Develop Reference

How get only 5mers from a sequence

I have a file that contains millions of sequences. What I want to do is to get 5mers from each sequence in every line of my file.
My file looks like this:
CGATGCATAGGAA
GCAGGAGTGATCC
my code is:
with open('test.txt','r') as file:
for line in file:
for i in range(len(line)):
kmer = str(line[i:i+5])
if len(kmer) == 5:
print(kmer)
else:
pass
with this code, I should not get 4 mers but I do even I have an if statement for the length of 5mers. Could anyone help me with this? Thanks
my out put is:
CGATG
GATGC
ATGCA
TGCAT
GCATA
CATAG
ATAGG
TAGGA
AGGAA
GGAA
GCAGG
CAGGA
AGGAG
GGAGT
GAGTG
AGTGA
GTGAT
TGATC
GATCC
ATCC
but the ideal output should be only the one with length equal to 5 (for each line separately):
CGATG
GATGC
ATGCA
TGCAT
GCATA
CATAG
ATAGG
TAGGA
AGGAA
GCAGG
CAGGA
AGGAG
GGAGT
GAGTG
AGTGA
GTGAT
TGATC
GATCC

When iterating through a file, every character is represented somewhere. In particular, the last character for each of those lines is a newline \n, which you're printing.
with open('test.txt') as f: data = list(f)
# data[0] == 'CGATGCATAGGAA\n'
# data[1] == 'GCAGGAGTGATCC\n'
So the very last substring you're trying to print from the first line is 'GGAA\n', which has a length of 5, but it's giving you the extra whitespace and the appearance of 4mers. One of the comments proposed a satisfactory solution, but when you know the root of the problem you have lots of options:
with open('test.txt', 'r') as file:
for line_no, line in enumerate(file):
if line_no: print() # for the space between chunks which you seem to want in your final output -- omit if not desired
line = line.strip() # remove surrounding whitespace, including the pesky newlines
for i in range(len(line)):
kmer = str(line[i:i+5])
if len(kmer) == 5:
print(kmer)
else:
pass

How to get first word from text file removing \n - python

If the text file is /n/n Hello world!/n I like python./n
How do I get the first word from that text?
I tried to code:
def word_file(file):
files = open(file, 'r')
l = files.readlines()
for i in range(len(l)):
a = l[i].rstrip("\n")
line = l[0]
word = line.strip().split(" ")[0]
return word
There is space in front Hello.
The result I get is NONE. How should I correct it?
Can anybody help?

Assuming there is a word in the file:
def word_file(f):
with open(f) as file:
return file.read().split()[0]
file.read reads the entire file as a string. Do a split with no parameters on that string (i.e. sep=None). Then according to the Python manual "runs of consecutive whitespace are regarded as a single separator, and the result will contain no empty strings at the start or end if the string has leading or trailing whitespace." So the splitting will be done on consecutive white space and there will be no empty strings returned as a result of the split. Therefore the first element of the returned list will be the first word in the file.
If there is a possibility that the file is empty or contains nothing but white space, then you would need to check the return value from file.read().split() to ensure it is not an empty list.
If you need to avoid having to read the entire file into memory at once, then the following, less terse code can be used:
def word_file(f):
with open(f) as file:
for line in file:
words = line.split()
if words:
return words[0]
return None # No words found

Edit: #Booboo answer is far better than my answer
This should work:
def word_file(file):
with open(file, 'r') as f:
for line in f:
for index, character in enumerate(line):
if not character.isspace():
line = line[index:]
for ind, ch in enumerate(line):
if ch.isspace():
return line[:ind]
return line # could not find whitespace character at end
return None # no words found
output:
Hello

