diff --git a/mavisp/modules.py b/mavisp/modules.py index c2c8c9c..40b7b83 100644 --- a/mavisp/modules.py +++ b/mavisp/modules.py @@ -1233,7 +1233,7 @@ class PTMs(MavispModule): 'T' : 'p', 'Y' : 'y'} protein_chain = 'A' - slim_pattern = re.compile('.* \((CLV|DEG|DOC|LIG|MOD|TRG)_[A-Za-z0-9_-]+\), [0-9]+-[0-9]+, (ggetELM|ELM)') + slim_pattern = re.compile(r'.* \((CLV|DEG|DOC|LIG|MOD|TRG)_[A-Za-z0-9_-]+\), [0-9]+-[0-9]+, (ggetELM|ELM)') def _assign_regulation_class(self, row): ref = row.name[0] @@ -1610,7 +1610,7 @@ def __init__(self, data_dir=None): def _process_sources(self, row): - manual_pattern = 'Manual annotations from (.+)\..+' + manual_pattern = r'Manual annotations from (.+)\..+' sources = row['sources'].split(',') for i,s in enumerate(sources): @@ -1726,7 +1726,7 @@ class ClinVar(MavispModule): module_dir = "clinvar" name = "clinvar" variants_fname = "variants_output.csv" - mutation_pattern = re.compile('\(p\.([A-Z][a-z]{2}[0-9]+[A-Z][a-z]{2})\)') + mutation_pattern = re.compile(r'\(p\.([A-Z][a-z]{2}[0-9]+[A-Z][a-z]{2})\)') def _get_mutation_string(self, row): matches = self.mutation_pattern.findall(row['variant_name']) @@ -2437,7 +2437,7 @@ class ExperimentalData(MavispModule): module_dir = "experimental_data" name = "experimental_data" - hgvsp_regexp = "p\.[A-Z][a-z][a-z][0-9]+[A-Z][a-z][a-z]" + hgvsp_regexp = r"p\.[A-Z][a-z][a-z][0-9]+[A-Z][a-z][a-z]" def _hgvs_to_mavisp(self, hgvsp, offset): return f"{three_to_one_hgvsp[hgvsp[2:5]]}{int(hgvsp[5:-3]) + int(offset)}{three_to_one_hgvsp[hgvsp[-3:]]}"