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minor comments and changes

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This commit is contained in:
Celine Mercier
2017-07-27 19:46:34 +02:00
parent c5f3fdc295
commit 9482c663c0
7 changed files with 59 additions and 73 deletions
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16
python/obitools3/commands/check.pyx
View File

@ -32,25 +32,15 @@ def addOptions(parser):
help="Name of the view.")
# group=parser.add_argument_group('obi check specific options')
# group.add_argument('--print',
# action="store", dest="less:print",
# metavar='<N>',
# default=None,
# type=int,
# help="Print N sequences (default: 10)")
def run(config):
# Open DMS
d = DMS.open(config['obi']['defaultdms'])
# Open input view uif there is one
if config['obi']['inputview'] is not None :
iview = View.open(d, config['obi']['view'])
print(repr(iview))
if 'view' in config['obi'] :
view = View.open(d, config['obi']['view'])
print(repr(view))
else :
for v in d :

2
python/obitools3/commands/count.py
View File

@ -1,3 +1,5 @@
#cython: language_level=3
'''
Created on 8 mars 2016

10
python/obitools3/commands/export.pyx
View File

@ -4,11 +4,8 @@
#
# import time
# import re
def run(config):
pass
#
#
# __title__="Export a NUC_SEQS view to a fasta or fastq file"
#
#
@ -44,7 +41,8 @@ def run(config):
# type=str,
# help="Export in the format <FORMAT>, 'fasta' or 'fastq'. Default: 'fasta'.") # TODO export in csv
#
# def run(config):
def run(config):
pass
#
# # TODO import doesn't work
# NUC_SEQUENCE_COLUMN = "NUC_SEQ"

4
python/obitools3/commands/import.pyx
View File

@ -20,10 +20,6 @@ from obitools3.dms.capi.obitypes cimport obitype_t, \
from obitools3.dms.capi.obierrno cimport obi_errno
import time
import pickle
__title__="Imports sequences from different formats into a DMS"

2
src/linked_list.c
View File

@ -117,7 +117,7 @@ Linked_list_node_p ll_get(Linked_list_node_p head, int idx)
// Delete a node
Linked_list_node_p ll_delete(Linked_list_node_p head, int idx) // TODO or with value?
Linked_list_node_p ll_delete(Linked_list_node_p head, int idx)
{
int i = 0;
Linked_list_node_p node = head;

2
src/linked_list.h
View File

@ -90,7 +90,7 @@ Linked_list_node_p ll_get(Linked_list_node_p head, int idx);
* @param idx The index of the node to delete.
*
* @returns A pointer on the new head node of the linked list.
* @retval NULL if an error occurred. // TODO or if list is now empty...
* @retval NULL if the list is now empty, or if the node did not exist. // TODO discuss
*
* @since February 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)

24
src/obi_align.c
View File

@ -154,35 +154,35 @@ static int create_alignment_output_columns(Obiview_p output_view,
bool normalize, int reference, bool similarity_mode)
{
// Create the column for the ids of the 1st sequence aligned
if (obi_view_add_column(output_view, ID1_COLUMN_NAME, -1, ID1_COLUMN_NAME, OBI_STR, 0, 1, NULL, id1_indexer_name, NULL, -1, ID1_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, ID1_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, id1_indexer_name, NULL, -1, ID1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the first column for the sequence ids when aligning");
return -1;
}
// Create the column for the ids of the 2nd sequence aligned
if (obi_view_add_column(output_view, ID2_COLUMN_NAME, -1, ID2_COLUMN_NAME, OBI_STR, 0, 1, NULL, id2_indexer_name, NULL, -1, ID2_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, ID2_COLUMN_NAME, -1, NULL, OBI_STR, 0, 1, NULL, id2_indexer_name, NULL, -1, ID2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the second column for the sequence ids when aligning");
return -1;
}
// Create the column for the index (in the input view) of the first sequences aligned
if (obi_view_add_column(output_view, IDX1_COLUMN_NAME, -1, IDX1_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, IDX1_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, IDX1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, IDX1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the first column for the sequence indices when aligning");
return -1;
}
// Create the column for the index (in the input view) of the second sequences aligned
if (obi_view_add_column(output_view, IDX2_COLUMN_NAME, -1, IDX2_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, IDX2_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, IDX2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, IDX2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the second column for the sequence indices when aligning");
return -1;
}
// Create the column for the LCS length
if (obi_view_add_column(output_view, LCS_LENGTH_COLUMN_NAME, -1, LCS_LENGTH_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, LCS_LENGTH_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, LCS_LENGTH_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, LCS_LENGTH_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the column for the LCS length when aligning");
return -1;
@ -191,7 +191,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
// Create the column for the alignment length if it is computed
if ((reference == ALILEN) && (normalize || !similarity_mode))
{
if (obi_view_add_column(output_view, ALI_LENGTH_COLUMN_NAME, -1, ALI_LENGTH_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, ALI_LENGTH_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, ALI_LENGTH_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, ALI_LENGTH_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the column for the alignment length when aligning");
return -1;
@ -200,7 +200,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
// Create the column for the alignment score
if (normalize)
{
if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, SCORE_COLUMN_NAME, OBI_FLOAT, 0, 1, NULL, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, NULL, OBI_FLOAT, 0, 1, NULL, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
{
obidebug(1, "\nError creating the column for the score when aligning");
return -1;
@ -208,7 +208,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
}
else
{
if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, SCORE_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
{
obidebug(1, "\nError creating the column for the score when aligning");
return -1;
@ -218,14 +218,14 @@ static int create_alignment_output_columns(Obiview_p output_view,
if (print_seq)
{
// Create the column for the first sequences aligned
if (obi_view_add_column(output_view, SEQ1_COLUMN_NAME, -1, SEQ1_COLUMN_NAME, OBI_SEQ, 0, 1, NULL, seq1_indexer_name, NULL, -1, SEQ1_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, SEQ1_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, seq1_indexer_name, NULL, -1, SEQ1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the first column for the sequences when aligning");
return -1;
}
// Create the column for the second sequences aligned
if (obi_view_add_column(output_view, SEQ2_COLUMN_NAME, -1, SEQ2_COLUMN_NAME, OBI_SEQ, 0, 1, NULL, seq2_indexer_name, NULL, -1, SEQ2_COLUMN_COMMENTS, true) < 0)
if (obi_view_add_column(output_view, SEQ2_COLUMN_NAME, -1, NULL, OBI_SEQ, 0, 1, NULL, seq2_indexer_name, NULL, -1, SEQ2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the second column for the sequences when aligning");
return -1;
@ -234,14 +234,14 @@ static int create_alignment_output_columns(Obiview_p output_view,
// if (print_count) // TODO count columns not implemented yet
// {
// // Create the column for the count of the first sequences aligned
// if (obi_view_add_column(output_view, COUNT1_COLUMN_NAME, -1, COUNT1_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, COUNT1_COLUMN_COMMENTS, true) < 0)
// if (obi_view_add_column(output_view, COUNT1_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, COUNT1_COLUMN_COMMENTS, true) < 0)
// {
// obidebug(1, "\nError creating the first column for the sequence counts when aligning");
// return -1;
// }
//
// // Create the column for the count of the second sequences aligned
// if (obi_view_add_column(output_view, COUNT2_COLUMN_NAME, -1, COUNT2_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, COUNT2_COLUMN_COMMENTS, true) < 0)
// if (obi_view_add_column(output_view, COUNT2_COLUMN_NAME, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, COUNT2_COLUMN_COMMENTS, true) < 0)
// {
// obidebug(1, "\nError creating the second column for the sequence counts when aligning");
// return -1;