diff --git a/PanACoTA/annotate_module/format_prokka.py b/PanACoTA/annotate_module/format_prokka.py
index 4faa26f2be9a50c5c5176c79a44e733fc59e3577..b3495da8bda3c2177892fc021e760b3f276e997d 100644
--- a/PanACoTA/annotate_module/format_prokka.py
+++ b/PanACoTA/annotate_module/format_prokka.py
@@ -23,6 +23,7 @@ April 2019
import os
import glob
+import sys
import shutil
import PanACoTA.utils as utils
import PanACoTA.annotate_module.general_format_functions as general
@@ -82,7 +83,7 @@ def format_one_genome(gpath, name, prok_path, lst_dir, prot_dir, gene_dir,
# Generate replicon file (same as input sequence but with gembase formatted headers). From
# this file, get contig names, to be used to generate gff file
- contigs = utils.get_genome_contigs_and_rename(name, gpath, res_rep_file)
+ contigs, sizes = utils.get_genome_contigs_and_rename(name, gpath, res_rep_file)
if not contigs:
try:
os.remove(res_lst_file)
@@ -96,13 +97,21 @@ def format_one_genome(gpath, name, prok_path, lst_dir, prot_dir, gene_dir,
return False
# Convert prokka tbl file to gembase .lst file format
- tbl2lst(prokka_tbl_file, res_lst_file, contigs, name, logger)
-
- import sys
- sys.exit(1)
+ ok_tbl = tbl2lst(prokka_tbl_file, res_lst_file, contigs, name, logger)
+ if not ok_tbl:
+ try:
+ 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 LSTINFO file for {}".format(name))
+ return False
# Create gff3 file for annotations
- ok_gff = generate_gff(gpath, prokka_gff_file, res_gff_file, res_lst_file, contigs, logger)
+ ok_gff = generate_gff(gpath, prokka_gff_file, res_gff_file, res_lst_file, sizes, logger)
if not ok_gff:
try:
os.remove(res_lst_file)
@@ -514,11 +523,12 @@ def tbl2lst(tblfile, lstfile, contigs, genome, logger):
with open(tblfile) as tblf, open(lstfile, "w") as lstf:
for line in tblf:
elems = line.strip().split("\t")
- # If new feature, write the previous one, and get information for this new one
+ # If new contig, write the previous one, and get information for this new one
# 2 elements: ">Feature" feature_name
if line.startswith(">Feature"):
- contig = line.strip().split()[-1]
cont_num += 1
+ cont_name = ">" + line.split()[-1] + "\n"
+ exp_cont_name = contigs[cont_num -1].split("\t")[1]
else:
# Get line type, and retrieve info according to it
# If it is not the line with start, end, type, there are only 2 elements
@@ -544,18 +554,28 @@ def tbl2lst(tblfile, lstfile, contigs, genome, logger):
# New contig
if cont_num != prev_cont_num:
# Check if
- # - it is not the first gene of the genome
- # - contig just following the previous one, or there are contigs
- # without any feature between them?
+ # - it is not the first gene of the genome (prev_cont_num =! -1)
+ # - current contig (name after 'feature') and contig corresponding
+ # to cont_num in contigs are the same? If not -> contigs without any gene
+ # without any feature between them
# - this new contig is as expected (next contig of the list of
# contigs generated during Replicons file generation)
- if prev_cont_num != -1 and cont_num != prev_cont_num + 1:
- logger.details("No feature found in contigs between contig {} and "
- "contig {}.".format(prev_cont_num, cont_num))
- cont_name_found = f"{genome}.{str(cont_num).zfill(4)}"
- cont_name_exp = contigs[prev_cont_num - 1]
- if cont_name_found != cont_name_exp:
+ # not first contig and cont_name not corresponding
+ if prev_cont_num != -1 and cont_name != exp_cont_name:
+ # Save current prev_cont_num to know from which contig there
+ # are no genes
+ save_prev_cont_num = prev_cont_num
+ # Find which cont_num corresponds to this cont_name
+ try:
+ while cont_name != exp_cont_name:
+ prev_cont_num += 1
+ exp_cont_name = contigs[prev_cont_num -1].split("\t")[1]
+ except IndexError:
+ logger.error(f"{cont_name} found in {tblfile} does not exist in genome {genome}.")
