GeoffSCollins
commented
8 months ago It looks like you need to fork the repository in order to contribute. I used this awhile ago but haven't looked at it in years.
Try pasting the code below in a file named modified_snapgene_reader.py and installing the necessary dependencies (pip install bipython, xmltodict, html2text). Then, change your import in your script to from modified_snapgene_reader import snapgene_file_to_dict.
When running your script on the attached plasmids, I get the following output in the terminal and in a file:
'''
snapgene reader main file
'''
import struct
import xmltodict
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation
import html2text
HTML_PARSER = html2text.HTML2Text()
HTML_PARSER.ignore_emphasis = True
HTML_PARSER.ignore_links = True
HTML_PARSER.body_width = 0
HTML_PARSER.single_line_break = True
def parse(val):
'''parse html'''
if isinstance(val, str):
return (HTML_PARSER.handle(val)
.strip()
.replace("\n", " ")
.replace('"', "'"))
else:
return val
# def parse(val):
# ss = re.sub(r'<br>', '\n', val)
# ss = re.sub(r'<.*?>', '', ss)
# return ss
def parse_dict(obj):
"""parse dict in the obj"""
if isinstance(obj, dict):
for key in obj:
if isinstance(obj[key], str):
obj[key] = parse(obj[key])
elif isinstance(obj[key], dict):
parse_dict(obj[key])
return obj
def snapgene_file_to_dict(filepath=None, fileobject=None):
"""Return a dictionnary containing the data from a ``*.dna`` file.
Parameters
----------
filepath
Path to a .dna file created with SnapGene
fileobject
On object-like pointing to the data of a .dna file created with
SnapGene
"""
if filepath is not None:
fileobject = open(filepath, 'rb')
if fileobject.read(1) != b'\t':
raise ValueError('Wrong format for a SnapGene file !')
def unpack(size, mode):
"""unpack the fileobject"""
return struct.unpack('>' + mode, fileobject.read(size))[0]
# READ THE DOCUMENT PROPERTIES
length = unpack(4, 'I')
title = fileobject.read(8).decode('ascii')
if length != 14 or title != 'SnapGene':
raise ValueError('Wrong format for a SnapGene file !')
data = dict(
isDNA=unpack(2, 'H'),
exportVersion=unpack(2, 'H'),
importVersion=unpack(2, 'H'),
features=[]
)
while True:
# READ THE WHOLE FILE, BLOCK BY BLOCK, UNTIL THE END
next_byte = fileobject.read(1)
# next_byte table
# 0: dna sequence
# 1: compressed DNA
# 2: unknown
# 3: unknown
# 5: primers
# 6: notes
# 7: history tree
# 8: additional sequence properties segment
# 9: file Description
# 10: features
# 11: history node
# 13: unknown
# 16: alignable sequence
# 17: alignable sequence
# 18: sequence trace
# 19: Uracil Positions
# 20: custom DNA colors
if next_byte == b'':
# END OF FILE
break
block_size = unpack(4, 'I')
if ord(next_byte) == 0:
# READ THE SEQUENCE AND ITS PROPERTIES
props = unpack(1, 'b')
data["dna"] = dict(
topology="circular" if props & 0x01 else "linear",
strandedness="double" if props & 0x02 > 0 else "single",
damMethylated=props & 0x04 > 0,
dcmMethylated=props & 0x08 > 0,
ecoKIMethylated=props & 0x10 > 0,
length=block_size - 1
)
data["seq"] = fileobject.read(block_size - 1).decode('ascii')
elif ord(next_byte) == 6:
# READ THE NOTES
block_content = fileobject.read(block_size).decode('utf-8')
note_data = parse_dict(xmltodict.parse(block_content))
data['notes'] = note_data['Notes']
elif ord(next_byte) == 10:
# READ THE FEATURES
strand_dict = {"0": ".", "1": "+", "2": "-", "3": "="}
format_dict = {'@text': parse, '@int': int, '@bool': bool }
