Develop Reference

Trouble parsing FASTA files in Python

dict = {}
tag = ""
with open('/storage/emulated/0/Download/sequence.fasta.txt','r') as sequence:
seq = sequence.readlines()
for line in seq:
if line.startswith(">"):
tag = line.replace("\n", "")
else:
seq = "".join(seq[1:])
dict[tag] = seq.replace("\n", "")
print(dict)
Background for those who arn't familiar with FASTA files. This format contains one or multiple DNA, RNA, or protein sequences with a one-line descriptive tag of the sequence that starts with a ">" and then the sequence in the following lines(Ex. For DNA it would be a lot of repeating of A, T, G, and C). It also comes with many unnecessary line breaks. So far this code works when I only have one sequence per file but it seems to ignore the if condition if there are multiple. For example it should add each new tag: sequence pair into the dictionary everytime it notices a ">" but instead it only runs once and puts the first description as the key in the dictionary and joins the rest of the file regardless of ">" characters and uses that as the value. How can I get this loop to notice a new ">" after the first occurrence?
I am purposefully steering away from the biopython module.

UPDATE: the code below now works for multiple-line sequences.
The following code works fine for me:
import re
from collections import defaultdict
sequences = defaultdict(str)
with open('fasta.txt') as f:
lines = f.readlines()
current_tag = None
for line in lines:
m = re.match('^>(.+)', line)
if m:
current_tag = m.group(1)
else:
sequences[current_tag] += line.strip()
for k, v in sequences.items():
print(f"{k}: {v}")
It uses a number of features you may be unfamiliar with, such as regular expressions (which are probably very useful in bioinformatics) and f-string formatting. If anything confuses you, ask away. One thing I should add is that you don't want to define a variable as dict because that will clobber something Python has defined at startup. I chose sequences, which doesn't do this and is more informative.
For reference, this is the content of the example FASTA file fasta.txt I used in this instance:
>seq0
FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
>seq1
KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKKIEKFHSQLMRLME LKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq2
EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK
>seq3
MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK
>seq4
EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVVSYEMRLFGVQKDNFALEHSLL
>seq5
SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKKIEKLTTLLMR
>seq6
FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKKLEKLSSTLLRSI
>seq7
SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKKMEKLNNIFF
>seq8
SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq9
KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK
>seq10
FDSWDEFVSKSVELFRNHPDTTRYVVKYRHCEGKLVLKVTDNHECLKFKTDQAQDAKKMEK

How to read variating data into dictionary?

I need to extract the name of the constants and their corresponding values from a .txt file into a dictionary. Where key = NameOfConstants and Value=float.
The start of the file looks like this:
speed of light 299792458.0 m/s
gravitational constant 6.67259e-11 m**3/kg/s**2
Planck constant 6.6260755e-34 J*s
elementary charge 1.60217733e-19 C
How do I get the name of the constants easy?
This is my attempt:
with open('constants.txt', 'r') as infile:
file1 = infile.readlines()
constants = {i.split()[0]: i.split()[1] for i in file1[2:]}
I'm not getting it right with the split(), and I need a little correction!

{' '.join(line.split()[:-2]):' '.join(line.split()[-2:]) for line in lines}

From your text file I'm unable to get the correct value of no of spaces to split. So below code is designed to help you. Please have a look, it worked for you above stated file.
import string
valid_char = string.ascii_letters + ' '
valid_numbers = string.digits + '.'
constants = {}
with open('constants.txt') as file1:
for line in file1.readlines():
key = ''
for index, char in enumerate(line):
if char in valid_char:
key += char
else:
key = key.strip()
break
value = ''
for char in line[index:]:
if char in valid_numbers:
value += char
else:
break
constants[key] = float(value)
print constants

Have You tried using regular expressions?
for example
([a-z]|\s)*
matches the first part of a line until the digits of the constants begin.
Python provides a very good tutorial on regular expressions (regex)
https://docs.python.org/2/howto/regex.html
You can try out your regex online as well
https://regex101.com/

with open('constants.txt', 'r') as infile:
lines = infile.readlines()
constants = {' '.join(line.split()[:-2]):float(' '.join(line.split()[-2:-1])) for line in lines[2:]}
Since there were two lines above not needed.

