cathalgarvey

{
  "binsi": {
    "target_site": "CCWGG", 
    "name": "BinSI", 
    "suppliers": [], 
    "source": "ATCC 15702", 
    "references": [
      "Khosaka, T., Kiwaki, M., Rak, B., (1983) FEBS Lett., vol. 163, pp. 170-174."
    ], 
    "prototype": "EcoRII", 

cathalgarvey

{
 "End": {
  "TAG": {
   "frequency": 0.0, 
   "relfreq": 0.0
  }, 
  "localfrequency": 2.74, 
  "TGA": {
   "frequency": 0.98, 
   "relfreq": 0.3576642335766423

cathalgarvey

#!/usr/bin/env python3
import os
from sys import argv

# Walk through folders recursively, list the full path and number of (extension) files found in each.

basefolder = os.path.expanduser(argv[1])
filetype = str(argv[2]).lower()
output = []

cathalgarvey

#!/usr/bin/env python3

import sys
fixfile = sys.argv[1]

with open(fixfile) as InputFile:
    word_soup = InputFile.read()

# Strip off excess whitespace and any trailing ellipsis.
word_soup = word_soup.strip().strip(".!?")

cathalgarvey

#!/usr/bin/env python3
import time
import datetime
import os
import json

timestamp_format = '%a %b %d %H:%M:%S %z %Y'
def twitter_timestamp_to_obj(time_string):
    'Returns a timezone-aware datetime object.'
    return datetime.datetime.strptime(time_string, timestamp_format)

cathalgarvey

#!/usr/bin/env python3
import time
import datetime
import json
import re

timestamp_format = '%a %b %d %H:%M:%S %z %Y'
def twitter_timestamp_to_obj(time_string):
    'Returns a timezone-aware datetime object.'
    return datetime.datetime.strptime(time_string, timestamp_format)

cathalgarvey

class VersionedDict(dict):
    '''A dictionary sublcass that remembers all or a defined number of prior entries for a key.
    Allows reversion by number from "head" or by absolute reference in revision list.
    Allows retrieval of currently retained revision history for a key.
    Deletion deletes all revisions, not merely the most recent.
    If instantiated with the "revisions" keyword and an integer argument, only retains that many revisions per entry.'''

    def __init__(self, *args, **kwargs):
        revisions = kwargs.pop('revisions', None)
        self._allowed_revisions = abs(int(revisions))

cathalgarvey

from Bio import SeqIO
from Bio.Seq import Seq

sequence_generator = SeqIO.parse("br_sequences.fasta", "fasta")
all_sequences = list(sequence_generator)

# * How many records are in the file?
print("Number of records:", len(all_sequences))

# * How many records have a sequence of length 249?

cathalgarvey

"Functions missing from Python's string/list types that are handy for bio-informatics."

def codonise(seq):
    '''Returns a list of codons, not including trailing 1/2n.
    To get codons starting from letter X, pass seq[X:].'''
    mylist = []
    for i in range(0, len(seq), 3):
        this_codon = seq[i:i+3]
        # This bit ensures that only whole codons,
        # not trailing bits, are added:

cathalgarvey

import sys
from Bio import SeqIO
from Bio.Seq import Seq

filename = sys.argv[1]
usersequence = Seq(sys.argv[2])
usersequence = usersequence.upper()
user_reverse = usersequence.reverse_complement()

records = SeqIO.parse(filename, "fasta")