Fix Contig Length Detection for GFF Parsing

ppanggolin/annotate/annotate.py

@@ -22,7 +22,7 @@
 # local libraries
 from ppanggolin.annotate.synta import (
     annotate_organism,
-    read_fasta,
+    get_contigs_from_fasta_file,
     get_dna_sequence,
     init_contig_counter,
     contig_counter,
@@ -1034,12 +1034,10 @@ def check_chevrons_in_start_and_stop(
                             dbxref_metadata
                         )
 
-                    if fields_gff[gff_seqname] in circular_contigs or (
+                    if contig is not None and (
                         "IS_CIRCULAR" in attributes
                         and attributes["IS_CIRCULAR"] == "true"
                     ):
-                        # WARNING: In case we have prodigal gff with is_circular attributes.
-                        # This would fail as contig is not defined. However, is_circular should not be found in prodigal gff
                         logging.getLogger("PPanGGOLiN").debug(
                             f"Contig {contig.name} is circular."
                         )
@@ -1120,9 +1118,9 @@ def check_chevrons_in_start_and_stop(
                             gene_frame = int(fields_gff[frame])
 
                         if (
-                            gene_id in id_attr_to_gene_id
+                            id_attribute in id_attr_to_gene_id
                         ):  # the ID has already been seen at least once in this genome
-                            existing_gene = id_attr_to_gene_id[gene_id]
+                            existing_gene = id_attr_to_gene_id[id_attribute]
                             new_gene_info = {
                                 "strand": fields_gff[gff_strand],
                                 "type": fields_gff[gff_type],
@@ -1141,7 +1139,7 @@ def check_chevrons_in_start_and_stop(
 
                         gene = Gene(org.name + "_CDS_" + str(gene_counter).zfill(4))
 
-                        id_attr_to_gene_id[gene_id] = gene
+                        id_attr_to_gene_id[id_attribute] = gene
 
                         # here contig is filled in order, so position is the number of genes already stored in the contig.
                         gene.fill_annotations(
@@ -1182,9 +1180,6 @@ def check_chevrons_in_start_and_stop(
                         rna_counter += 1
                         contig.add_rna(rna)
 
-    # Correct coordinates of genes that overlap the edge of circulars contig
-    correct_putative_overlaps(org.contigs)
-
     # Fix partial genes coordinates
     for contig in org.contigs:
         for gene in contig.genes:
@@ -1201,14 +1196,11 @@ def check_chevrons_in_start_and_stop(
         has_fasta = False
 
     if has_fasta:
-        contig_sequences = read_fasta(
-            org, fasta_string.split("\n")
-        )  # _ is total contig length
+        contig_sequences = get_contigs_from_fasta_file(org, fasta_string.split("\n"))
+
+        correct_putative_overlaps(org.contigs)
+
         for contig in org.contigs:
-            if contig.length != len(contig_sequences[contig.name]):
-                raise ValueError(
-                    "The contig length defined is different than the sequence length"
-                )
 
             for gene in contig.genes:
                 gene.add_sequence(get_dna_sequence(contig_sequences[contig.name], gene))
@@ -1220,7 +1212,7 @@ def check_chevrons_in_start_and_stop(
         add_metadata_from_gff_file(contig_name_to_region_info, org, gff_file_path)
 
     if used_transl_table_arg:
-        logging.getLogger("PPanGGOLiN").info(
+        logging.getLogger("PPanGGOLiN").debug(
             f"transl_table tag was not found for {used_transl_table_arg} CDS "
             f"in {gff_file_path}. Provided translation_table argument value was used instead: {translation_table}."
         )
@@ -1616,7 +1608,15 @@ def get_gene_sequences_from_fastas(
                 f"your fasta file are different."
             )
         with read_compressed_or_not(Path(elements[1])) as currFastaFile:
-            fasta_dict[org] = read_fasta(org, currFastaFile)
+            fasta_dict[org] = get_contigs_from_fasta_file(org, currFastaFile)
+
+            # When dealing with GFF files, some genes may have coordinates extending beyond the actual
+            # length of contigs, especially when they overlap the edges. This usually needs to be split
+            # into two parts to handle the circular genome wrapping.
+            # If the GFF file lacks associated FASTA sequences and it was not possible to determine the
+            # contig length from the GFF file, we must apply this correction while parsing the external FASTA file.
+
+            correct_putative_overlaps(org.contigs)
 
     if set(pangenome.organisms) > set(fasta_dict.keys()):
         missing = pangenome.number_of_organisms - len(

ppanggolin/annotate/synta.py

@@ -9,7 +9,7 @@
 from subprocess import Popen, PIPE
 import ast
 from collections import defaultdict
-from typing import Dict, List, Optional, Union
+from typing import Dict, List, Optional, Union, Generator, Tuple
 from pathlib import Path
 
 # install libraries
@@ -245,49 +245,65 @@ def launch_infernal(
     return gene_objs
 
 
-def read_fasta(org: Organism, fna_file: Union[TextIOWrapper, list]) -> Dict[str, str]:
-    """Reads a fna file (or stream, or string) and stores it in a dictionary with contigs as key and sequence as value.
+def parse_fasta(
+    fna_file: Union[TextIOWrapper, list]
+) -> Generator[Tuple[str, str], None, None]:
+    """Yields each header and sequence from a FASTA file or stream as a tuple.
 