This would best be solved using a regexp.
Focussing on your question (how to get the names) and your desires (have something shorter):
import re
# Regular expression fetches all characters
# until the first occurence of a number
REGEXP = re.compile('^([a-zA-Z\s]+)\d.*$')
with open('tst.txt', 'r') as f:
for line in f:
match = REGEXP.match(line)
if match:
# On a match the part between parentheses
# are copied to the first group
name = match.group(1).strip()
else:
# Raise something, or change regexp :)
pass

What about re.split-
import re
lines = open(r"C:\txt.txt",'r').readlines()
for line in lines:
data = re.split(r'\s{3,}',line)
print "{0} : {1}".format(data[0],''.join(data[1:]))
Or use oneliner to make dictionary-
{k:v.strip() for k,v in [(re.split(r'\s{3,}',line)[0],''.join(re.split(r'\s{3,}',line)[1:])) for line in open(r"C:\txt.txt",'r').readlines() ]}
Output-
gravitational constant : 6.67259e-11m**3/kg/s**2
Planck constant : 6.6260755e-34J*s
elementary charge : 1.60217733e-19C
Dictionary-
{'Planck constant': '6.6260755e-34J*s', 'elementary charge': '1.60217733e-19C', 'speed of light': '299792458.0m/s', 'gravitational constant': '6.67259e-11m**3/kg/s**2'}

Counting words in a dictionary (Python)

I have this code, which I want to open a specified file, and then every time there is a while loop it will count it, finally outputting the total number of while loops in a specific file. I decided to convert the input file to a dictionary, and then create a for loop that every time the word while followed by a space was seen it would add a +1 count to WHILE_ before finally printing WHILE_ at the end.
However this did not seem to work, and I am at a loss as to why. Any help fixing this would be much appreciated.
This is the code I have at the moment:
WHILE_ = 0
INPUT_ = input("Enter file or directory: ")
OPEN_ = open(INPUT_)
READLINES_ = OPEN_.readlines()
STRING_ = (str(READLINES_))
STRIP_ = STRING_.strip()
input_str1 = STRIP_.lower()
dic = dict()
for w in input_str1.split():
if w in dic.keys():
dic[w] = dic[w]+1
else:
dic[w] = 1
DICT_ = (dic)
for LINE_ in DICT_:
if ("while\\n',") in LINE_:
WHILE_ += 1
elif ('while\\n",') in LINE_:
WHILE_ += 1
elif ('while ') in LINE_:
WHILE_ += 1
print ("while_loops {0:>12}".format((WHILE_)))
This is the input file I was working from:
'''A trivial test of metrics
Author: Angus McGurkinshaw
Date: May 7 2013
'''
def silly_function(blah):
'''A silly docstring for a silly function'''
def nested():
pass
print('Hello world', blah + 36 * 14)
tot = 0 # This isn't a for statement
for i in range(10):
tot = tot + i
if_im_done = false # Nor is this an if
print(tot)
blah = 3
while blah > 0:
silly_function(blah)
blah -= 1
while True:
if blah < 1000:
break
The output should be 2, but my code at the moment prints 0

This is an incredibly bizarre design. You're calling readlines to get a list of strings, then calling str on that list, which will join the whole thing up into one big string with the quoted repr of each line joined by commas and surrounded by square brackets, then splitting the result on spaces. I have no idea why you'd ever do such a thing.
Your bizarre variable names, extra useless lines of code like DICT_ = (dic), etc. only serve to obfuscate things further.
But I can explain why it doesn't work. Try printing out DICT_ after you do all that silliness, and you'll see that the only keys that include while are while and 'while. Since neither of these match any of the patterns you're looking for, your count ends up as 0.
It's also worth noting that you only add 1 to WHILE_ even if there are multiple instances of the pattern, so your whole dict of counts is useless.
This will be a lot easier if you don't obfuscate your strings, try to recover them, and then try to match the incorrectly-recovered versions. Just do it directly.
While I'm at it, I'm also going to fix some other problems so that your code is readable, and simpler, and doesn't leak files, and so on. Here's a complete implementation of the logic you were trying to hack up by hand:
import collections
filename = input("Enter file: ")
counts = collections.Counter()
with open(filename) as f:
for line in f:
counts.update(line.strip().lower().split())
print('while_loops {0:>12}'.format(counts['while']))
When you run this on your sample input, you correctly get 2. And extending it to handle if and for is trivial and obvious.
However, note that there's a serious problem in your logic: Anything that looks like a keyword but is in the middle of a comment or string will still get picked up. Without writing some kind of code to strip out comments and strings, there's no way around that. Which means you're going to overcount if and for by 1. The obvious way of stripping—line.partition('#')[0] and similarly for quotes—won't work. First, it's perfectly valid to have a string before an if keyword, as in "foo" if x else "bar". Second, you can't handle multiline strings this way.
These problems, and others like them, are why you almost certainly want a real parser. If you're just trying to parse Python code, the ast module in the standard library is the obvious way to do this. If you want to be write quick&dirty parsers for a variety of different languages, try pyparsing, which is very nice, and comes with some great examples.
Here's a simple example:
import ast
filename = input("Enter file: ")
with open(filename) as f:
tree = ast.parse(f.read())
while_loops = sum(1 for node in ast.walk(tree) if isinstance(node, ast.While))
print('while_loops {0:>12}'.format(while_loops))
Or, more flexibly:
import ast
import collections
filename = input("Enter file: ")
with open(filename) as f:
tree = ast.parse(f.read())
counts = collections.Counter(type(node).__name__ for node in ast.walk(tree))
print('while_loops {0:>12}'.format(counts['While']))
print('for_loops {0:>14}'.format(counts['For']))
print('if_statements {0:>10}'.format(counts['If']))

