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Find first line of text according to value in Python

How can I do a search of a value of the first "latitude, longitude" coordinate in a "file.txt" list in Python and get 3 rows above and 3 rows below?
Value
37.0459
file.txt
37.04278,-95.58895
37.04369,-95.58592
37.04369,-95.58582
37.04376,-95.58557
37.04376,-95.58546
37.04415,-95.58429
37.0443,-95.5839
37.04446,-95.58346
37.04461,-95.58305
37.04502,-95.58204
37.04516,-95.58184
37.04572,-95.58139
37.04597,-95.58127
37.04565,-95.58073
37.04546,-95.58033
37.04516,-95.57948
37.04508,-95.57914
37.04494,-95.57842
37.04483,-95.5771
37.0448,-95.57674
37.04474,-95.57606
37.04467,-95.57534
37.04462,-95.57474
37.04458,-95.57396
37.04454,-95.57274
37.04452,-95.57233
37.04453,-95.5722
37.0445,-95.57164
37.04448,-95.57122
37.04444,-95.57054
37.04432,-95.56845
37.04432,-95.56834
37.04424,-95.5668
37.044,-95.56251
37.04396,-95.5618
Expected Result
37.04502,-95.58204
37.04516,-95.58184
37.04572,-95.58139
37.04597,-95.58127
37.04565,-95.58073
37.04546,-95.58033
37.04516,-95.57948
Additional information
In linux I can get the closest line and do the treatment I need using grep, sed, cut and others, but I'd like in Python.
Any help will be greatly appreciated!
Thank you.

How can I do a search of a value of the first "latitude, longitude"
coordinate in a "file.txt" list in Python and get 3 rows above and 3
rows below?*
You can try:
with open("text_filter.txt") as f:
text = f.readlines() # read text lines to list
filter= "37.0459"
match = [i for i,x in enumerate(text) if filter in x] # get list index of item matching filter
if match:
if len(text) >= match[0]+3: # if list has 3 items after filter, print it
print("".join(text[match[0]:match[0]+3]).strip())
print(text[match[0]].strip())
if match[0] >= 3: # if list has 3 items before filter, print it
print("".join(text[match[0]-3:match[0]]).strip())
Output:
37.04597,-95.58127
37.04565,-95.58073
37.04546,-95.58033
37.04597,-95.58127
37.04502,-95.58204
37.04516,-95.58184
37.04572,-95.58139

You can use pandas to import the data in a dataframe and then easily manipulate it. As per your question the value to check is not the exact match and therefore I have converted it to string.
import pandas as pd
data = pd.read_csv("file.txt", header=None, names=["latitude","longitude"]) #imports text file as dataframe
value_to_check = 37.0459 # user defined
for i in range(len(data)):
if str(value_to_check) == str(data.iloc[i,0])[:len(str(value_to_check))]:
break
print(data.iloc[i-3:i+4,:])
output
latitude longitude
9 37.04502 -95.58204
10 37.04516 -95.58184
11 37.04572 -95.58139
12 37.04597 -95.58127
13 37.04565 -95.58073
14 37.04546 -95.58033
15 37.04516 -95.57948

A solution with iterators, that only keeps in memory the necessary lines and doesn't load the unnecessary part of the file:
from collections import deque
from itertools import islice
def find_in_file(file, target, before=3, after=3):
queue = deque(maxlen=before)
with open(file) as f:
for line in f:
if target in map(float, line.split(',')):
out = list(queue) + [line] + list(islice(f, 3))
return out
queue.append(line)
else:
raise ValueError('target not found')
Some tests:
print(find_in_file('test.txt', 37.04597))
# ['37.04502,-95.58204\n', '37.04516,-95.58184\n', '37.04572,-95.58139\n', '37.04597,-95.58127\n',
# '37.04565,-95.58073\n', '37.04565,-95.58073\n', '37.04565,-95.58073\n']
print(find_in_file('test.txt', 37.044)) # Only one line after the match
# ['37.04432,-95.56845\n', '37.04432,-95.56834\n', '37.04424,-95.5668\n', '37.044,-95.56251\n',
# '37.04396,-95.5618\n']
Also, it works if there is less than the expected number of lines before or after the match. We match floats, not strings, as '37.04' would erroneously match '37.0444' otherwise.

