end of tests for format_prodigal functions

PanACoTA/annotate_module/format_prodigal.py

@@ -84,11 +84,11 @@ def format_one_genome(gpath, name, prod_path, lst_dir, prot_dir, gene_dir,
     contigs, sizes = utils.get_genome_contigs_and_rename(name, gpath, res_rep_file)
     if not contigs:
         try:
+            os.remove(res_rep_file)
             os.remove(res_lst_file)
             os.remove(res_gff_file)
             os.remove(res_gene_file)
             os.remove(res_prt_file)
-            os.remove(res_rep_file)
         except OSError:
             pass
         logger.error("Problems while generating Replicon file for {}".format(name))
@@ -99,8 +99,11 @@ def format_one_genome(gpath, name, prod_path, lst_dir, prot_dir, gene_dir,
     ok = create_gene_lst(contigs, gen_file, res_gene_file, res_lst_file, gpath, name)
     if not ok:
         try:
+            os.remove(res_rep_file)
             os.remove(res_gene_file)
             os.remove(res_lst_file)
+            os.remove(res_gff_file)
+            os.remove(res_prot_file)
         except OSError:
             pass
         logger.error(f"Problems while generating .gen and .lst files for {name}")
@@ -116,10 +119,11 @@ def format_one_genome(gpath, name, prod_path, lst_dir, prot_dir, gene_dir,
             os.remove(res_lst_file)
             os.remove(res_rep_file)
             os.remove(res_gff_file)
+            os.remove(res_prot_file)
         except OSError:
             pass
-        logger.error("Problems while generating .fna (Replicons folder) and .gff (gff3 folder) "
-                     "files for {}".format(name))
+        logger.error("Problems while generating .gff (gff3 folder) "
+                     "file for {}".format(name))
         return False
 
     # Generate .prt files (in Proteins directory)
@@ -135,7 +139,7 @@ def format_one_genome(gpath, name, prod_path, lst_dir, prot_dir, gene_dir,
             os.remove(res_prot_file)
         except OSError:
             pass
-        logger.error("Problems while generating .prt files (Proteins folder) "
+        logger.error("Problems while generating .prt file (Proteins folder) "
                      "for {}".format(name))
         return False
     return ok
@@ -209,8 +213,11 @@ def create_gene_lst(contigs, gen_file, res_gen_file, res_lst_file, gpath, name):
                 (gname, start, end, strand, info) = lineffn.strip().split(">")[-1].split("#")
                 # Get contig number from prodigal gene header: prodigal first part of header is:
                 #  <original genome name contig name>_<protein number>
-                contig_name = "_".join(gname.strip().split("_")[:-1])
-
+                contig_name = gname.strip().split("_")
+                if len(contig_name) > 1:
+                    contig_name = "_".join(contig_name[:-1])
+                else:
+                    contig_name = contig_name[0]
                 # If new contig:
                 # - previous gene was the last of its contig -> prev_loc = "b" ;
                 # - the current gene is the first of its contig (loc = "b")
@@ -221,7 +228,8 @@ def create_gene_lst(contigs, gen_file, res_gen_file, res_lst_file, gpath, name):
                         contig_num = contigs[contig_name].split(".")[-1]
                     # if not in the list, problem, return false
                     else:
-                        logger.error(f"{contig_name} found in {gen_file} does not exist in {gpath}.")
+                        logger.error(f"'{contig_name}' found in {gen_file} does not exist in "
+                                     f"{gpath}.")
                         return False
                     prev_loc = 'b'
                     loc = 'b'

PanACoTA/utils.py

@@ -1135,10 +1135,11 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
                     cont = "\t".join([prev_cont, str(cont_size)]) + "\n"
                     prevcont_nohead = "".join(prev_cont.split(">")[1:])
                     prev_orig_name_nohead = "".join(prev_orig_name.split(">")[1:])
-                    sizes[prevcont_nohead] = cont_size
-                    contigs[prev_orig_name_nohead] = prevcont_nohead
-                    grf.write(cont)
-                    grf.write(seq)
+                    if prev_orig_name_nohead:
+                        sizes[prevcont_nohead] = cont_size
+                        contigs[prev_orig_name_nohead] = prevcont_nohead
+                        grf.write(cont)
+                        grf.write(seq)
                 prev_cont = ">" + gembase_name + "." + str(contig_num).zfill(4)
                 prev_orig_name = line.strip()
                 contig_num += 1
@@ -1152,10 +1153,11 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
         cont = "\t".join([prev_cont, str(cont_size)]) + "\n"
         prevcont_nohead = "".join(prev_cont.split(">")[1:])
         prev_orig_name_nohead = "".join(prev_orig_name.split(">")[1:])
-        contigs[prev_orig_name_nohead] = prevcont_nohead
-        sizes[prevcont_nohead] = cont_size
-        grf.write(cont)
-        grf.write(seq)
+        if prev_orig_name_nohead:
+            contigs[prev_orig_name_nohead] = prevcont_nohead
+            sizes[prevcont_nohead] = cont_size
+            grf.write(cont)
+            grf.write(seq)
     return contigs, sizes
 