Unable to remove line breaks in a text file in python

At the risk of losing reputation I did not know what else to do. My file is not showing any hidden characters and I have tried every .replace and .strip I can think of. My file is UTF-8 encoded and I am using python/3.6.1
I have a file with the format:
>header1
AAAAAAAA
TTTTTTTT
CCCCCCCC
GGGGGGGG
>header2
CCCCCC
TTTTTT
GGGGGG
AAAAAA
I am trying to remove line breaks from the end of the file to make each line a continuous string. (This file is actually thousands of lines long).
My code is redundant in the sense that I typed in everything I could think of to remove line breaks:
fref = open(ref)
for line in fref:
sequence = 0
header = 0
if line.startswith('>'):
header = ''.join(line.splitlines())
print(header)
else:
sequence = line.strip("\n").strip("\r")
sequence = line.replace('\n', ' ').replace('\r', '').replace(' ', '').replace('\t', '')
print(len(sequence))
output is:
>header1
8
8
8
8
>header2
6
6
6
6
But if I manually go in and delete the end of line to make it a continuous string it shows it as a congruent string.
Expected output:
>header1
32
>header2
24
Thanks in advance for any help,
Dennis

There are several approaches to parsing this kind of input. In all cases, I would recommend isolating the open and print side-effects outside of a function that you can unit test to convince yourself of the proper behavior.
You could iterate over each line and handle the case of empty lines and end-of-file separately. Here, I use yield statements to return the values:
def parse(infile):
for line in infile:
if line.startswith(">"):
total = 0
yield line.strip()
elif not line.strip():
yield total
else:
total += len(line.strip())
if line.strip():
yield total
def test_parse(func):
with open("input.txt") as infile:
assert list(parse(infile)) == [
">header1",
32,
">header2",
24,
]
Or, you could handle both empty lines and end-of-file at the same time. Here, I use an output array to which I append headers and totals:
def parse(infile):
output = []
while True:
line = infile.readline()
if line.startswith(">"):
total = 0
header = line.strip()
elif line and line.strip():
total += len(line.strip())
else:
output.append(header)
output.append(total)
if not line:
break
return output
def test_parse(func):
with open("input.txt") as infile:
assert parse(infile) == [
">header1",
32,
">header2",
24,
]
Or, you could also split the whole input file into empty-line-separated blocks and parse them independently. Here, I use an output stream to which I write the output; in production, you could pass the sys.stdout stream for example:
import re
def parse(infile, outfile):
content = infile.read()
for block in re.split(r"\r?\n\r?\n", content):
header, *lines = re.split(r"\s+", block)
total = sum(len(line) for line in lines)
outfile.write("{header}\n{total}\n".format(
header=header,
total=total,
))
from io import StringIO
def test_parse(func):
with open("/tmp/a.txt") as infile:
outfile = StringIO()
parse(infile, outfile)
outfile.seek(0)
assert outfile.readlines() == [
">header1\n",
"32\n",
">header2\n",
"24\n",
]
Note that my tests use open("input.txt") for brevity but I would actually recommend passing a StringIO(...) instance instead to see the input being tested more easily, to avoid hitting the filesystem and to make the tests faster.

From my understanding of your question you would like something like this:
Note how the sequence is build over multiple iteration steps of the loop, as you wish to combine multiple lines.
with open(ref) as f:
sequence = "" # reset sequence
header = None
for line in f:
if line.startswith('>'):
if header:
print(header) # print last header
print(len(sequence)) # print last sequence
sequence = "" # reset sequence
header = line[1:] # store header
else:
sequence += line.rstrip() # append line to sequence

how to count empty lines in python file

I would like to print the total empty lines using python. I have been trying to print using:
f = open('file.txt','r')
for line in f:
if (line.split()) == 0:
but not able to get proper output
I have been trying to print it.. it does print the value as 0.. not sure what wrong with code..
print "\nblank lines are",(sum(line.isspace() for line in fname))
it printing as:
blank lines are 0
There are 7 lines in the file.
There are 46 characters in the file.
There are 8 words in the file.

