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OBITools3
Commit 9ccddd52 authored by Celine Mercier's avatar Celine Mercier
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better cfiles

parent e026e9ec
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Showing with 2332 additions and 22 deletions
python/obitools3/commands/align.cfiles 0 → 100644
View file @ 9ccddd52
../../../src/obi_lcs.h
../../../src/obi_lcs.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/utils.h
../../../src/utils.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/libjson/json_utils.h
../../../src/libjson/json_utils.c
../../../src/libjson/cJSON.h
../../../src/libjson/cJSON.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/bloom.h
../../../src/bloom.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/linked_list.h
../../../src/linked_list.c
../../../src/obidmscolumn_array.h
../../../src/obidmscolumn_array.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn_str.c
../../../src/array_indexer.h
../../../src/array_indexer.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.c
../../../src/encode.h
../../../src/uint8_indexer.c
../../../src/uint8_indexer.h
../../../src/build_reference_db.c
../../../src/build_reference_db.h
../../../src/kmer_similarity.c
../../../src/kmer_similarity.h
../../../src/obi_clean.c
../../../src/obi_clean.h
../../../src/obi_ecopcr.c
../../../src/obi_ecopcr.h
../../../src/obi_ecotag.c
../../../src/obi_ecotag.h
../../../src/obidms_taxonomy.c
../../../src/obidms_taxonomy.h
../../../src/obilittlebigman.c
../../../src/obilittlebigman.h
../../../src/_sse.h
../../../src/obidebug.h
../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../src/libecoPCR/libapat/apat_parse.c
../../../src/libecoPCR/libapat/apat_search.c
../../../src/libecoPCR/libapat/apat.h
../../../src/libecoPCR/libapat/Gmach.h
../../../src/libecoPCR/libapat/Gtypes.h
../../../src/libecoPCR/libapat/libstki.c
../../../src/libecoPCR/libapat/libstki.h
../../../src/libecoPCR/libthermo/nnparams.h
../../../src/libecoPCR/libthermo/nnparams.c
../../../src/libecoPCR/ecoapat.c
../../../src/libecoPCR/ecodna.c
../../../src/libecoPCR/ecoError.c
../../../src/libecoPCR/ecoMalloc.c
../../../src/libecoPCR/ecoPCR.h
python/obitools3/commands/pouic.pyx → python/obitools3/commands/align.pyx
View file @ 9ccddd52
......@@ -9,8 +9,8 @@ from obitools3.dms.view import RollbackException
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes, str2bytes
from obitools3.dms.capi.obialign cimport obi_lcs_align_one_column, \
obi_lcs_align_two_columns
from obitools3.dms.capi.obilcsalign cimport obi_lcs_align_one_column, \
obi_lcs_align_two_columns
import time
import sys
......@@ -27,14 +27,14 @@ def addOptions(parser):
group=parser.add_argument_group('obi align specific options')
group.add_argument('--input-2', '-I',
action="store", dest="pouic:inputuri2",
action="store", dest="align:inputuri2",
metavar='<INPUT URI>',
default="",
type=str,
help="Eventually, the URI of the second input to align with the first one.")
group.add_argument('--threshold','-t',
action="store", dest="pouic:threshold",
action="store", dest="align:threshold",
metavar='<THRESHOLD>',
default=0.0,
type=float,
......@@ -48,41 +48,41 @@ def addOptions(parser):
" (no threshold).")
group.add_argument('--longest-length','-L',
action="store_const", dest="pouic:reflength",
action="store_const", dest="align:reflength",
default=0,
const=1,
help="The reference length is the length of the longest sequence."
" Default: the reference length is the length of the alignment.")
group.add_argument('--shortest-length','-l',
action="store_const", dest="pouic:reflength",
action="store_const", dest="align:reflength",
default=0,
const=2,
help="The reference length is the length of the shortest sequence."
