diff --git a/PanACoTA/annotate_module/format_prodigal.py b/PanACoTA/annotate_module/format_prodigal.py
index 374fe545e8f01fbc46655ae748cb27499494e976..30679831ce87064a8216cb72a7f5d8c5a9f96514 100644
--- a/PanACoTA/annotate_module/format_prodigal.py
+++ b/PanACoTA/annotate_module/format_prodigal.py
@@ -52,6 +52,7 @@ July 2019
import os
import shutil
+import glob
import logging
import PanACoTA.utils as utils
@@ -100,9 +101,9 @@ def format_one_genome(gpath, name, prod_path, lst_dir, prot_dir, gene_dir,
prodigal_dir = os.path.join(prod_path, os.path.basename(gpath) + "-prodigalRes")
# Get prodigal result files
- prot_file = os.path.join(prodigal_dir, name + ".faa")
- gen_file = os.path.join(prodigal_dir, name + ".ffn")
- gff_file = os.path.join(prodigal_dir, name + ".gff")
+ prot_file = glob.glob(os.path.join(prodigal_dir, "*.faa"))[0]
+ gen_file = glob.glob(os.path.join(prodigal_dir, "*.ffn"))[0]
+ gff_file = glob.glob(os.path.join(prodigal_dir, "*.gff"))[0]
# Define names for generated gembase files
res_prot_file = os.path.join(prot_dir, name + ".prt")
@@ -275,9 +276,9 @@ def create_gene_lst(contigs, gen_file, res_gen_file, res_lst_file, gpath, name):
# If it is not the first gene of the genome, write previous gene information
if prev_start != "":
# Write line in LSTINFO file, + header and sequence to the gene file
- _, lstline = gfunc.write_gene("CDS", locus_num, "NA", "NA", 0,
- prev_loc, name, prev_cont_num, "NA", prev_info,
- "NA", prev_strand, prev_start, prev_end, r_lst)
+ lstline = gfunc.write_gene("CDS", locus_num, "NA", "NA",
+ prev_loc, name, prev_cont_num, "NA", prev_info,
+ "NA", prev_strand, prev_start, prev_end, r_lst)
gfunc.write_header(lstline, r_gen)
r_gen.write(seq)
# -> get new information, save it for the next gene, and go to next line
@@ -302,9 +303,9 @@ def create_gene_lst(contigs, gen_file, res_gen_file, res_lst_file, gpath, name):
# Otherwise, nothing to write
if prev_start != "":
prev_loc = "b"
- _, lstline = gfunc.write_gene("CDS", locus_num, "NA", "NA", 0,
- prev_loc, name, prev_cont_num, "NA", prev_info, "NA",
- prev_strand, prev_start, prev_end, r_lst)
+ lstline = gfunc.write_gene("CDS", locus_num, "NA", "NA",
+ prev_loc, name, prev_cont_num, "NA", prev_info, "NA",
+ prev_strand, prev_start, prev_end, r_lst)
gfunc.write_header(lstline, r_gen)
r_gen.write(seq)
return True
diff --git a/PanACoTA/annotate_module/format_prokka.py b/PanACoTA/annotate_module/format_prokka.py
index fc3cc146601996da30e2c763a9b10c8c76ee523a..33ec320449b8e1f50af4a12ddfb1cf3b525d50b1 100644
--- a/PanACoTA/annotate_module/format_prokka.py
+++ b/PanACoTA/annotate_module/format_prokka.py
@@ -238,9 +238,6 @@ def tbl2lst(tblfile, lstfile, contigs, genome, gpath):
bool :
True if genome name used in lstfile and prokka tblfile are the same, False otherwise
"""
- # Number CRISPRs. By default, 0 CRISPR -> next one will be CRISPR1
- crispr_num = 1
- crispr = False
# Protein localisation in contig (b = border ; i = inside)
cont_loc = "b"
prev_cont_loc = "b"
@@ -325,11 +322,11 @@ def tbl2lst(tblfile, lstfile, contigs, genome, gpath):
# If not first gene of the contig, write the previous gene to .lst file
# The first gene will be written while reading the 2nd gene
if start != "-1" and end != "-1" and not crispr:
- crispr_num, lstline = general.write_gene(feature_type, locus_num,
- gene_name, product, crispr_num,
- prev_cont_loc, genome,
- prev_cont_num, ecnum, inf2,
- db_xref, strand, start, end, lstf)
+ lstline = general.write_gene(feature_type, locus_num,