This solution will print the before and after elements even if they are less than 3.
Also I am using string as it is implied from the question that you want partial matches also. ie. 37.0459 will match 37.04597
search_term='37.04462'
with open('file.txt') as f:
lines = f.readlines()
lines = [line.strip().split(',') for line in lines] #remove '\n'
for lat,lon in lines:
if search_term in lat:
index=lines.index([lat,lon])
break
left=0
right=0
for k in range (1,4): #bcoz last one is not included
if index-k >=0:
left+=1
if index+k<=(len(lines)-1):
right+=1
for i in range(index-left,index+right+1): #bcoz last one is not included
print(lines[i][0],lines[i][1])

How to make a list a string and then an array

import csv
with open('data1.txt', 'r') as f:
fread = csv.reader(f, delimiter='\t')
output = []
for line in fread:
output.append(line)
data_values = str(output[1:17]) #skip the first line and grab relevant data from lines 1 to 16
print(data_values)
usable_data_values = float(data_values)
Right now I'm trying to convert a .txt file with two columns of data into an array with two columns of data. At this point I've extracted the data and have this:
[['0.0000', '1.06E+05'], ['0.0831', '93240'], ['0.1465', '1.67E+05'],
['0.2587', '1.54E+05'], ['0.4828', '1.19E+05'], ['0.7448', '1.17E+05'],
['0.9817', '1.10E+05'], ['1.2563', '1.11E+05'], ['1.4926', '74388'], ['1.7299', '83291'],
['1.9915', '66435'], ['3.0011', '35407'], ['4.0109', '21125'], ['5.0090', '20450'],
['5.9943', '15798'], ['7.0028', '4785.2']]
I'm trying to get that data into something usable (I think I need to get rid of the commas but I'm new to Python and don't even know how to do this). Any help would be appreciated on getting these numbers into a usable form for operations(multiply, add, divide, etc.)!

I believe this is the best you can do. The commas are fine, they just indicate separate elements of a python list. Notice the quotation marks disappear to indicate you are no longer dealing with text strings.
lst = [['0.0000', '1.06E+05'], ['0.0831', '93240'], ['0.1465', '1.67E+05'],
['0.2587', '1.54E+05'], ['0.4828', '1.19E+05'], ['0.7448', '1.17E+05'],
['0.9817', '1.10E+05'], ['1.2563', '1.11E+05'], ['1.4926', '74388'], ['1.7299', '83291'],
['1.9915', '66435'], ['3.0011', '35407'], ['4.0109', '21125'], ['5.0090', '20450'],
['5.9943', '15798'], ['7.0028', '4785.2']]
[list(map(float, i)) for i in lst]
# [[0.0, 106000.0],
# [0.0831, 93240.0],
# [0.1465, 167000.0],
# [0.2587, 154000.0],
# [0.4828, 119000.0],
# [0.7448, 117000.0],
# [0.9817, 110000.0],
# [1.2563, 111000.0],
# [1.4926, 74388.0],
# [1.7299, 83291.0],
# [1.9915, 66435.0],
# [3.0011, 35407.0],
# [4.0109, 21125.0],
# [5.009, 20450.0],
# [5.9943, 15798.0],
# [7.0028, 4785.2]]

Trying to split a txt file into multiple variables

So I'm making a program where it reads a text file and I need to separate all the info into their own variables. It looks like this:
>1EK9:A.41,52; B.61,74; C.247,257; D.279,289
ENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGAD
YTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQ
DVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTT
QRFNVGLVAITDVQNARAQYDTVLANEVTARNNLDNAVEQLRQITGN
YYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLARE
QIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQN
KVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRS
SFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDAT
TTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPV
STNPENVAPQTPEQNAIADGYAPDSPAPVVQQTSARTTTSNGHNPFRN
The code after the > is a title, the next bit that looks like this "A.41,52" are numbered positions in the sequence I need to save to use, and everything after that is an amino acid sequence. I know how to deal with the amino acid sequence, I just need to know how to separate the important numbers in the first line.
In the past when I just had a title and sequence I did something like this:
for line in nucfile:
if line.startswith(">"):
headerline=line.strip("\n")[1:]
else:
nucseq+=line.strip("\n")
Am I on the right track here? This is my first time, any advice would be fantastic and thanks for reading :)

I suggest you use the split() method.
split() allows you to specify the separator of your choice. Provided the sequence title (here 1EK9) is always separated from the rest of the sequence by a colon, you could first pass ":" as your separator. You could then split the remainder of the sequence to recover the numbered positions (e.g. A.41,52) using ";" as a separator.
I hope this helps!

