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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

@ -30,16 +30,6 @@ def addOptions(parser):
default=None,
type=str,
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):
@ -48,9 +38,9 @@ def run(config):
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

82
python/obitools3/commands/export.pyx
View File

@ -1,32 +1,29 @@
# from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
# from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
# from obitools3.utils cimport bytes2str
#
#
# import time
# import re
def run(config):
pass
#
#
# __title__="Export a NUC_SEQS view to a fasta or fastq file"
#
#
#
#
# default_config = { 'inputview' : None,
# }
#
#
# def addOptions(parser):
#
#
# # TODO put this common group somewhere else but I don't know where
# group=parser.add_argument_group('DMS and view options')
#
#
# group.add_argument('--default-dms','-d',
# action="store", dest="obi:defaultdms",
# metavar='<DMS NAME>',
# default=None,
# type=str,
# help="Name of the default DMS for reading and writing data.")
#
#
# group.add_argument('--input-view','-i',
# action="store", dest="obi:inputview",
# metavar='<INPUT VIEW NAME>',
@ -34,76 +31,77 @@ def run(config):
# type=str,
# help="Name of the input view, either raw if the view is in the default DMS,"
# " or in the form 'dms:view' if it is in another DMS.")
#
#
# group=parser.add_argument_group('obi export specific options')
#
#
# group.add_argument('--format','-f',
# action="store", dest="export:format",
# metavar='<FORMAT>',
# default="fasta",
# 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"
# ID_COLUMN = "ID"
# DEFINITION_COLUMN = "DEFINITION"
# QUALITY_COLUMN = "QUALITY"
#
#
# special_columns = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
#
#
# # Open DMS
# d = OBIDMS(config['obi']['defaultdms'])
#
#
# # Open input view
# iview = d.open_view(config['obi']['inputview'])
#
#
# print(iview.type)
#
#
# # TODO check that the view has the type NUC_SEQS
# if ((config['export']['format'] == "fasta") or (config['export']['format'] == "fastq")) and (iview.type != "NUC_SEQS_VIEW") : # TODO find a way to import those macros
# raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
#
#
# # Initialize the progress bar
# pb = ProgressBar(len(iview), config, seconde=5)
#
#
# i=0
# for seq in iview :
# pb(i)
#
#
# toprint = ">"+seq.id+" "
#
#
# for col_name in seq :
# if col_name not in special_columns :
# toprint = toprint + col_name + "=" + str(seq[col_name]) + "; "
#
#
# if DEFINITION_COLUMN in seq :
# toprint = toprint + seq.definition
#
#
# nucseq = bytes2str(seq.nuc_seq)
#
#
# if config['export']['format'] == "fasta" :
# nucseq = re.sub("(.{60})", "\\1\n", nucseq, 0, re.DOTALL)
#
#
# toprint = toprint + "\n" + nucseq
#
#
# if config['export']['format'] == "fastq" :
# toprint = toprint + "\n" + "+" + "\n" + seq.get_str_quality()
#
#
# print(toprint)
# i+=1
#
#
# iview.close()
# d.close()
#
#
# print("Done.")
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#

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;