features_data = xmltodict.parse(fileobject.read(block_size))
features = features_data["Features"]["Feature"]
if not isinstance(features, list):
features = [features]
for feature in features:
segments = feature["Segment"]
if not isinstance(segments, list):
segments = [segments]
segments_ranges = [
sorted([int(e) for e in segment['@range'].split('-')])
for segment in segments
]
qualifiers = feature.get('Q', [])
if not isinstance(qualifiers, list):
qualifiers = [qualifiers]
parsed_qualifiers = {}
for qualifier in qualifiers:
if qualifier['V'] is None:
pass
elif isinstance(qualifier['V'], list):
if len(qualifier['V'][0].items()) == 1:
parsed_qualifiers[qualifier['@name']] = l_v = []
for e_v in qualifier['V']:
fmt, value = e_v.popitem()
fmt = format_dict.get(fmt, parse)
l_v.append(fmt(value))
else:
parsed_qualifiers[qualifier['@name']] = d_v = {}
for e_v in qualifier['V']:
(fmt1, value1), (_, value2), *_ = e_v.items()
fmt = format_dict.get(fmt1, parse)
d_v[value2] = fmt(value1)
else:
fmt, value = qualifier['V'].popitem()
fmt = format_dict.get(fmt, parse)
parsed_qualifiers[qualifier['@name']] = fmt(value)
if 'label' not in parsed_qualifiers:
parsed_qualifiers['label'] = feature['@name']
if 'note' not in parsed_qualifiers:
parsed_qualifiers['note'] = []
if not isinstance(parsed_qualifiers['note'], list):
parsed_qualifiers['note'] = [parsed_qualifiers['note']]
color = segments[0]['@color']
parsed_qualifiers['note'].append("color: " + color)
data["features"].append(dict(
start=min([start - 1 for (start, end) in segments_ranges]),
end=max([end for (start, end) in segments_ranges]),
strand=strand_dict[feature.get('@directionality', "0")],
type=feature['@type'],
name=feature['@name'],
color=segments[0]['@color'],
textColor='black',
segments=segments,
row=0,
isOrf=False,
qualifiers=parsed_qualifiers
))
else:
# WE IGNORE THE WHOLE BLOCK
fileobject.read(block_size)
pass
fileobject.close()
return data
def snapgene_file_to_seqrecord(filepath=None, fileobject=None):
"""Return a BioPython SeqRecord from the data of a ``*.dna`` file.
Parameters
----------
filepath
Path to a .dna file created with SnapGene
fileobject
On object-like pointing to the data of a .dna file created with
SnapGene
"""
data = snapgene_file_to_dict(filepath=filepath, fileobject=fileobject)
strand_dict = {'+': 1, '-': -1, '.': 0}
return SeqRecord(
seq=Seq(data['seq']),
features=[
SeqFeature(
location=FeatureLocation(
start=feature['start'],
end=feature['end'],
strand=strand_dict[feature['strand']]
),
strand=strand_dict[feature['strand']],
type=feature['type'],
qualifiers=feature['qualifiers']
)
for feature in data['features']
],
annotations=dict(data['notes'])
)
def snapgene_file_to_gbk(read_file_object, write_file_object):
'''
convert a file object
'''
def analyse_gs(dic, *args, **kwargs):
'''extract gs block in the document'''
if 'default' not in kwargs:
kwargs['default'] = None
for arg in args:
if arg in dic:
dic = dic[arg]
else:
return kwargs['default']
return dic
data = snapgene_file_to_dict(fileobject=read_file_object)
wfo = write_file_object
wfo.write(
('LOCUS Exported {0:>6} bp ds-DNA {1:>8} SYN \
15-APR-2012\n').format(len(data['seq']), data['dna']['topology']))
definition = analyse_gs(data, 'notes', 'Description',
default='.').replace('\n', '\n ')
wfo.write('DEFINITION {}\n'.format(definition))
wfo.write('ACCESSION .\n')
wfo.write('VERSION .\n')
wfo.write('KEYWORDS {}\n'.format(
analyse_gs(data, 'notes', 'CustomMapLabel', default='.')))