I think what you are trying to do is extract certain parts of the sequence based on their identifiers given to you on the first line (the line starting with >).
This line contains your title, then a sequence name and the data range you need to extract.
Try this:
sequence_pairs = {}
with open('somefile.txt') as f:
header_line = next(f)
sequence = f.read()
title,components = header_line.split(':')
pairs = components.split(';')
for pair in pairs:
start,end = pair[2:-1].split(',')
sequence_pars[pair[:1]] = sequence[start:int(end)+1]
for sequence,data in sequence_pairs.iteritems():
print('{} - {}'.format(sequence, data))

As the other answer may be very good to tackle the assumed problem in it's entirety - but the OP has requested for pointers or an example of the tpyical split-unsplit transform which is often so successful I hereby provide some ideas and working code to show this (based on the example of the question).
So let us focus on the else branch below:
from __future__ import print_function
nuc_seq = [] # a list
title_token = '>'
with open('some_file_of_a_kind.txt', 'rt') as f:
for line in f.readlines():
s_line = line.strip() # this strips whitespace
if line.startswith(title_token):
headerline = line.strip("\n")[1:]
else:
nuc_seq.append(s_line) # build list
# now nuc_seq is a list of strings like:
# ['ENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGAD',
# 'YTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQ',
# ...
# ]
demo_nuc_str = ''.join(nuc_seq)
# now:
# demo_nuc_str == 'ENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGADYTYSNGYR ...'
That is fast and widely deployed paradigm in Python programming (and programming with powerful datatypes in general).
If the split-unsplit ( a.k.a. join) method is still unclear, just ask or try to sear SO on excellent answers to related questions.
Also note, that there is no need to line.strip('\n') as \nis considered whitespace like ' ' (string with a space only) or a tabulator '\t', sample:
>>> a = ' \t \n '
>>> '+'.join(a.split())
''
So the "joining character" only appears, if there are at least two element sto join and in this case, strip removed all whits space and left us with the empty string.
Upate:
As requested a further analysis of the "coordinate part" in the line called headline of the question:
>1EK9:A.41,52; B.61,74; C.247,257; D.279,289
If you want to retrieve the:
A.41,52; B.61,74; C.247,257; D.279,289
and assume you have (as above the complete line in headline string):
title, coordinate_string = headline.split(':')
# so now title is '1EK9' and
# coordinates == 'A.41,52; B.61,74; C.247,257; D.279,289'
Now split on the semi colons, trim the entries:
het_seq = [z.strip() for z in coordinates.split(';')]
# now het_seq == ['A.41,52', 'B.61,74', 'C.247,257', 'D.279,289']
If 'a', 'B', 'C', and 'D' are well known dimensions, than you can "lose" the ordering info from input file (as you could always reinforce what you already know ;-) and might map the coordinats as key: (ordered coordinate-pair):
>>> coord_map = dict(
(a, tuple(int(k) for k in bc.split(',')))
for a, bc in (abc.split('.') for abc in het_seq))
>>> coord_map
{'A': (41, 52), 'C': (247, 257), 'B': (61, 74), 'D': (279, 289)}
In context of a micro program:
#! /usr/bin/enc python
from __future__ import print_function
het_seq = ['A.41,52', 'B.61,74', 'C.247,257', 'D.279,289']
coord_map = dict(
(a, tuple(int(k) for k in bc.split(',')))
for a, bc in (abc.split('.') for abc in het_seq))
print(coord_map)
yields:
{'A': (41, 52), 'C': (247, 257), 'B': (61, 74), 'D': (279, 289)}
Here one might write this explicit a nested for loop but it is a late european evening so trick is to read it from right:
for all elements of het_seq
split on the dot and store left in a and right in b
than further split the bc into a sequence of k's, convert to integer and put into tuple (ordered pair of integer coordinates)
arrived on the left you build a tuple of the a ("The dimension like 'A' and the coordinate tuple from 3.
In the end call the dict() function that constructs a dictionary using here the form dict(key_1, value_1, hey_2, value_2, ...) which gives {key_1: value1, ...}
So all coordinates are integers, stored ordered pairs as tuples.
I'ld prefer tuples here, although split() generates lists, because
You will keep those two coordinates not extend or append that pair
In python mapping and remapping is often performed and there a hashable (that is immutable type) is ready to become a key in a dict.
One last variant (with no knoted comprehensions):
coord_map = {}
for abc in het_seq:
a, bc = abc.split('.')
coord_map[a] = tuple(int(k) for k in bc.split(','))
print(coord_map)
The first four lines produce the same as above minor obnoxious "one liner" (that already had been written on three lines kept together within parentheses).
HTH.

