add locus prefix checks

oschwengers · Nov 23, 2021 · 8c58851 · 8c58851
1 parent 8e27f68
commit 8c58851
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/bakta/config.py b/bakta/config.py
@@ -208,6 +208,9 @@ def setup(args):
         if(' ' in locus):
             log.error("Whitespace character in 'locus' parameter! locus=%s", locus)
             sys.exit(f"ERROR: whitespace character ({locus}) in 'locus' parameter!")
+        if(bc.RE_INSDC_ID_PREFIX.fullmatch(locus) is None):
+            log.error("Invalid 'locus' parameter! locus=%s", locus)
+            sys.exit(f"ERROR: invalid 'locus' parameter ({locus})!\nLocus prefixes must contain between 1 and 20 alphanumeric and '-_' characters.")
     log.info('locus=%s', locus)
     locus_tag = args.locus_tag
     if(locus_tag is not None):

diff --git a/bakta/constants.py b/bakta/constants.py
@@ -5,6 +5,8 @@
 # Common regex
 ############################################################################
 RE_MULTIWHITESPACE = re.compile(r'\s+')
+RE_INSDC_ID_PREFIX = re.compile(r'[A-Za-z\d_.:*#-]{1,20}')  # https://www.ncbi.nlm.nih.gov/WebSub/html/help/fasta.html
+RE_INSDC_ID = re.compile(r'[A-Za-z\d_.:*#-]{1,25}')  # https://www.ncbi.nlm.nih.gov/WebSub/html/help/fasta.html
 RE_INSDC_LOCUSTAG_PREFIX = re.compile(r'[A-Z][A-Z0-9]{2,11}')  # https://ena-docs.readthedocs.io/en/latest/faq/locus_tags.html
 
 ############################################################################

diff --git a/bakta/utils.py b/bakta/utils.py
@@ -43,9 +43,6 @@ def print_version(self):
 DEPENDENCY_AMRFINDERPLUS = (Version(3, 10, 16), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('amrfinder', '--version'), ['--skip-cds'])
 
 
-INSDC_ID_REGEX = re.compile(r'[^A-Za-z\d_.:*#-]')  # https://www.ncbi.nlm.nih.gov/WebSub/html/help/fasta.html
-
-
 def init_parser():
     parser = argparse.ArgumentParser(
         prog='bakta',
@@ -441,8 +438,7 @@ def qc_contigs(contigs, replicons):
                 if(len(contig['id']) > 25):  # max 25 characters
                     log.error('INSDC compliance: contig id larger than 25! contig-id=%s', contig['id'])
                     sys.exit(f"ERROR: INSDC compliance failed! Contig ID ({contig['id']}) larger than 25 characers!")
-                unvalid_char_match = INSDC_ID_REGEX.search(contig['id'])
-                if(unvalid_char_match is not None):  # invalid characters
+                if(bc.RE_INSDC_ID.fullmatch(contig['id']) is None):  # invalid characters
                     log.error('INSDC compliance: contig id contains invalid characters! contig-id=%s', contig['id'])
                     sys.exit(f"ERROR: INSDC compliance failed! Contig ID ({contig['id']}) contains invalid characters!")