" Default: the reference length is the length of the alignment.")
group.add_argument('--raw','-r',
action="store_false", dest="pouic:normalize",
action="store_false", dest="align:normalize",
default=True,
help="Raw score, not normalized. Default: score is normalized with the reference sequence length.")
group.add_argument('--distance','-D',
action="store_false", dest="pouic:similarity",
action="store_false", dest="align:similarity",
default=True,
help="Score is expressed in distance. Default: score is expressed in similarity.")
group.add_argument('--print-seq','-s',
action="store_true", dest="pouic:printseq",
action="store_true", dest="align:printseq",
default=False,
help="The nucleotide sequences are written in the output view. Default: they are not written.")
group.add_argument('--print-count','-n',
action="store_true", dest="pouic:printcount",
action="store_true", dest="align:printcount",
default=False,
help="Sequence counts are written in the output view. Default: they are not written.")
group.add_argument('--thread-count','-p', # TODO should probably be in a specific option group
action="store", dest="pouic:threadcount",
action="store", dest="align:threadcount",
metavar='<THREAD COUNT>',
default=1,
type=int,
......@@ -168,8 +168,8 @@ def run(config):
i_view_name_2 = b""
i_column_name_2 = b""
i_element_name_2 = b""
if config['pouic']['inputuri2']:
input_2 = open_uri(config['pouic']['inputuri2'],
if config['align']['inputuri2']:
input_2 = open_uri(config['align']['inputuri2'],
dms_only=True)
if input_2 is None:
raise Exception("Could not read second input")
......@@ -182,7 +182,7 @@ def run(config):
if len(i_uri_2.split(b"/")) == 3:
i_element_name_2 = i_uri_2.split(b"/")[2]
if len(i_uri_2.split(b"/")) > 3:
raise Exception("Input URI contains too many elements:", config['pouic']['inputuri2'])
raise Exception("Input URI contains too many elements:", config['align']['inputuri2'])
# If the 2 input DMS are not the same, temporarily import 2nd input view in first input DMS
if i_dms != i_dms_2:
......@@ -225,7 +225,7 @@ def run(config):
i_view_list = [i_view_name]
if original_i_view_name_2:
i_view_list.append(original_i_view_name_2)
comments = View.print_config(config, "pouic", command_line, input_dms_name=i_dms_list, input_view_name=i_view_list)
comments = View.print_config(config, "align", command_line, input_dms_name=i_dms_list, input_view_name=i_view_list)
# Call cython alignment function
# Using default ID columns of the view. TODO discuss adding option
......@@ -239,14 +239,14 @@ def run(config):
input_elt_2_n = i_element_name_2, \
id_column_1_n = b"", \
id_column_2_n = b"", \
threshold = config['pouic']['threshold'], \
normalize = config['pouic']['normalize'], \
reference = config['pouic']['reflength'], \
similarity_mode = config['pouic']['similarity'], \
print_seq = config['pouic']['printseq'], \
print_count = config['pouic']['printcount'], \
threshold = config['align']['threshold'], \
normalize = config['align']['normalize'], \
reference = config['align']['reflength'], \
similarity_mode = config['align']['similarity'], \
print_seq = config['align']['printseq'], \
print_count = config['align']['printcount'], \
comments = comments, \
thread_count = config['pouic']['threadcount'])
thread_count = config['align']['threadcount'])
# If the input and output DMS are not the same, export result view to output DMS
if i_dms != o_dms:
......