So I'm assuming you are trying to process a Fasta like file and so the way I would do it is to first get the header and separate the pieces with Regex. Following that you can store the A:42.52 B... in a list for easy access. The code is as follows.
import re
def processHeader(line):
positions = re.search(r':(.*)', line).group(1)
positions = positions.split('; ')
return positions
dnaSeq = ''
positions = []
with open('myFasta', 'r') as infile:
for line in infile:
if '>' in line:
positions = processHeader(line)
else:
dnaSeq += line.strip()

I am not sure I completely understand the goal (and I think this post is more suitable for a comment, but I do not have enough privileges) but I think that the key to you solution is using .split(). You can then join the elements of the resulting list just by using + similar to this:
>>> result = line.split(' ')
>>> result
['1EK9:A.41,52;', 'B.61,74;', 'C.247,257;', 'D.279,289', 'ENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGAD', 'YTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQ', 'DVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTT', 'QRFNVGLVAITDVQNARAQYDTVLANEVTARNNLDNAVEQLRQITGN',
'YYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLARE', 'QIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQN', 'KVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRS', 'SFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDAT', 'TTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPV', 'STNPENVAPQTPEQNAIADGYAPDSPAPVVQQTSARTTTSNGHNPFRN']
>>> result[3]+result[4]
'D.279,289ENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGAD'
>>>
etc. You can also use the usual following syntax to extract the elements of the list that you need:
>>> result[5:]
['YTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQ', 'DVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTT', 'QRFNVGLVAITDVQNARAQYDTVLANEVTARNNLDNAVEQLRQITGN', 'YYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLARE', 'QIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQN', 'KVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRS', 'SFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDAT', 'TTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPV', 'STNPENVAPQTPEQNAIADGYAPDSPAPVVQQTSARTTTSNGHNPFRN']
and join them together:
>>> reduce(lambda x, y: x+y, result[5:])
'YTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQDVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTTQRFNVGLVAITDVQNARAQYDTVLANEVTARNNLDNAVEQLRQITGNYYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLAREQIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQNKVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRSSFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDATTTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPVSTNPENVAPQTPEQNAIADGYAPDSPAPVVQQTSARTTTSNGHNPFRN'
remember that + on lists produces a list.
By the way I would not remove '\n' to start with as you may try to use it to extract the first line similar to the above with using space to extract "words".
UPDATE (starting from result):
#getting A indexes
letter_seq=result[5:]
ind=result[:4]
Aind=ind[0].split('.')[1].replace(';', '')
#getting one long letter seq
long_letter_seq=reduce(lambda x, y: x+y, letter_seq)
#extracting the final seq fromlong_letter_seq using Aind
output = long_letter_seq[int(Aind.split(',')[0]):int(Aind.split(',')[1])]
the last line is just a union of several operations that were also used earlier.
Same for B C D etc -- so a lot of manual work and calculations...
BE CAREFUL with indexes of A -- numbering in python starts from 0 which may not be the case in your numbering system.
The more elegant solution would be using re (https://docs.python.org/2/library/re.html) to find pettern using a mask, but this requires very well defined rules for how to look up the sequence needed.
UPDATE2: it is also not clear to me what is the role of spaces -- so far I removed them but they may matter when counting the letters in the original string.

