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Use raw string literals for regex in parsers #38

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Use raw string literals for regex in parsers #38

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32 changes: 16 additions & 16 deletions pyir/parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ class QueryParser(BaseParser):
def __init__(self, seq_dict):
# self.args = args
self.required = True
self.regex = re.compile('^Query= ((\S| )*)')
self.regex = re.compile(r'^Query= ((\S| )*)')
self.seq_dict = seq_dict

def parse(self, line, out_d):
Expand Down Expand Up @@ -79,10 +79,10 @@ class SignificantAlignmentParser(BaseParser):
This parser is responsible for the 'Hits' field along with its' subfields"""
def __init__(self):
self.required = True
self.failure_regex = re.compile('^.+No hits found.+$')
self.trigger_regex = re.compile('^Sequences producing significant alignments')
self.hit_regex = re.compile('(.*?)[ ]+([0-9.\-e]+)[ ]+([0-9.\-e]+)')
self.halt_regex = re.compile('^Domain classification requested')
self.failure_regex = re.compile(r'^.+No hits found.+$')
self.trigger_regex = re.compile(r'^Sequences producing significant alignments')
self.hit_regex = re.compile(r'(.*?)[ ]+([0-9.\-e]+)[ ]+([0-9.\-e]+)')
self.halt_regex = re.compile(r'^Domain classification requested')
self.hits = []
self.triggered = False

Expand Down Expand Up @@ -123,7 +123,7 @@ class VDJSummaryParser(BaseParser):
'V family', 'J family', 'D family', 'Top V gene e_value', 'Top D gene e_value', and 'Top J gene e_value'
fields as well as overall informational fields 'Chain type', 'stop codon', 'V-J frame', and 'Strand'"""
def __init__(self):
self.regex = re.compile('^V-\(D\)-J rearrangement summary for query sequence \((.*)\)\.')
self.regex = re.compile(r'^V-\(D\)-J rearrangement summary for query sequence \((.*)\)\.')
self.required = True
self.triggered = False
self.fields = None
Expand Down Expand Up @@ -196,7 +196,7 @@ class SubRegionParser(BaseParser):
'V family', 'J family', 'D family', 'Top V gene e_value', 'Top D gene e_value', and 'Top J gene e_value'
fields"""
def __init__(self):
self.regex = re.compile('^Sub-region sequence details \((.*)\)')
self.regex = re.compile(r'^Sub-region sequence details \((.*)\)')
self.required = False
self.triggered = False
self.fields = None
Expand Down Expand Up @@ -227,9 +227,9 @@ class AlignmentSummaryParser(BaseParser):
This parser is responsible for the alignment summary table fields from IgBlast, which can include:
'FR1', 'FR2', 'FR3', 'FR4', 'CDR1', 'CDR2', 'CDR3', and 'Total' fields."""
def __init__(self):
self.regex = re.compile('^Alignment summary between query and top germline V gene hit \((.*)\)')
self.regex = re.compile(r'^Alignment summary between query and top germline V gene hit \((.*)\)')
self.required = True
self.alignment_type_regex = re.compile('(\w*)-IMGT')
self.alignment_type_regex = re.compile(r'(\w*)-IMGT')
self.triggered = False
self.frameworks_found = []

Expand Down Expand Up @@ -287,9 +287,9 @@ def __init__(self, line):
self.is_header = False
self.is_translation = False
self.appended_count = 0
self.hit_regex = re.compile('([VDJ])\s+(\S*)\s+(\S*)\s+(\S*)\s+([0-9]+)\s+(\S*)\s+([0-9]+)')
self.query_regex = re.compile('(\S*Query\S*)\s+([0-9]+)\s+(\S*)\s+([0-9]+)')
self.header_regex = re.compile('[<\->]')
self.hit_regex = re.compile(r'([VDJ])\s+(\S*)\s+(\S*)\s+(\S*)\s+([0-9]+)\s+(\S*)\s+([0-9]+)')
self.query_regex = re.compile(r'(\S*Query\S*)\s+([0-9]+)\s+(\S*)\s+([0-9]+)')
self.header_regex = re.compile(r'[<\->]')
self.read_line(line)

def read_line(self, line):
Expand Down Expand Up @@ -348,9 +348,9 @@ class AlignmentParser(BaseParser):
This parser is responsible for the 'Alignments' field as well as the 'NT', 'sequence_aa', and 'AA_Length' fields in
'CDR1', 'CDR2', 'CDR3', 'FR1', 'FR2', 'FR3', and 'FR4'"""
def __init__(self, input_type, seqs_dict):
self.trigger_regex = re.compile('^Alignments')
self.halt_regex = re.compile('^Lambda')
self.alignments_regex = re.compile('(<[-\w]*>)')
self.trigger_regex = re.compile(r'^Alignments')
self.halt_regex = re.compile(r'^Lambda')
self.alignments_regex = re.compile(r'(<[-\w]*>)')
self.required = True
self.alignments = []
self.alignment_span = None
Expand Down Expand Up @@ -585,7 +585,7 @@ def __init__(self, seq_dict, out_file, args):

self.total_parsed = 0
self.total_passed = 0
self.end_regex = re.compile('^Effective search space used:.*$')
self.end_regex = re.compile(r'^Effective search space used:.*$')

# The parsers must be initialized in order of appearance in BLAST output for PyIR to work
self.parsers = [
Expand Down