/usr/lib/python3/dist-packages/screed/seqparse.py is in python3-screed 0.9-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 | # Copyright (c) 2008-2010, Michigan State University
"""
seqparse contains custom sequence parsers for extending screed's
functionality to arbitrary sequence formats. An example 'hava'
parser is included for API reference
"""
from __future__ import absolute_import
import os
from .createscreed import create_db
from .openscreed import ScreedDB
from . import openscreed
from . import fastq
from . import fasta
from . import hava
# [AN] these functions look strangely similar
def read_fastq_sequences(filename):
"""
Function to parse text from the given FASTQ file into a screed database
"""
# Will raise an exception if the file doesn't exist
iterfunc = openscreed.open(filename, parse_description=True)
# Create the screed db
create_db(filename, fastq.FieldTypes, iterfunc)
return ScreedDB(filename)
def read_fasta_sequences(filename):
"""
Function to parse text from the given FASTA file into a screed database
"""
# Will raise an exception if the file doesn't exist
iterfunc = openscreed.open(filename, parse_description=True)
# Create the screed db
create_db(filename, fasta.FieldTypes, iterfunc)
return ScreedDB(filename)
def read_hava_sequences(filename):
"""
Function to parse text from the given HAVA file into a screed database
"""
# Will raise an exception if the file doesn't exist
theFile = open(filename, "rb")
# Setup the iterator function
iterfunc = hava.hava_iter(theFile)
# Create the screed db
create_db(filename, hava.FieldTypes, iterfunc)
theFile.close()
return ScreedDB(filename)
|