Python: How split data into different data types into 2D array

I’m trying to split downloaded data to an 2D array into different datatypes. The downloaded data looks like this:
000|17:40
000|17:45
010|17:50
025|17:55
056|18:00
178|18:05
202|18:10
203|18:15
190|18:20
072|18:25
013|18:30
002|18:35
000|18:40
000|18:45
000|18:50
000|18:55
000|19:00
000|19:05
000|19:10
000|19:15
000|19:20
000|19:25
000|19:30
000|19:35
000|19:40
I’m using the following code to parse this into a two dimensional array:
#!/usr/bin/python
import urllib2
response = urllib2.urlopen('http://gps.buienradar.nl/getrr.php?lat=52&lon=4')
html = response.read()
htmlsplit = []
for record in html.split("\r\n"):
htmlsplit.append(record.split("|"))
print htmlsplit
This is working great, but as expected, it treats it as a string. I’ve found some examples that splits into integers. That’s great if both sides where integers. But in my case it’s an integer | string (or maybe some kind of Python time format)
How can I split this directly into different data types?

Something like this?
for record in html.split("\r\n"): # beware, newlines are treacherous!
s = record.split("|")
htmlsplit.append((int(s[0]), s[1]))
Just write a parser for each record, if you have data this simple. However, I would add some try/except clause to catch errors for non-conforming lines, empty lines, etc. which may be present in the data. The code above is very fragile. Also, you might want to break at only \n and then clean your strings by strip() (i.e. replace s[1] by s[1].strip()). The integer conversion takes care of it automatically.

Use str.splitlines instead of splitting on \r\n
Use the csv module to iterate over the lines:
import csv
txt = '000|17:40\n000|17:45\n000|17:50\n000|17:55\n000|18:00\n000|18:05\n000|18:10\n000|18:15\n000|18:20\n000|18:25\n000|18:30\n000|18:35\n000|18:40\n000|18:45\n000|18:50\n000|18:55\n000|19:00\n000|19:05\n000|19:10\n000|19:15\n000|19:20\n000|19:25\n000|19:30\n000|19:35\n000|19:40\n'
reader = csv.reader(txt.splitlines(), delimiter='|')
column1 = []
column2 = []
for c1, c2 in reader:
column1.append(c1)
column2.append(c2)
You can also use the DictReader
import StringIO
reader2 = csv.DictReader(StringIO.StringIO(txt),
fieldnames=['int', 'time'],
delimiter='|')
column1 = []
column2 = []
for row in reader2:
column1.append(row['time'])
column2.append(row['int'])

Writing csv with python

I wrote a python script in which I generate a csv from numbers I computed.
The rows I write are:
writeRow = [str(t), len(c) , {k for k in c.keys()}, {k for k in c.values()}]
I have two problems:
t is a number that can begin by 0. But in that case, the 0 is deleted.
I tried without str() but it doesn't change...
the sets are printed as sets in the cells. However, I want to write these numbers separated by commas in the same cell and without the {} How can I do that?
edit
I am using the csv module; In the code, I create lists for each row to write and then write them with csv.writerow
I'm gonna post more code:
from csv import reader, writer
with open(fileName1) as inp, open(fileName2,'w') as o:
I then define the reader, writer, and the variables t,c
writeRow = [str(t), len(c) , {k for k in c.keys()}, {k for k in c.values()}]
Then I write the result in the output file
Edit
form of t and what a row should look like
t = 023
t = 123
t is an int
The line in the end should look like:
cell1 cell2 cell3 cell4
123 2 string1,string2 num1,num2
string1 and str2 are the dict keys; num1,num2 the corresponding values

For starters, you can take advantage of the join() method (assuming keys and values are strings):
",".join(c.keys()) + "," + ",".join(c.values())
This will take care of commas. However, this will break very easily for any non-trivial data, so consider using csv module instead, which would take care of escaping dangerous characters.

Use string formatting for the padding with 0s, and join for the sets:
writeRow = ['{:0>3}'.format(t), len(c) , ','.join(c.keys()), ','.join(c.values())]
note that you should not enter your value for t with a leading 0:
>>>t = 023
>>>t
19

What about using format strings?
'%s,%i'%(t,c)
might do what you want. You could also use '%03i' or something similar to produce some padding zeros before your number. Or, I might misunderstand your question. Try posting a more complete (runnable) example.