python/obitools3/commands/alignpairedend.cfiles 0 → 100644
View file @ 9ccddd52
../../../src/obi_lcs.h
../../../src/obi_lcs.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/utils.h
../../../src/utils.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/libjson/json_utils.h
../../../src/libjson/json_utils.c
../../../src/libjson/cJSON.h
../../../src/libjson/cJSON.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/bloom.h
../../../src/bloom.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/linked_list.h
../../../src/linked_list.c
../../../src/obidmscolumn_array.h
../../../src/obidmscolumn_array.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn_str.c
../../../src/array_indexer.h
../../../src/array_indexer.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.c
../../../src/encode.h
../../../src/uint8_indexer.c
../../../src/uint8_indexer.h
../../../src/build_reference_db.c
../../../src/build_reference_db.h
../../../src/kmer_similarity.c
../../../src/kmer_similarity.h
../../../src/obi_clean.c
../../../src/obi_clean.h
../../../src/obi_ecopcr.c
../../../src/obi_ecopcr.h
../../../src/obi_ecotag.c
../../../src/obi_ecotag.h
../../../src/obidms_taxonomy.c
../../../src/obidms_taxonomy.h
../../../src/obilittlebigman.c
../../../src/obilittlebigman.h
../../../src/_sse.h
../../../src/obidebug.h
../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../src/libecoPCR/libapat/apat_parse.c
../../../src/libecoPCR/libapat/apat_search.c
../../../src/libecoPCR/libapat/apat.h
../../../src/libecoPCR/libapat/Gmach.h
../../../src/libecoPCR/libapat/Gtypes.h
../../../src/libecoPCR/libapat/libstki.c
../../../src/libecoPCR/libapat/libstki.h
../../../src/libecoPCR/libthermo/nnparams.h
../../../src/libecoPCR/libthermo/nnparams.c
../../../src/libecoPCR/ecoapat.c
../../../src/libecoPCR/ecodna.c
../../../src/libecoPCR/ecoError.c
../../../src/libecoPCR/ecoMalloc.c
../../../src/libecoPCR/ecoPCR.h
python/obitools3/commands/annotate.cfiles 0 → 100644
View file @ 9ccddd52
../../../src/obi_lcs.h
../../../src/obi_lcs.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/utils.h
../../../src/utils.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/libjson/json_utils.h
../../../src/libjson/json_utils.c
../../../src/libjson/cJSON.h
../../../src/libjson/cJSON.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/bloom.h
../../../src/bloom.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/linked_list.h
../../../src/linked_list.c
../../../src/obidmscolumn_array.h
../../../src/obidmscolumn_array.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn_str.c
../../../src/array_indexer.h
../../../src/array_indexer.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.c
../../../src/encode.h
../../../src/uint8_indexer.c
../../../src/uint8_indexer.h
../../../src/build_reference_db.c
../../../src/build_reference_db.h
../../../src/kmer_similarity.c
../../../src/kmer_similarity.h
../../../src/obi_clean.c
../../../src/obi_clean.h
../../../src/obi_ecopcr.c
../../../src/obi_ecopcr.h
../../../src/obi_ecotag.c
../../../src/obi_ecotag.h
../../../src/obidms_taxonomy.c
../../../src/obidms_taxonomy.h
../../../src/obilittlebigman.c
../../../src/obilittlebigman.h
../../../src/_sse.h
../../../src/obidebug.h
../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../src/libecoPCR/libapat/apat_parse.c
../../../src/libecoPCR/libapat/apat_search.c
../../../src/libecoPCR/libapat/apat.h
../../../src/libecoPCR/libapat/Gmach.h
../../../src/libecoPCR/libapat/Gtypes.h
../../../src/libecoPCR/libapat/libstki.c
../../../src/libecoPCR/libapat/libstki.h
../../../src/libecoPCR/libthermo/nnparams.h
../../../src/libecoPCR/libthermo/nnparams.c