+ gene_name, product,
+ prev_cont_loc, genome,
+ prev_cont_num, ecnum, inf2,
+ db_xref, strand, start, end, lstf)
# Get new values for the next gene: start, end, strand and feature type
start, end, feature_type = elems
@@ -359,9 +356,9 @@ def tbl2lst(tblfile, lstfile, contigs, genome, gpath):
# Write last feature
if start != -1 and end != -1:
prev_cont_loc = "b"
- crispr_num, _ = general.write_gene(feature_type, locus_num, gene_name, product,
- crispr_num, prev_cont_loc, genome, prev_cont_num,
- ecnum, inf2, db_xref, strand, start, end, lstf)
+ general.write_gene(feature_type, locus_num, gene_name, product,
+ prev_cont_loc, genome, prev_cont_num,
+ ecnum, inf2, db_xref, strand, start, end, lstf)
return True
@@ -516,7 +513,6 @@ def create_gen(ffnseq, lstfile, genseq):
"""
problem = False
write = True # Write next sequence
- crispr_id = 1
with open(ffnseq) as ffn, open(lstfile) as lst, open(genseq, "w") as gen:
for line_ffn in ffn:
# Ignore gene that we do not want to write (should be a crispr)
diff --git a/PanACoTA/annotate_module/general_format_functions.py b/PanACoTA/annotate_module/general_format_functions.py
index c11c0560605f2fc4d06e44c849897776d76697ff..68dd0c4cee9dab4202677b0b995493005b9720ff 100644
--- a/PanACoTA/annotate_module/general_format_functions.py
+++ b/PanACoTA/annotate_module/general_format_functions.py
@@ -65,8 +65,7 @@ from PanACoTA.annotate_module import format_prodigal as fprodigal
main_logger = logging.getLogger("annotate.geneffunc")
-def format_genomes(genomes_ok, res_path, annot_path, prodigal_only, threads=1, quiet=False,
- changed_name=False):
+def format_genomes(genomes_ok, res_path, annot_path, prodigal_only, threads=1, quiet=False):
"""
For all genomes which were annotated (by prokka or prodigal), reformat them
in order to have, in 'res_path', the following folders:
@@ -80,7 +79,8 @@ def format_genomes(genomes_ok, res_path, annot_path, prodigal_only, threads=1, q
Parameters
----------
genomes_ok : dict
- genomes to format (annotation was OK) -> {genome: [name, gpath, size, nbcont, l90]}
+ genomes to format (annotation was OK) ->
+ {genome: [name, gpath, to_annot, size, nbcont, l90]}
res_path : str
path to folder where the 4 directories must be created
annot_path : str
@@ -91,9 +91,6 @@ def format_genomes(genomes_ok, res_path, annot_path, prodigal_only, threads=1, q
number of threads to use to while formatting genomes
quiet : bool
True if nothing must be sent to stderr/stdout, False otherwise
- changed_name : bool
- True if contig names have been changed (cutn != 0) -> contig names end by '_num',
- False otherwise.
Returns
-------
@@ -216,7 +213,7 @@ def handle_genome(args):
return ok_format, genome
-def write_gene(gtype, locus_num, gene_name, product, crispr_num, cont_loc,
+def write_gene(gtype, locus_num, gene_name, product, cont_loc,
genome, cont_num, ecnum, inf2, db_xref, strand, start, end, lstopenfile):
"""
Write given gene to output file
@@ -231,11 +228,6 @@ def write_gene(gtype, locus_num, gene_name, product, crispr_num, cont_loc,
gene name found by prokka/prodigal ("NA" if no gene name -> Always the case with Prodigal)
product : str
found by prokka/Prodigal, "NA" if no product (always the case for prodigal)
- crispr_num : int
- current crispr number. In prokka tbl, CRISPRs are not numbered, they all
- have the same name. We name them by adding a unique number to each CRISPR. If the current
- gene to add is a CRISPR, this number will be incremented and returned. If not, this same
- number will be returned.