Since the empty string is a falsy value, you may use .strip():
for line in f:
if not line.strip():
....
The above ignores lines with only whitespaces.
If you want completely empty lines you may want to use this instead:
if line in ['\r\n', '\n']:
...

Please use a context manager (with statement) to open files:
with open('file.txt') as f:
print(sum(line.isspace() for line in f))
line.isspace() returns True (== 1) if line doesn't have any non-whitespace characters, and False (== 0) otherwise. Therefore, sum(line.isspace() for line in f) returns the number of lines that are considered empty.
line.split() always returns a list. Both
if line.split() == []:
and
if not line.split():
would work.

FILE_NAME = 'file.txt'
empty_line_count = 0
with open(FILE_NAME,'r') as fh:
for line in fh:
# The split method will split the word into list. if the line is
# empty the split will return an empty list. ' == [] ' this will
# check the list is empty or not.
if line.split() == []:
empty_line_count += 1
print('Empty Line Count : ' , empty_line_count)

Python: List not correct after appending lines

I'm trying to append lines to an empty list reading from a file, and I've already stripped the lines of returns and newlines, but what should be one line is being entered as two separate items into the list.
DNA = open('DNAGCex.txt')
DNAID = []
DNASEQ = []
for line in DNA:
line = line.rstrip()
line = line.lstrip()
if line.startswith('>')==True:
DNAID.append(line)
if line.startswith('>')==False:
DNASEQ.append(line)
print DNAID
print DNASEQ
And here's the output
['>Rosalind_6404', '>Rosalind_5959', '>Rosalind_0808']
['CCTGCGGAAGATCGGCACTAGA', 'TCCCACTAATAATTCTGAGG', 'CCATCGGTAGCGCATCCTTAGTCCA', 'ATATCCATTTGTCAGCAGACACGC', 'CCACCCTCGTGGTATGGCTAGGCATTCAG', 'TGGGAACCTGCGGGCAGTAGGTGGAAT']
I want it to look like this:
['>Rosalind_6404', '>Rosalind_5959', '>Rosalind_0808']
['CCTGCGGAAGATCGGCACTAGATCCCACTAATAATTCTGAGG', 'CCATCGGTAGCGCATCCTTAGTCCAATATCCATTTGTCAGCAGACACGC', 'CCACCCTCGTGGTATGGCTAGGCATTCAGTGGGAACCTGCGGGCAGTAGGTGGAAT']
Here is the source material, just remove the ''s:
['>Rosalind_6404'
CCTGCGGAAGATCGGCACTAGA
TCCCACTAATAATTCTGAGG
'>Rosalind_5959'
CCATCGGTAGCGCATCCTTAGTCCA
ATATCCATTTGTCAGCAGACACGC
'>Rosalind_0808'
CCACCCTCGTGGTATGGCTAGGCATTCAG
TGGGAACCTGCGGGCAGTAGGTGGAAT]

You can combine the .lstrip() and .rstrip() into a single .strip() call.
Then, you were thinking that .append() both added lines to a list and joined lines into a single line. Here, we start DNASEQ with an empty string and use += to join the lines into a long string:
DNA = open('DNAGCex.txt')
DNAID = []
DNASEQ = []
for line in DNA:
line = line.strip()
if line.startswith('>'):
DNAID.append(line)
DNASEQ.append('')
else:
DNASEQ[-1] += line
print DNAID
print DNASEQ

Within each iteration of the loop, you're only looking at a certain line from the file. This means that, although you certainly are appending lines that don't contain a linefeed at the end, you're still appending one of the file's lines at a time. You'll have to let the interpreter know that you want to combine certain lines, by doing something like setting a flag when you first start to read in a DNASEQ and clearing it when the next DNAID starts.
for line in DNA:
line = line.strip() # gets both sides
if line.startswith('>'):
starting = True
DNAID.append(line)
elif starting:
starting = False
DNASEQ.append(line)
else:
DNASEQ[-1] += line