+ sys.exit(1)
+ logger.details("No feature found in contigs between contig {} and "
+ "contig {}.".format(save_prev_cont_num, prev_cont_num))
# Previous loc was 'i' (because we were in the same contig).
# But we now change contig, so this previous feature was the last
# of its contigs -> prev_loc = "b"
@@ -568,11 +588,12 @@ def tbl2lst(tblfile, lstfile, contigs, genome, logger):
if prev_cont_loc == "b":
cont_loc = "i"
# If we are in the first contig, prev = current
- if prev_cont_num == "-1":
+ if prev_cont_num == -1:
+
prev_cont_num = cont_num
prev_cont_loc = cont_loc
- # If not first feature, write the previous feature to .lst file
+ # If not first feature of the contig, write the previous feature to .lst file
# (The first feature will be written once 2nd feature as been read)
if start != -1 and end != -1:
crispr_num, lstline = general.write_gene(feature_type, locus_num,
@@ -580,10 +601,7 @@ def tbl2lst(tblfile, lstfile, contigs, genome, logger):
prev_cont_loc, genome,
prev_cont_num, ecnum, inf2,
db_xref, strand, start, end, lstf)
- print(cont_name)
- print(f"contig name from rep file {}")
- import sys
- sys.exit(1)
+
# Get new values for start, end, strand and feature type
start, end, feature_type = elems
# Get strain of gene
@@ -596,6 +614,7 @@ def tbl2lst(tblfile, lstfile, contigs, genome, logger):
# and feature type which just calculated)
prev_cont_num = cont_num
prev_cont_loc = cont_loc
+ cont_name = exp_cont_name
locus_num = "NA"
gene_name = "NA"
product = "NA"
diff --git a/PanACoTA/utils.py b/PanACoTA/utils.py
index eccdf21489c91acf9c764a9e612507e4bd96d980..0f2b5a4c7e7218dbd9d7804d38b5ac06967169f0 100755
--- a/PanACoTA/utils.py
+++ b/PanACoTA/utils.py
@@ -1040,8 +1040,11 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
Returns
-------
- list
- List of all contigs with their size ["contig1'\t'size1", "contig2'\t'size2" ...]
+ tuple
+ - List of all contigs with their original and new name:
+ ["contig1'\t'orig_name1", "contig2'\t'orig_name2" ...]
+ - List of all contigs with their size:
+ ["contig1'\t'size1", "contig2'\t'size2" ...]
"""
# Initialize variables
@@ -1049,11 +1052,14 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
contig_num = 1
# contig size
cont_size = 0
- # List of contigs [<name>\t<size>]
+ # List of contigs [<name>\t<orig_name>]
contigs = []
+ # List of contigs with their sizes [<name>\t<size>]
+ sizes = []
# Name of previous contig (to put to contigs, as we need to wait for the next
# contig to know the size of the previous one)
prev_cont = ""
+ prev_orig_name = ""
# sequence of previous contig
seq = ""
@@ -1066,13 +1072,17 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
if line.startswith(">") :
# If not first contig (contigs not empty):
# - add its name as well as its size to contigs list
+ # - add its name with its original name to
# - write header ("<contig name> <size>") to replicon file
if prev_cont:
cont = "\t".join([prev_cont, str(cont_size)]) + "\n"
- contigs.append(cont)
+ sizes.append(cont)
+ cor = "\t".join([prev_cont, prev_orig_name])
+ contigs.append(cor)
grf.write(cont)
grf.write(seq)
prev_cont = ">" + gembase_name + "." + str(contig_num).zfill(4)
+ prev_orig_name = line
contig_num += 1
cont_size = 0
seq = ""
@@ -1082,10 +1092,12 @@ def get_genome_contigs_and_rename(gembase_name, gpath, outfile):
cont_size += len(line.strip())
# Write last contig
cont = "\t".join([prev_cont, str(cont_size)]) + "\n"
- contigs.append(cont)
+ sizes.append(cont)
+ cor = "\t".join([prev_cont, prev_orig_name])
+ contigs.append(cor)
grf.write(cont)
grf.write(seq)
- return contigs
+ return contigs, sizes
def logger_thread(q):