little improvements for lst/gen generation

PanACoTA/annotate_module/format_prodigal.py

@@ -5,7 +5,7 @@
 Functions to convert prodigal result files to gembase format.
 
     * Proteins: multifasta with all CDS in aa
-    * Replicons: multifasta of genome
+    * Replicons: (multi)fasta of genome sequences
     * Genes: multifasta of all genes in nuc
     * gff3: gff files without sequence
     * LSTINFO: information on annotation. Columns are: "start end strand type locus
@@ -42,7 +42,8 @@ def format_one_genome(gpath, name, prod_path, lst_dir, prot_dir, gene_dir,
     name : str
         gembase name of the genome
     prod_path : str
-        directory where prodigal folders are saved
+        directory where all tmp_files for all sequences are saved (sequences cut at each set
+        of 5N, prodigal results and logs)
     name : str
         gembase name of the genome
     lst_dir : srt
@@ -63,11 +64,15 @@ def format_one_genome(gpath, name, prod_path, lst_dir, prot_dir, gene_dir,
     bool :
         True if genome was correctly formatted, False otherwise
     """
+    # Get directory where prodigal results for the current genome are saved
     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")
 
+    # Define names for generated gembase files
     res_prot_file = os.path.join(prot_dir, name + ".prt")
     res_gene_file = os.path.join(gene_dir, name + ".gen")
     res_lst_file = os.path.join(lst_dir, name + ".lst")
@@ -75,15 +80,16 @@ def format_one_genome(gpath, name, prod_path, lst_dir, prot_dir, gene_dir,
     res_gff_file = os.path.join(gff_dir, name + ".gff")
 
 
-    # First, create gen and lst files, and get genome contig names
+    # First, create .gen and .lst files,
     ok = create_gene_lst(gen_file, res_gene_file, res_lst_file, name, logger)
     if not ok:
         os.remove(res_gene_file)
         os.remove(res_lst_file)
-        logger.error("Problems while generating gene and lst files for {}".format(name))
+        logger.error("Problems while generating .gen and .lst files for {}".format(name))
         return False
 
     # Create replicon file. Same as input sequence but with gembase formatted headers
+    # From Replicon file, get contig names, and use them to generate gff file
     ok = create_rep_gff(gpath, res_rep_file, res_gff_file, res_lst_file, gff_file, name, logger)
 
     # ok = create_prt(prot_file, res_prot_file, res_lst_file, logger)
@@ -94,14 +100,14 @@ def create_gene_lst(gen_file, res_gene_file, res_lst_file, name, logger):
     """
     Generate .gen file, from sequences contained in .ffn, but changing the
     headers to match with gembase format.
-    At the same time, generate lst file
+    At the same time, generate .lst file, from the information given in prodigal ffn headers
 
     Parameters
     ----------
     gen_file : str
         .ffn file generated by prodigal
     res_gene_file : str
-        output file, to write in Genes directory
+        output .gen file, to write in Genes directory
     res_lst_file : str
         .lst file to write in LSTINFO directory
     name : str
@@ -115,7 +121,7 @@ def create_gene_lst(gen_file, res_gene_file, res_lst_file, name, logger):
         True if conversion went well, False otherwise
     """
 
-    # Variable which will contain the current sequence
+    # Variable which will contain the current gene sequence
     seq = ""
     # number of the current gene (first gene is 1, 2nd is 2 etc. each number is unique: do not
     # re-start at 1 for each new contig)
@@ -167,6 +173,7 @@ def create_gene_lst(gen_file, res_gene_file, res_lst_file, name, logger):
                     prev_end = end
                     prev_cont_num = contig_num
                     prev_annot = annot
+                    # Convert strand 1/-1 to D/C
                     if int(strand) == 1:
                         strand = "D"
                     else:
@@ -261,7 +268,7 @@ def create_rep_gff(gpath, res_rep_file, res_gff_file, res_lst_file, gff_file, na
             path to the genome sequence
         res_rep_file : str
             path to the new file, containing 'gpath' sequence, but with 'gembase_name' in headers
-        res-gff_file : str
+        res_gff_file : str
             path to the gff file that must be created in result database
         res_lst_file : str
             path to the lst file that was created in result database in the previous step
@@ -274,13 +281,14 @@ def create_rep_gff(gpath, res_rep_file, res_gff_file, res_lst_file, gff_file, na
 
     Returns
     -------
-    list :
+    bool :
         True if everything went well, False otherwise
 
     """
     contigs = create_replicons(gpath, res_rep_file, name)
-    if contigs:
-        return create_gff(gpath, gff_file, res_gff_file, res_lst_file, name, contigs, logger)
+    logger.info(contigs)
+    # if contigs:
+    #     return create_gff(gpath, gff_file, res_gff_file, res_lst_file, name, contigs, logger)
 
 
 def create_replicons(gpath, res_rep_file, name):
@@ -294,18 +302,20 @@ def create_replicons(gpath, res_rep_file, name):
     ----------
         gpath : str
             path to the genome sequence
+        res_rep_file : str
+            path to the new file, containing 'gpath' sequence, but with 'gembase_named' headers
         name : str
             genome name to use (species.date.strain)
-        res_rep_file : str
-            path to the new file, containing 'gpath' sequence, but with 'gembase_name' in headers
+
     Returns
     -------
     list :
         List of all contigs with their size ["contig1;size1", "contig2;size2" ...]
 
     """
-    # Change headers to put into gembase format
+    # Change headers of replicon file to put into gembase format, and save it in res_rep_file
     contigs = utils.get_genome_contigs_and_rename(name, gpath, res_rep_file)
+    # Return each contig name with its size.
     return contigs
 
 
@@ -349,7 +359,7 @@ def create_gff(gpath, gff_file, res_gff_file, res_lst_file, name, contigs, logge
     Returns
     -------
     bool
-        True if everythin went well, False if any problem
+        True if everything went well, False if any problem
 
     """
     # open gff generated by prodigal to read it

PanACoTA/utils.py

@@ -850,7 +850,10 @@ def check_out_dirs(resdir):
 def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
     """
     For the given genome (sequence in gpath), rename all its contigs
-    with the new name: 'gembase_name', and save the output sequence in outfile
+    with the new name: 'gembase_name', and save the output sequence in outfile.
+
+    For each contig renamed, save its new name as well as its size. This will be used to generate
+    gff files
 
     Parameters
     ----------
@@ -861,22 +864,30 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
     outfile : str
         path to the new file, containing 'gpath' sequence, but with 'gembase_name' in headers
 
+    Returns
+    -------
+    list
+        List of all contigs with their size ["contig1;size1", "contig2;size2" ...]
     """
+    # Initialize variables
     contig_num = 1
     cont_size = 0
     contigs = []
+    # Read input sequence given to prodigal, and open file where sequences with new
+    # headers must be written.
     with open(gpath, "r") as gpf, open(outfile, "w") as grf:
         for line in gpf:
             # When we find a new header line, convert its name to gembase format, and write it
-            # to the list of contigs, as well as its size (calculated before)
+            # to output replicon file
             if line.startswith(">") :
                 new_cont = ">" + gembase_name + "." + str(contig_num).zfill(4)
                 grf.write(new_cont + "\n")
-                # If first contig, just convert its name, but no size yet
+                # If not first contig (size != 0), add its name as well as its size to contigs list
                 if cont_size != 0:
                     contigs.append("{};{}".format(new_cont, cont_size))
                 contig_num += 1
                 cont_size = 0
+            # Sequence line: write it as is in replicon file, and add its size to cont_size.
             else:
                 grf.write(line)
                 cont_size += len(line.strip())