Matching in Python lists when there are extra characters

I am trying to write a python code to match things from two lists in python.
One tab-delimited file looks like this:
COPB2
KLMND7
BLCA8
while the other file2 has a long list of similar looking "names", if you will. There should be some identical matches in the file, which I have succeeded in identifying and writing out to a new file. The problem is when there are additional characters at the end of one of the "names". For example, COPB2 from above should match COPB2A in file2, but it does not. Similarly KLMND7 should match KLMND79. Should I use regular expressions? Make them into strings? Any ideas are helpful, thank you!
What I have worked on so far, after the first response seen below:
with open(in_file1, "r") as names:
for line in names:
file1_list = [i.strip() for i in line.split()]
file1_str = str(file1_list)
with open(in_file2, "r") as symbols:
for line in symbols:
items = line.split("\t")
items = str(items)
matches = items.startswith(file1_str)
print matches
This code returns False when I know there should be some matches.

string.startswith() No need for regex, if it's only trailing characters
>>> g = "COPB2A"
>>> f = "COPB2"
>>> g.startswith(f)
True
Here is a working piece of code:
file1_list = []
with open(in_file1, "r") as names:
for line in names:
line_items = line.split()
for item in line_items:
file1_list.append(item)
matches = []
with open(in_file2, "r") as symbols:
for line in symbols:
file2_items = line.split()
for file2_item in file2_items:
for file1_item in file1_list:
if file2_item.startswith(file1_item):
matches.append(file2_item)
print file2_item
print matches
It may be quite slow for large files. If it's unacceptable, I could try to think about how to optimize it.

You might take a look at difflib if you need a more generic solution. Keep in mind it is a big import with lots of overhead so only use it if you really need to. Here is another question that is somewhat similar.
https://stackoverflow.com/questions/1209800/difference-between-two-strings-in-python-php

Assuming you loaded the files into lists X, Y.
## match if a or b is equal to or substring of one another in a case-sensitive way
def Match( a, b):
return a.find(b[0:min(len(a),len(b))-1])
common_words = {};
for a in X:
common_words[a]=[];
for b in Y:
if ( Match( a, b ) ):
common_words[a].append(b);
If you want to use regular expressions to do the matching, you want to use "beginning of word match" operator "^".
import re
def MatchRe( a, b ):
# make sure longer string is in 'a'.
if ( len(a) < len(b) ):
a, b = b, a;
exp = "^"+b;
q = re.match(exp,a);
if ( not q ):
return False; #no match
return True; #access q.group(0) for matches

Help parsing text file in python

Really been struggling with this one for some time now, i have many text files with a specific format from which i need to extract all the data and file into different fields of a database. The struggle is tweaking the parameters for parsing, ensuring i get all the info correctly.
the format is shown below:
WHITESPACE HERE of unknown length.
K PA DETAILS
2 4565434 i need this sentace as one DB record
2 4456788 and this one
5 4879870 as well as this one, content will vary!
X Max - there sometimes is a line beginning with 'Max' here which i don't need
There is a Line here that i do not need!
WHITESPACE HERE of unknown length.
The tough parts were 1) Getting rid of whitespace, and 2)defining the fields from each other, see my best attempt, below:
dict = {}
XX = (open("XX.txt", "r")).readlines()
for line in XX:
if line.isspace():
pass
elif line.startswith('There is'):
pass
elif line.startswith('Max', 2):
pass
elif line.startswith('K'):
pass
else:
for word in line.split():
if word.startswith('4'):
tmp_PA = word
elif word == "1" or word == "2" or word == "3" or word == "4" or word == "5":
tmp_K = word
else:
tmp_DETAILS = word
cu.execute('''INSERT INTO bugInfo2 (pa, k, details) VALUES(?,?,?)''',(tmp_PA,tmp_K,tmp_DETAILS))
At the minute, i can pull the K & PA fields no problem using this, however my DETAILS is only pulling one word, i need the entire sentance, or at least 25 chars of it.
Thanks very much for reading and I hope you can help! :)
K

