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Fix invalid regex escape warnings #462

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Fix invalid regex escape warnings #462

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8 changes: 4 additions & 4 deletions mavisp/modules.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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]
Expand Down Expand Up @@ -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):
Expand Down Expand Up @@ -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'])
Expand Down Expand Up @@ -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:]]}"
Expand Down