wfo.write('SOURCE .\n')
wfo.write(' ORGANISM .\n')
references = analyse_gs(data, 'notes', 'References')
reference_count = 0
if references:
for key in references:
reference_count += 1
ref = references[key]
wfo.write('REFERENCE {} (bases 1 to {} )\n'.format(
reference_count, analyse_gs(data, 'dna', 'length')))
for key2 in ref:
gb_key = key2.replace('@', '').upper()
wfo.write(' {} {}\n'.format(gb_key, ref[key2]))
# generate special reference
reference_count += 1
wfo.write('REFERENCE {} (bases 1 to {} )\n'.format(
reference_count, analyse_gs(data, 'dna', 'length')))
wfo.write(' AUTHORS IssacLuo\'s SnapGeneReader\n')
wfo.write(' TITLE Direct Submission\n')
wfo.write((' JOURNAL Exported Monday, Nov 20, 2017 from SnapGene File\
Reader\n'))
wfo.write(' https://github.com/IsaacLuo/SnapGeneFileReader\n')
wfo.write('COMMENT {}\n'.format(
analyse_gs(data, 'notes', 'Comments', default='.').replace(
'\n', '\n ').replace('\\', '')))
wfo.write('FEATURES Location/Qualifiers\n')
features = analyse_gs(data, 'features')
for feature in features:
strand = analyse_gs(feature, 'strand', default='')
segments = analyse_gs(feature, 'segments', default=[])
segments = [x for x in segments if x['@type'] == 'standard']
if len(segments) > 1:
line = 'join('
for segment in segments:
segment_range = analyse_gs(segment, '@range').replace('-', '..')
if analyse_gs(segment, '@type') == 'standard':
line += segment_range
line += ','
line = line[:-1] + ')'
else:
line = '{}..{}'.format(
analyse_gs(feature, 'start', default=' '),
analyse_gs(feature, 'end', default=' ')
)
if strand == '-':
wfo.write(' {} complement({})\n'.format(
analyse_gs(feature, 'type', default=' ').ljust(15),
line,
))
else:
wfo.write(' {} {}\n'.format(
analyse_gs(feature, 'type', default=' ').ljust(15),
line,
))
strand = analyse_gs(feature, 'strand', default='')
# if strand == '-':
# wfo.write(' /direction=LEFT\n')
# name
wfo.write(' /note="{}"\n'.format(
analyse_gs(feature, 'name', default='feature')
))
# qualifiers
for q_key in analyse_gs(feature, 'qualifiers', default={}):
# do not write label, because it has been written at first.
if q_key == 'label':
pass
elif q_key == 'note':
for note in analyse_gs(feature, 'qualifiers', q_key, default=[]):
# do note write color, because it will be written later
if note[:6] != 'color:':
wfo.write(' /note="{}"\n'.format(
note))
else:
wfo.write(' /{}="{}"\n'.format(
q_key, analyse_gs(feature, 'qualifiers', q_key, default='')
))
if len(segments) > 1:
wfo.write((' /note="This feature \
has {} segments:').format(len(segments)))
for seg_i, seg in enumerate(segments):
segment_name = analyse_gs(seg, '@name', default='')
if segment_name:
segment_name = ' / {}'.format(segment_name)
wfo.write('\n {}: {} / {}{}'.format(
seg_i,
seg['@range'].replace('-', ' .. '),
seg['@color'],
segment_name,
)
)
wfo.write('"\n')
else:
# write colors and direction
wfo.write(
21 * ' ' + '/note="color: {}'.format(
analyse_gs(feature, 'color', default='#ffffff')))
if strand == '-':
wfo.write('; direction: LEFT"\n')
# wfo.write('"\n')
elif strand == '+':
wfo.write('; direction: RIGHT"\n')
else:
wfo.write('"\n')
# sequence
wfo.write('ORIGIN\n')
seq = analyse_gs(data, 'seq')
# devide rows
for i in range(0, len(seq), 60):
wfo.write(str(i).rjust(9))
for j in range(i, min(i + 60, len(seq)), 10):
wfo.write(' {}'.format(seq[j:j + 10]))
wfo.write('\n')
wfo.write('//\n')
Hello,
I am using snapgene_reader to extract the plasmid name and length from a list of files to populate a database. I have been using it for a while without problems. Here is the script:
However, for one of the files, I get the following error:
It seems that this file might have two names? I have tracked the files that give the problem but I cannot find any possible cause (I am attaching them). It seems these two plasmid files contain a gene sequence that was downloaded from NCBI, so there might be the issue. plasmids.zip