cont_loc : str
'i' if the gene is inside a contig, 'b' if its on the border (first or last gene
of the contig)
@@ -260,16 +252,9 @@ def write_gene(gtype, locus_num, gene_name, product, crispr_num, cont_loc,
Returns
-------
- tuple :
- Current crispr number, lstline
+ str :
+ lstline
"""
- # if last gene was a crispr
- if gtype == "repeat_region":
- gtype = "CRISPR"
- locus_num = "CRISPR" + str(crispr_num)
- gene_name = "crispr"
- product = "crispr-array"
- crispr_num += 1
locus_name = "{}.{}{}_{}".format(genome, str(cont_num).zfill(4), cont_loc,
str(locus_num).zfill(5))
# If '|' character found in those fields, replace by '_' to avoid problems while parsing
@@ -279,7 +264,7 @@ def write_gene(gtype, locus_num, gene_name, product, crispr_num, cont_loc,
db_xref.replace("|", "_"))
lst_line = "\t".join([start, end, strand, gtype, locus_name, gene_name, more_info])
lstopenfile.write(lst_line + "\n")
- return crispr_num, lst_line
+ return lst_line
def write_header(lstline, outfile):
diff --git a/test/data/annotate/exp_files/res_create_gff_prodigal.gff b/test/data/annotate/exp_files/res_create_gff_prodigal.gff
index ebf97f8c9e8f22f15fe2eac1b8320a30c51d8ba7..5ec00adf5f8ab81d91ef00803ba931a6c04dc26d 100644
--- a/test/data/annotate/exp_files/res_create_gff_prodigal.gff
+++ b/test/data/annotate/exp_files/res_create_gff_prodigal.gff
@@ -1,11 +1,11 @@
##gff-version 3
-##sequence-region test.0417.00002.0001 1 14000
-##sequence-region test.0417.00002.0002 1 5000
-##sequence-region test.0417.00002.0003 1 4600
-##sequence-region test.0417.00002.0004 1 8000
-##sequence-region test.0417.00002.0005 1 1
-##sequence-region test.0417.00002.0006 1 10
-##sequence-region test.0417.00002.0007 1 15000
+##sequence-region test.0417.00002.0001 1 84
+##sequence-region test.0417.00002.0002 1 103
+##sequence-region test.0417.00002.0003 1 122
+##sequence-region test.0417.00002.0004 1 35
+##sequence-region test.0417.00002.0005 1 198
+##sequence-region test.0417.00002.0006 1 128
+##sequence-region test.0417.00002.0007 1 85
test.0417.00002.0001 Prodigal:2.6 CDS 287 787 . + 0 ID=test.0417.00002.0001b_00001;inference=ab initio prediction:Prodigal:2.6;locus_tag=EPKOMDHM_00001;product=hypothetical protein
test.0417.00002.0001 Prodigal:2.6 CDS 4416 6068 . + 0 ID=test.0417.00002.0001i_00002;Name=yiaD;gene=yiaD;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P37665;locus_tag=EPKOMDHM_00005;product=putative lipoprotein YiaD
test.0417.00002.0001 Prodigal:2.6 CDS 9000 12002 . - 0 ID=test.0417.00002.0001b_00003;Name=vgrG1;gene=vgrG1;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:Q9HI36;locus_tag=EPKOMDHM_00006;product=Major exported protein
diff --git a/test/test_unit/test_annotate/test_format_prodigal.py b/test/test_unit/test_annotate/test_format_prodigal.py
index 09b89e85de0b5d35a5f8e9e63a51a3506ea46466..9644df5e6ffd5acfe5d23e46fc1148161740820e 100644
--- a/test/test_unit/test_annotate/test_format_prodigal.py
+++ b/test/test_unit/test_annotate/test_format_prodigal.py
@@ -129,13 +129,13 @@ def test_create_gff(caplog):
"ter": "test.0417.00002.0006",
"contname": "test.0417.00002.0007"
}
- sizes = {"test.0417.00002.0001": 14000,
- "test.0417.00002.0002": 5000,
- "test.0417.00002.0003": 4600,
- "test.0417.00002.0004": 8000,
- "test.0417.00002.0005": 1,
- "test.0417.00002.0006": 10,
- "test.0417.00002.0007": 15000,
+ sizes = {"test.0417.00002.0001": 84,
+ "test.0417.00002.0002": 103,
+ "test.0417.00002.0003": 122,
+ "test.0417.00002.0004": 35,
+ "test.0417.00002.0005": 198,
+ "test.0417.00002.0006": 128,
+ "test.0417.00002.0007": 85,
}
res_gff_file = os.path.join(GENEPATH, "prodigal_res.gff")
exp_lst = os.path.join(EXP_ANNOTE, "res_create_gene_lst_prodigal.lst")
@@ -383,7 +383,15 @@ def test_format_1genome_emptygpath(caplog):
# Create empty file, that we give to prodigal for formatting step
gpath = os.path.join(GENEPATH, "original_name-empty.fna")