../../../src/libecoPCR/ecoapat.c
../../../src/libecoPCR/ecodna.c
../../../src/libecoPCR/ecoError.c
../../../src/libecoPCR/ecoMalloc.c
../../../src/libecoPCR/ecoPCR.h
python/obitools3/commands/build_ref_db.cfiles 0 → 100644
View file @ 9ccddd52
../../../src/obi_lcs.h
../../../src/obi_lcs.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/utils.h
../../../src/utils.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/libjson/json_utils.h
../../../src/libjson/json_utils.c
../../../src/libjson/cJSON.h
../../../src/libjson/cJSON.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/bloom.h
../../../src/bloom.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/linked_list.h
../../../src/linked_list.c
../../../src/obidmscolumn_array.h
../../../src/obidmscolumn_array.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_qual.h
../../../src/obidmscolumn_qual.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_str.h
../../../src/obidmscolumn_str.c
../../../src/array_indexer.h
../../../src/array_indexer.c
../../../src/char_str_indexer.h
../../../src/char_str_indexer.c
../../../src/dna_seq_indexer.h
../../../src/dna_seq_indexer.c
../../../src/encode.c
../../../src/encode.h
../../../src/uint8_indexer.c
../../../src/uint8_indexer.h
../../../src/build_reference_db.c
../../../src/build_reference_db.h
../../../src/kmer_similarity.c
../../../src/kmer_similarity.h
../../../src/obi_clean.c
../../../src/obi_clean.h
../../../src/obi_ecopcr.c
../../../src/obi_ecopcr.h
../../../src/obi_ecotag.c
../../../src/obi_ecotag.h
../../../src/obidms_taxonomy.c
../../../src/obidms_taxonomy.h
../../../src/obilittlebigman.c
../../../src/obilittlebigman.h
../../../src/_sse.h
../../../src/obidebug.h
../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../src/libecoPCR/libapat/apat_parse.c
../../../src/libecoPCR/libapat/apat_search.c
../../../src/libecoPCR/libapat/apat.h
../../../src/libecoPCR/libapat/Gmach.h
../../../src/libecoPCR/libapat/Gtypes.h
../../../src/libecoPCR/libapat/libstki.c
../../../src/libecoPCR/libapat/libstki.h
../../../src/libecoPCR/libthermo/nnparams.h
../../../src/libecoPCR/libthermo/nnparams.c
../../../src/libecoPCR/ecoapat.c
../../../src/libecoPCR/ecodna.c
../../../src/libecoPCR/ecoError.c
../../../src/libecoPCR/ecoMalloc.c
../../../src/libecoPCR/ecoPCR.h
python/obitools3/commands/clean.cfiles 0 → 100644
View file @ 9ccddd52
../../../src/obi_lcs.h
../../../src/obi_lcs.c
../../../src/obierrno.h
../../../src/obierrno.c
../../../src/upperband.h
../../../src/upperband.c
../../../src/sse_banded_LCS_alignment.h
../../../src/sse_banded_LCS_alignment.c
../../../src/obiblob.h
../../../src/obiblob.c
../../../src/utils.h
../../../src/utils.c
../../../src/obidms.h
../../../src/obidms.c
../../../src/libjson/json_utils.h
../../../src/libjson/json_utils.c
../../../src/libjson/cJSON.h
../../../src/libjson/cJSON.c
../../../src/obiavl.h
../../../src/obiavl.c
../../../src/bloom.h
../../../src/bloom.c
../../../src/crc64.h
../../../src/crc64.c
../../../src/murmurhash2.h
../../../src/murmurhash2.c
../../../src/obidmscolumn.h
../../../src/obidmscolumn.c
../../../src/obitypes.h
../../../src/obitypes.c
../../../src/obidmscolumndir.h
../../../src/obidmscolumndir.c
../../../src/obiblob_indexer.h
../../../src/obiblob_indexer.c
../../../src/obiview.h
../../../src/obiview.c
../../../src/hashtable.h
../../../src/hashtable.c
../../../src/linked_list.h
../../../src/linked_list.c
../../../src/obidmscolumn_array.h
../../../src/obidmscolumn_array.c
../../../src/obidmscolumn_blob.h
../../../src/obidmscolumn_blob.c
../../../src/obidmscolumn_idx.h
../../../src/obidmscolumn_idx.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_qual.h