From 9482c663c0eb0d2ce113a1063045c691c2386c94 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Thu, 27 Jul 2017 19:46:34 +0200 Subject: [PATCH] minor comments and changes --- python/obitools3/commands/check.pyx | 16 +----- python/obitools3/commands/count.py | 2 + python/obitools3/commands/export.pyx | 82 ++++++++++++++-------------- python/obitools3/commands/import.pyx | 4 -- src/linked_list.c | 2 +- src/linked_list.h | 2 +- src/obi_align.c | 24 ++++---- 7 files changed, 59 insertions(+), 73 deletions(-) diff --git a/python/obitools3/commands/check.pyx b/python/obitools3/commands/check.pyx index d1db019..b513438 100644 --- a/python/obitools3/commands/check.pyx +++ b/python/obitools3/commands/check.pyx @@ -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='', -# 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 : diff --git a/python/obitools3/commands/count.py b/python/obitools3/commands/count.py index 28bd996..af9d317 100644 --- a/python/obitools3/commands/count.py +++ b/python/obitools3/commands/count.py @@ -1,3 +1,5 @@ +#cython: language_level=3 + ''' Created on 8 mars 2016 diff --git a/python/obitools3/commands/export.pyx b/python/obitools3/commands/export.pyx index b3b0212..24c670a 100644 --- a/python/obitools3/commands/export.pyx +++ b/python/obitools3/commands/export.pyx @@ -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='', # 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='', @@ -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='', # default="fasta", # type=str, # help="Export in the 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.") -# -# -# -# -# -# -# -# \ No newline at end of file +# +# +# +# +# +# +# +# \ No newline at end of file diff --git a/python/obitools3/commands/import.pyx b/python/obitools3/commands/import.pyx index 15c8625..7badd0e 100644 --- a/python/obitools3/commands/import.pyx +++ b/python/obitools3/commands/import.pyx @@ -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" diff --git a/src/linked_list.c b/src/linked_list.c index 17a2d51..9e81251 100644 --- a/src/linked_list.c +++ b/src/linked_list.c @@ -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; diff --git a/src/linked_list.h b/src/linked_list.h index 6356cd0..bd305ed 100644 --- a/src/linked_list.h +++ b/src/linked_list.h @@ -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) diff --git a/src/obi_align.c b/src/obi_align.c index a160ce6..db07274 100644 --- a/src/obi_align.c +++ b/src/obi_align.c @@ -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;