 

test/test_unit/test_annotate/test_format_prodigal.py

@@ -108,7 +108,7 @@ def test_create_gen_lst_cont_unknown(caplog):
     gpath = "original_genome_name"
     assert not prodigalfunc.create_gene_lst(contigs, genfile, res_gen_file, res_lst_file,
                                             gpath, name)
-    assert ("my_contig found in test/data/annotate/test_files/original_name.fna-prodigalRes/"
+    assert ("'my_contig' found in test/data/annotate/test_files/original_name.fna-prodigalRes/"
             "prodigal.outtest.ok.faa does not exist in original_genome_name") in caplog.text
 
 
@@ -292,9 +292,191 @@ def test_format_1genome(caplog):
     os.makedirs(gff_dir)
 
     assert prodigalfunc.format_one_genome(gpath, name, prod_path, lst_dir, prot_dir, gene_dir,
-                      rep_dir, gff_dir, logger)
+                                          rep_dir, gff_dir, logger)
 
 
+def test_format_1genome_emptygpath(caplog):
+    """
+    Test on formatting prodigal results, when ffn file is empty -> error message,
+    and no file generated
+    """
+    caplog.set_level(logging.DEBUG)
+    logger = logging.getLogger("test_prodigal")
+    name = "prodigal.outtest.ok"
+    # 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
+    prot_dir = os.path.join(GENEPATH, "Proteins")
+    lst_dir = os.path.join(GENEPATH, "LSTINFO")
+    rep_dir = os.path.join(GENEPATH, "Replicons")
+    gene_dir = os.path.join(GENEPATH, "Genes")
+    gff_dir = os.path.join(GENEPATH, "gff")
+    os.makedirs(rep_dir)
+
+    assert not prodigalfunc.format_one_genome(gpath, name, prod_path, lst_dir, prot_dir, gene_dir,
+                                              rep_dir, gff_dir, logger)
+    assert ("Problems while generating Replicon file for prodigal.outtest.ok") in caplog.text
+
+
+def test_format_1genome_wrongffn(caplog):
+    """
+    Test on formatting prodigal results, when the file given to prodigal was empty
+    -> error message,
+    -> no file generated
+    """
+    caplog.set_level(logging.DEBUG)
+    logger = logging.getLogger("test_prodigal")
+    name = "prodigal.outtest.ok"
+    # path to original genome, given to prodigal for annotation
+    orig_gpath =  os.path.join(TEST_ANNOTE, "original_name.fna")
+    # 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)
+    shutil.copyfile(orig_gpath, used_gpath)
+    # 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")
+    prod_path = GENEPATH
+    prot_dir = os.path.join(GENEPATH, "Proteins")
+    lst_dir = os.path.join(GENEPATH, "LSTINFO")
+    rep_dir = os.path.join(GENEPATH, "Replicons")
+    gene_dir = os.path.join(GENEPATH, "Genes")
+    gff_dir = os.path.join(GENEPATH, "gff")
+    os.makedirs(rep_dir)
+    os.makedirs(gene_dir)
+    os.makedirs(lst_dir)
+
+    assert not prodigalfunc.format_one_genome(used_gpath, name, prod_path, lst_dir, prot_dir,
+                                              gene_dir, rep_dir, gff_dir, logger)
+    # # Check that replicon file was removed
+    # assert len(os.listdir(rep_dir) ) == 0
+    assert ("'wrongheader' found in test/data/annotate/generated_by_unit-tests/"
+            "original_name.fna-prodigalRes/prodigal.outtest.ok.ffn does not exist in "
+            "test/data/annotate/generated_by_unit-tests/original_name.fna") in caplog.text
+    assert ("Problems while generating .gen and .lst files for prodigal.outtest.ok") in caplog.text
+
+
+def test_format_1genome_wronglst(caplog):
+    """
+    Test on formatting prodigal results, when the file given to prodigal was empty
+    -> error message,
+    -> no file generated
+    """
+    caplog.set_level(logging.DEBUG)
+    logger = logging.getLogger("test_prodigal")
+    name = "prodigal.outtest.ok"
+
+    # path to original genome, given to prodigal for annotation
+    orig_gpath =  os.path.join(TEST_ANNOTE, "original_name.fna")
+    # 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)
