obitools/obitools3
2
0 Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

minor comments and changes

Browse Source
This commit is contained in:
Celine Mercier committed 2017-07-27 19:46:34 +02:00
1 parent c5f3fdc295
commit 9482c663c0
7 files changed
+23 -37
Download Patch File Download Diff File Expand all files Collapse all files

No files matched your search

python/obitools3/commands/check.pyx
+3 -13
View File
@@ -32,25 +32,15 @@ def addOptions(parser):
help="Name of the view.") 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): def run(config):
# Open DMS # Open DMS
d = DMS.open(config['obi']['defaultdms']) d = DMS.open(config['obi']['defaultdms'])
# Open input view uif there is one # Open input view uif there is one
if config['obi']['inputview'] is not None : if 'view' in config['obi'] :
iview = View.open(d, config['obi']['view']) view = View.open(d, config['obi']['view'])
print(repr(iview)) print(repr(view))
else : else :
for v in d : for v in d :
python/obitools3/commands/count.py
+2
View File
@@ -1,3 +1,5 @@
#cython: language_level=3
''' '''
Created on 8 mars 2016 Created on 8 mars 2016
python/obitools3/commands/export.pyx
+4 -6
View File
@@ -4,11 +4,8 @@
# #
# import time # import time
# import re # import re
#
#
def run(config):
pass
# __title__="Export a NUC_SEQS view to a fasta or fastq file" # __title__="Export a NUC_SEQS view to a fasta or fastq file"
# #
# #
@@ -44,7 +41,8 @@ def run(config):
# type=str, # type=str,
# help="Export in the format <FORMAT>, 'fasta' or 'fastq'. Default: 'fasta'.") # TODO export in csv # 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 # # TODO import doesn't work
# NUC_SEQUENCE_COLUMN = "NUC_SEQ" # NUC_SEQUENCE_COLUMN = "NUC_SEQ"
python/obitools3/commands/import.pyx
-4
View File
@@ -20,10 +20,6 @@ from obitools3.dms.capi.obitypes cimport obitype_t, \
from obitools3.dms.capi.obierrno cimport obi_errno from obitools3.dms.capi.obierrno cimport obi_errno
import time
import pickle
__title__="Imports sequences from different formats into a DMS" __title__="Imports sequences from different formats into a DMS"
src/linked_list.c
+1 -1
View File
@@ -117,7 +117,7 @@ Linked_list_node_p ll_get(Linked_list_node_p head, int idx)
// Delete a node // 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; int i = 0;
Linked_list_node_p node = head; Linked_list_node_p node = head;
src/linked_list.h
+1 -1
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. * @param idx The index of the node to delete.
* *
* @returns A pointer on the new head node of the linked list. * @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 * @since February 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org) * @author Celine Mercier (celine.mercier@metabarcoding.org)
src/obi_align.c
+12 -12
View File
@@ -154,35 +154,35 @@ static int create_alignment_output_columns(Obiview_p output_view,
bool normalize, int reference, bool similarity_mode) bool normalize, int reference, bool similarity_mode)
{ {
// Create the column for the ids of the 1st sequence aligned // 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"); obidebug(1, "\nError creating the first column for the sequence ids when aligning");
return -1; return -1;
} }
// Create the column for the ids of the 2nd sequence aligned // 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"); obidebug(1, "\nError creating the second column for the sequence ids when aligning");
return -1; return -1;
} }
// Create the column for the index (in the input view) of the first sequences aligned // 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"); obidebug(1, "\nError creating the first column for the sequence indices when aligning");
return -1; return -1;
} }
// Create the column for the index (in the input view) of the second sequences aligned // 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"); obidebug(1, "\nError creating the second column for the sequence indices when aligning");
return -1; return -1;
} }
// Create the column for the LCS length // 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"); obidebug(1, "\nError creating the column for the LCS length when aligning");
return -1; 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 // Create the column for the alignment length if it is computed
if ((reference == ALILEN) && (normalize || !similarity_mode)) 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"); obidebug(1, "\nError creating the column for the alignment length when aligning");
return -1; return -1;
@@ -200,7 +200,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
// Create the column for the alignment score // Create the column for the alignment score
if (normalize) 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"); obidebug(1, "\nError creating the column for the score when aligning");
return -1; return -1;
@@ -208,7 +208,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
} }
else 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"); obidebug(1, "\nError creating the column for the score when aligning");
return -1; return -1;
@@ -218,14 +218,14 @@ static int create_alignment_output_columns(Obiview_p output_view,
if (print_seq) if (print_seq)
{ {
// Create the column for the first sequences aligned // 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"); obidebug(1, "\nError creating the first column for the sequences when aligning");
return -1; return -1;
} }
// Create the column for the second sequences aligned // 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"); obidebug(1, "\nError creating the second column for the sequences when aligning");
return -1; 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 // if (print_count) // TODO count columns not implemented yet
// { // {
// // Create the column for the count of the first sequences aligned // // 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"); // obidebug(1, "\nError creating the first column for the sequence counts when aligning");
// return -1; // return -1;
// } // }
// //
// // Create the column for the count of the second sequences aligned // // 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"); // obidebug(1, "\nError creating the second column for the sequence counts when aligning");
// return -1; // return -1;