open(gpath, "w").close()
- prod_path = TEST_ANNOTE
+ prod_path = GENEPATH
+ # Create prodigal result files (empty, then won't be read)
+ prodigal_dir = gpath + "-prodigalRes"
+ os.makedirs(prodigal_dir)
+ prodigal_faa = os.path.join(gpath + "-prodigalRes", "notread.faa")
+ prodigal_ffn = os.path.join(gpath + "-prodigalRes", "notread.ffn")
+ prodigal_gff = os.path.join(gpath + "-prodigalRes", "notread.gff")
+ for file in [prodigal_faa, prodigal_gff, prodigal_ffn]:
+ open(file, "w").close()
# Generate result folders
prot_dir = os.path.join(GENEPATH, "Proteins")
lst_dir = os.path.join(GENEPATH, "LSTINFO")
@@ -428,12 +436,14 @@ def test_format_1genome_wrongffn(caplog):
name = "prodigal.outtest.ok"
# path to original genome, given to prodigal for annotation
orig_gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
- # In GENEPATH folder, create the original genome given to prodigal
- # (copy from test_file)
+ orig_prodpath = orig_gpath + "-prodigalRes"
used_gpath = os.path.join(GENEPATH, "original_name.fna")
used_respath = used_gpath + "-prodigalRes"
- os.makedirs(used_respath)
+ # Add original genome, and prodigal results to result folder
shutil.copyfile(orig_gpath, used_gpath)
+ shutil.copytree(orig_prodpath, used_respath)
+ # In GENEPATH folder, create the original genome given to prodigal
+ # (copy from test_file)
# Create gen_file with a header not existing
with open(os.path.join(used_respath, "prodigal.outtest.ok.ffn"), "w") as ori:
ori.write(">wrongheader # 1 # 2 # 1 # toto")
@@ -481,16 +491,14 @@ def test_format_1genome_wronggff(caplog):
# path to original genome, given to prodigal for annotation
orig_gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
+ orig_prodpath = orig_gpath + "-prodigalRes"
# In generated_by_tests folder, create the original genome given to prodigal
# (copy from test_file)
used_gpath = os.path.join(GENEPATH, "original_name.fna")
used_respath = used_gpath + "-prodigalRes"
- os.makedirs(used_respath)
+ # Add original genome, and prodigal results to result folder
shutil.copyfile(orig_gpath, used_gpath)
- # Copy ffn file generated by prodigal:
- orig_ffn = os.path.join(orig_gpath + "-prodigalRes", "prodigal.outtest.ok.ffn")
- used_ffn = os.path.join(used_respath, "prodigal.outtest.ok.ffn")
- shutil.copyfile(orig_ffn, used_ffn)
+ shutil.copytree(orig_prodpath, used_respath)
# Copy gff file, but modify to get wrong start position
orig_gff = os.path.join(orig_gpath + "-prodigalRes", "prodigal.outtest.ok.gff")
used_gff = os.path.join(used_respath, "prodigal.outtest.ok.gff")
@@ -548,21 +556,14 @@ def test_format_1genome_wrongprt(caplog):
# path to original genome, given to prodigal for annotation
orig_gpath = os.path.join(TEST_ANNOTE, "original_name.fna")
+ orig_prodpath = orig_gpath + "-prodigalRes"
# In generated_by_tests folder, create the original genome given to prodigal
# (copy from test_file)
used_gpath = os.path.join(GENEPATH, "original_name.fna")
used_respath = used_gpath + "-prodigalRes"
- os.makedirs(used_respath)
+ # Add original genome, and prodigal results to result folder
shutil.copyfile(orig_gpath, used_gpath)
- # Copy ffn file generated by prodigal:
- orig_ffn = os.path.join(orig_gpath + "-prodigalRes", "prodigal.outtest.ok.ffn")
- used_ffn = os.path.join(used_respath, "prodigal.outtest.ok.ffn")
- shutil.copyfile(orig_ffn, used_ffn)
- # Copy gff file generated by prodigal:
- orig_gff = os.path.join(orig_gpath + "-prodigalRes", "prodigal.outtest.ok.gff")
- used_gff = os.path.join(used_respath, "prodigal.outtest.ok.gff")
- shutil.copyfile(orig_gff, used_gff)
- # Copy prt file, but removing first proteins
+ shutil.copytree(orig_prodpath, used_respath)
orig_faa = os.path.join(orig_gpath + "-prodigalRes", "prodigal.outtest.ok.faa")
used_faa = os.path.join(used_respath, "prodigal.outtest.ok.faa")
with open(orig_faa, "r") as faa, open(used_faa, "w") as faar: