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

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

@ -1,3 +1,5 @@
#cython: language_level=3
''' '''
Created on 8 mars 2016 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.apps.progress cimport ProgressBar # @UnresolvedImport
# from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work # from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
# from obitools3.utils cimport bytes2str # from obitools3.utils cimport bytes2str
# #
# 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"
# #
# #
# default_config = { 'inputview' : None, # default_config = { 'inputview' : None,
# } # }
# #
# def addOptions(parser): # def addOptions(parser):
# #
# # TODO put this common group somewhere else but I don't know where # # TODO put this common group somewhere else but I don't know where
# group=parser.add_argument_group('DMS and view options') # group=parser.add_argument_group('DMS and view options')
# #
# group.add_argument('--default-dms','-d', # group.add_argument('--default-dms','-d',
# action="store", dest="obi:defaultdms", # action="store", dest="obi:defaultdms",
# metavar='<DMS NAME>', # metavar='<DMS NAME>',
# default=None, # default=None,
# type=str, # type=str,
# help="Name of the default DMS for reading and writing data.") # help="Name of the default DMS for reading and writing data.")
# #
# group.add_argument('--input-view','-i', # group.add_argument('--input-view','-i',
# action="store", dest="obi:inputview", # action="store", dest="obi:inputview",
# metavar='<INPUT VIEW NAME>', # metavar='<INPUT VIEW NAME>',
@ -34,76 +31,77 @@ def run(config):
# type=str, # type=str,
# help="Name of the input view, either raw if the view is in the default DMS," # 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.") # " or in the form 'dms:view' if it is in another DMS.")
# #
# group=parser.add_argument_group('obi export specific options') # group=parser.add_argument_group('obi export specific options')
# #
# group.add_argument('--format','-f', # group.add_argument('--format','-f',
# action="store", dest="export:format", # action="store", dest="export:format",
# metavar='<FORMAT>', # metavar='<FORMAT>',
# default="fasta", # default="fasta",
# 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"
# ID_COLUMN = "ID" # ID_COLUMN = "ID"
# DEFINITION_COLUMN = "DEFINITION" # DEFINITION_COLUMN = "DEFINITION"
# QUALITY_COLUMN = "QUALITY" # QUALITY_COLUMN = "QUALITY"
# #
# special_columns = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN] # special_columns = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
# #
# # Open DMS # # Open DMS
# d = OBIDMS(config['obi']['defaultdms']) # d = OBIDMS(config['obi']['defaultdms'])
# #
# # Open input view # # Open input view
# iview = d.open_view(config['obi']['inputview']) # iview = d.open_view(config['obi']['inputview'])
# #
# print(iview.type) # print(iview.type)
# #
# # TODO check that the view has the type NUC_SEQS # # 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 # 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") # raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
# #
# # Initialize the progress bar # # Initialize the progress bar
# pb = ProgressBar(len(iview), config, seconde=5) # pb = ProgressBar(len(iview), config, seconde=5)
# #
# i=0 # i=0
# for seq in iview : # for seq in iview :
# pb(i) # pb(i)
# #
# toprint = ">"+seq.id+" " # toprint = ">"+seq.id+" "
# #
# for col_name in seq : # for col_name in seq :
# if col_name not in special_columns : # if col_name not in special_columns :
# toprint = toprint + col_name + "=" + str(seq[col_name]) + "; " # toprint = toprint + col_name + "=" + str(seq[col_name]) + "; "
# #
# if DEFINITION_COLUMN in seq : # if DEFINITION_COLUMN in seq :
# toprint = toprint + seq.definition # toprint = toprint + seq.definition
# #
# nucseq = bytes2str(seq.nuc_seq) # nucseq = bytes2str(seq.nuc_seq)
# #
# if config['export']['format'] == "fasta" : # if config['export']['format'] == "fasta" :
# nucseq = re.sub("(.{60})", "\\1\n", nucseq, 0, re.DOTALL) # nucseq = re.sub("(.{60})", "\\1\n", nucseq, 0, re.DOTALL)
# #
# toprint = toprint + "\n" + nucseq # toprint = toprint + "\n" + nucseq
# #
# if config['export']['format'] == "fastq" : # if config['export']['format'] == "fastq" :
# toprint = toprint + "\n" + "+" + "\n" + seq.get_str_quality() # toprint = toprint + "\n" + "+" + "\n" + seq.get_str_quality()
# #
# print(toprint) # print(toprint)
# i+=1 # i+=1
# #
# iview.close() # iview.close()
# d.close() # d.close()
# #
# print("Done.") # 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 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"

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 // 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;

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. * @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)

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) 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;