+    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, 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")
+    with open(orig_gff, "r") as orig, open(used_gff, "w") as gffw:
+        for line in orig:
+            if line.startswith("#"):
+                gffw.write(line)
+            else:
+                fields_g = line.split("\t")
+                (contig_name, source, type_g, start_g, end_g,
+                 score, strand_g, phase, attributes) = fields_g
+                gffw.write("\t".join([contig_name, source, type_g, "12", end_g, score, strand_g,
+                                      phase, attributes]))
+                break
+    prod_path = GENEPATH
+    prot_dir = os.path.join(GENEPATH, "Proteins")
+    lst_dir = os.path.join(GENEPATH, "LSTINFO")
+    rep_dir = os.path.join(GENEPATH, "Replicons")
+    gene_dir = os.path.join(GENEPATH, "Genes")
+    gff_dir = os.path.join(GENEPATH, "gff3")
+    os.makedirs(rep_dir)
+    os.makedirs(gene_dir)
+    os.makedirs(lst_dir)
+    os.makedirs(gff_dir)
+    # Copy generated lstfile, but modify first line to have a difference between gff and lst starts
+
+    assert not prodigalfunc.format_one_genome(used_gpath, name, prod_path, lst_dir, prot_dir,
+                                              gene_dir, rep_dir, gff_dir, logger)
+    # # # Check that replicon file was removed
+    # # assert len(os.listdir(rep_dir) ) == 0
+    assert ("Files prodigal.outtest.ok.ffn and prodigal.outtest.ok.gff (in prodigal tmp_files: "
+            "test/data/annotate/generated_by_unit-tests/original_name.fna-prodigalRes) do "
+            "not have the same start value for gene EPKOMDHM_00001 "
+            "(12 in gff, 287 in ffn)") in caplog.text
+    assert ("Problems while generating .gff (gff3 folder) file for "
+            "prodigal.outtest.ok") in caplog.text
+
+
+
+def test_format_1genome_wrongprt(caplog):
+    """
+    Test on formatting prodigal results, when the file given to prodigal was empty
+    -> error message,
+    -> no file generated
+    """
+    caplog.set_level(logging.DEBUG)
+    logger = logging.getLogger("test_prodigal")
+    name = "prodigal.outtest.ok"
+
+    # path to original genome, given to prodigal for annotation
+    orig_gpath =  os.path.join(TEST_ANNOTE, "original_name.fna")
+    # 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)
+    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 protein
+    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:
+        for i in range(7):
+            faa.readline()
+        for line in faa:
+            faar.write(line)
+
+    prod_path = GENEPATH
+    prot_dir = os.path.join(GENEPATH, "Proteins")
+    lst_dir = os.path.join(GENEPATH, "LSTINFO")
+    rep_dir = os.path.join(GENEPATH, "Replicons")
+    gene_dir = os.path.join(GENEPATH, "Genes")
+    gff_dir = os.path.join(GENEPATH, "gff3")
+    gff_dir = os.path.join(GENEPATH, "Proteins")
+    os.makedirs(rep_dir)
+    os.makedirs(gene_dir)
+    os.makedirs(lst_dir)
+    os.makedirs(gff_dir)
+    # Copy generated lstfile, but modify first line to have a difference between gff and lst starts
+
+    assert not prodigalfunc.format_one_genome(used_gpath, name, prod_path, lst_dir, prot_dir,
+                                              gene_dir, rep_dir, gff_dir, logger)
+    # # # Check that replicon file was removed
+    # # assert len(os.listdir(rep_dir) ) == 0
+    assert ("Protein prodigal.outtest.ok.0007b_00013 is in .lst file but its sequence is not in "
+            "the protein file generated by prodigal.") in caplog.text
+    assert ("Problems while generating .prt file (Proteins folder) for "
+            "prodigal.outtest.ok") in caplog.text
+
 # # def test_tbl_to_lst_not_changed_names(caplog):
 #     """
 #     Check that generated lstinfo file is as expected, when the genome name is the same as