-    :param org: Organism corresponding to fasta file
-    :param fna_file: Input fasta file with sequences or list of each line as sequence
+    :param fna_file: Input FASTA file or list of lines as sequences.
+    :yield: Tuple with contig header (without '>') and sequence.
+    """
+    header = None
+    sequence = []
+
+    for line in fna_file:
+        line = line.strip()
+        if line.startswith(">"):  # New header
+            if header:  # Yield previous header and sequence
+                yield (header, "".join(sequence))
+            header = line[1:]  # Strip '>'
+            sequence = []
+        else:
+            sequence.append(line)
+
+    if header:  # Yield the final contig
+        yield (header, "".join(sequence))
 
-    :return: Dictionary with contig_name as keys and contig sequence in values
+
+def get_contigs_from_fasta_file(
+    org: Organism, fna_file: Union[TextIOWrapper, list]
+) -> Dict[str, str]:
+    """Processes contigs from a parsed FASTA generator and stores in a dictionary.
+
+    :param org: Organism instance to update with contig info.
+    :param fna_file: Input FASTA file or list of lines as sequences.
+    :return: Dictionary with contig names as keys and sequences as values.
     """
+
     global contig_counter
-    try:
-        contigs = {}
-        contig_seq = ""
-        contig = None
-        for line in fna_file:
-            if line.startswith(">"):
-                if len(contig_seq) >= 1:  # contig filter = 1
-                    contigs[contig.name] = contig_seq.upper()
-                    contig.length = len(contig_seq)
-                contig_seq = ""
-                try:
-                    contig = org.get(line.split()[0][1:])
-                except KeyError:
-                    with contig_counter.get_lock():
-                        contig = Contig(contig_counter.value, line.split()[0][1:])
-                        contig_counter.value += 1
-                    org.add(contig)
-            else:
-                contig_seq += line.strip()
-        if len(contig_seq) >= 1:  # processing the last contig
-            contigs[contig.name] = contig_seq.upper()
-            contig.length = len(contig_seq)
-
-    except AttributeError as e:
-        raise AttributeError(
-            f"{e}\nAn error was raised when reading file: '{fna_file.name}'. "
-            f"One possibility for this error is that the file did not start with a '>' "
-            f"as it would be expected from a fna file."
-        )
-    except Exception as err:  # To manage other exception which can occur
-        raise Exception(
-            f"{err}: Please check your input file and if everything looks fine, "
-            "please post an issue on our github"
-        )
+    contigs = {}
+
+    for header, sequence in parse_fasta(fna_file):
+        contig_name = header.split()[0]
+
+        # Retrieve or create the contig
+        try:
+            contig = org.get(contig_name)
+        except KeyError:
+            with contig_counter.get_lock():
+                contig = Contig(contig_counter.value, contig_name)
+                contig_counter.value += 1
+            org.add(contig)
+
+        # Update contig information
+        if contig.length is not None and contig.length != len(sequence):
+            raise ValueError(
+                f"Length mismatch for contig {contig_name}: expected {contig.length}, found {len(sequence)} from the fasta sequence."
+            )
+
+        contig.length = len(sequence)
+        contigs[contig_name] = sequence.upper()
+
     return contigs
 
 
@@ -464,7 +480,7 @@ def annotate_organism(
 
     fasta_file = read_compressed_or_not(file_name)
 
-    contig_sequences = read_fasta(org, fasta_file)
+    contig_sequences = get_contigs_from_fasta_file(org, fasta_file)
     if is_compressed(file_name):  # TODO simply copy file with shutil.copyfileobj
         fasta_file = write_tmp_fasta(contig_sequences, tmpdir)
     if procedure is None:  # prodigal procedure is not force by user

ppanggolin/genome.py

@@ -553,8 +553,6 @@ def __setitem__(self, coordinate: Tuple[int, int, str], gene: Gene):
     @property
     def length(self) -> Union[int, None]:
         """Get the length of the contig"""
-        if self._length is None:
-            logging.getLogger("PPanGGOLiN").warning("Contig length is unknown")
         return self._length
 
     @length.setter

ppanggolin/projection/projection.py

@@ -20,7 +20,7 @@
 import yaml
 
 # # local libraries
-from ppanggolin.annotate.synta import read_fasta, get_dna_sequence
+from ppanggolin.annotate.synta import get_contigs_from_fasta_file, get_dna_sequence
 from ppanggolin.annotate.annotate import (
     init_contig_counter,
     read_anno_file,
@@ -679,7 +679,7 @@ def get_gene_sequences_from_fasta_files(organisms, genome_name_to_annot_path):
         org_fasta_file = genome_name_to_annot_path[org.name]["path"]
 
         with read_compressed_or_not(org_fasta_file) as currFastaFile:
-            org_contig_to_seq = read_fasta(org, currFastaFile)
+            org_contig_to_seq = get_contigs_from_fasta_file(org, currFastaFile)
 
         for contig in org.contigs:
             try:
@@ -997,7 +997,7 @@ def retrieve_gene_sequences_from_fasta_file(input_organism, fasta_file):
     """
 
     with read_compressed_or_not(fasta_file) as currFastaFile:
-        contig_id2seq = read_fasta(input_organism, currFastaFile)
+        contig_id2seq = get_contigs_from_fasta_file(input_organism, currFastaFile)
 
     for contig in input_organism.contigs:
         try: