82d2642000
commit 89168271ef
4 changed files with 26 additions and 4 deletions
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11
python/obitools3/commands/ecopcr.pyx
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@ -175,6 +175,14 @@ def run(config):
o_dms_name = output[0].name
o_view_name = output[1]
# Open the taxonomy DMS
taxdms = open_uri(config['obi']['taxoURI'],
dms_only=True)
if taxdms is None:
raise Exception("Could not open taxonomy DMS")
tax_dms = taxdms[0]
tax_dms_name = taxdms[0].name
# Read taxonomy name
taxonomy_name = config['obi']['taxoURI'].split("/")[-1] # Robust in theory
@ -197,7 +205,8 @@ def run(config):
# TODO: primers in comments?
if obi_ecopcr(i_dms.name_with_full_path, tobytes(i_view_name), tobytes(taxonomy_name), \
if obi_ecopcr(i_dms.name_with_full_path, tobytes(i_view_name),
tax_dms.name_with_full_path, tobytes(taxonomy_name), \
o_dms.name_with_full_path, tobytes(o_view_name), comments, \
tobytes(config['ecopcr']['primer1']), tobytes(config['ecopcr']['primer2']), \
config['ecopcr']['error'], \

1
python/obitools3/dms/capi/obiecopcr.pxd
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@ -8,6 +8,7 @@ cdef extern from "obi_ecopcr.h" nogil:
int obi_ecopcr(const char* input_dms_name,
const char* i_view_name,
const char* tax_dms_name,
const char* taxonomy_name,
const char* output_dms_name,
const char* o_view_name,

14
src/obi_ecopcr.c
View File

@ -645,7 +645,8 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
int obi_ecopcr(const char* i_dms_name,
const char* i_view_name,
const char* taxonomy_name, // TODO discuss that input dms assumed
const char* tax_dms_name,
const char* taxonomy_name,
const char* o_dms_name,
const char* o_view_name,
const char* o_view_comments,
@ -678,6 +679,7 @@ int obi_ecopcr(const char* i_dms_name,
OBIDMS_p i_dms = NULL;
OBIDMS_p o_dms = NULL;
OBIDMS_p tax_dms = NULL;
OBIDMS_taxonomy_p taxonomy = NULL;
Obiview_p i_view = NULL;
Obiview_p o_view = NULL;
@ -965,8 +967,16 @@ int obi_ecopcr(const char* i_dms_name,
return -1;
}
// Open taxonomy DMS
tax_dms = obi_open_dms(tax_dms_name, false);
if (tax_dms == NULL)
{
obidebug(1, "\nError opening the taxonomy DMS");
return -1;
}
// Open the taxonomy
taxonomy = obi_read_taxonomy(i_dms, taxonomy_name, false);
taxonomy = obi_read_taxonomy(tax_dms, taxonomy_name, false);
if (taxonomy == NULL)
{
obidebug(1, "\nError opening the taxonomy");

4
src/obi_ecopcr.h
View File

@ -77,7 +77,8 @@
*
* @param i_dms_name The path to the input DMS.
* @param i_view_name The name of the input view.
* @param taxonomy_name The name of the taxonomy in the input DMS.
* @param tax_dms_name The path to the DMS containing the taxonomy.
* @param taxonomy_name The name of the taxonomy.
* @param o_dms_name The path to the output DMS.
* @param o_view_name The name of the output view.
* @param o_view_comments The comments to associate with the output view.
@ -106,6 +107,7 @@
*/
int obi_ecopcr(const char* i_dms_name,
const char* i_view_name,
const char* tax_dms_name,
const char* taxonomy_name,
const char* o_dms_name,
const char* o_view_name,