You are splitting the whole line into words. You need to split into first word, second word and the rest. Like line.split(None, 2).
It would probably use regular expressions. And use the oposite logic, that is if it starts with number 1 through 5, use it, otherwise pass. Like:
pattern = re.compile(r'([12345])\s+\(d+)\s+\(.*\S)')
f = open('XX.txt', 'r') # No calling readlines; lazy iteration is better
for line in f:
m = pattern.match(line)
if m:
cu.execute('''INSERT INTO bugInfo2 (pa, k, details) VALUES(?,?,?)''',
(m.group(2), m.group(1), m.group(3)))
Oh, and of course, you should be using prepared statement. Parsing SQL is orders of magnitude slower than executing it.

If I understand correctly your file format, you can try this script
filename = 'bug.txt'
f = file(filename,'r')
foundHeaders = False
records = []
for rawline in f:
line = rawline.strip()
if not foundHeaders:
tokens = line.split()
if tokens == ['K','PA','DETAILS']:
foundHeaders = True
continue
else:
tokens = line.split(None,2)
if len(tokens) != 3:
break
try:
K = int(tokens[0])
PA = int(tokens[1])
except ValueError:
break
records.append((K,PA,tokens[2]))
f.close()
for r in records:
print r # replace this by your DB insertion code
This will start reading the records when it encounters the header line, and stop as soon as the format of the line is no longer (K,PA,description).
Hope this helps.

Here is my attempt using re
import re
stuff = open("source", "r").readlines()
whitey = re.compile(r"^[\s]+$")
header = re.compile(r"K PA DETAILS")
juicy_info = re.compile(r"^(?P<first>[\d])\s(?P<second>[\d]+)\s(?P<third>.+)$")
for line in stuff:
if whitey.match(line):
pass
elif header.match(line):
pass
elif juicy_info.match(line):
result = juicy_info.search(line)
print result.group('third')
print result.group('second')
print result.group('first')
Using re I can pull the data out and manipulate it on a whim. If you only need the juicy info lines, you can actually take out all the other checks, making this a REALLY concise script.
import re
stuff = open("source", "r").readlines()
#create a regular expression using subpatterns.
#'first, 'second' and 'third' are our own tags ,
# we could call them Adam, Betty, etc.
juicy_info = re.compile(r"^(?P<first>[\d])\s(?P<second>[\d]+)\s(?P<third>.+)$")
for line in stuff:
result = juicy_info.search(line)
if result:#do stuff with data here just use the tag we declared earlier.
print result.group('third')
print result.group('second')
print result.group('first')

import re
reg = re.compile('K[ \t]+PA[ \t]+DETAILS[ \t]*\r?\n'\
+ 3*'([1-5])[ \t]+(\d+)[ \t]*([^\r\n]+?)[ \t]*\r?\n')
with open('XX.txt') as f:
mat = reg.search(f.read())
for tripl in ((2,1,3),(5,4,6),(8,7,9)):
cu.execute('''INSERT INTO bugInfo2 (pa, k, details) VALUES(?,?,?)''',
mat.group(*tripl)
I prefer to use [ \t] instead of \s because \s matches the following characters:
blank , '\f', '\n', '\r', '\t', '\v'
and I don't see any reason to use a symbol representing more that what is to be matched, with risks to match erratic newlines at places where they shouldn't be
Edit
It may be sufficient to do:
import re
reg = re.compile(r'^([1-5])[ \t]+(\d+)[ \t]*([^\r\n]+?)[ \t]*$',re.MULTILINE)
with open('XX.txt') as f:
for mat in reg.finditer(f.read()):
cu.execute('''INSERT INTO bugInfo2 (pa, k, details) VALUES(?,?,?)''',
mat.group(2,1,3)