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  • Python - from file to data structure?

    - by Seafoid
    Hi, I have large file comprising ~100,000 lines. Each line corresponds to a cluster and each entry within each line is a reference i.d. for another file (protein structure in this case), e.g. 1hgn 1dju 3nmj 8kfn 9opu 7gfb 4bui I need to read in the file as a list of lists where each line is a sublist, thus preserving the integrity of the cluster, e.g. nested_list = [['1hgn', '1dju', '3nmj', '8kfn'], ['9opu', '7gfb'], ['4bui']] My current code creates a nested list but the entries within each list are a single string and not comma separated. Therefore, I cannot splice the list with indices so easily. Any help greatly appreciated. Thanks, S :-)

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  • Cant overload python socket.send

    - by ralu
    Code from socket import socket class PolySocket(socket): def __init__(self,*p): print "PolySocket init" socket.__init__(self,*p) def sendall(self,*p): print "PolySocket sendall" return socket.sendall(self,*p) def send(self,*p): print "PolySocket send" return socket.send(self,*p) def connect(self,*p): print "connecting..." socket.connect(self,*p) print "connected" HOST="stackoverflow.com" PORT=80 readbuffer="" s=PolySocket() s.connect((HOST, PORT)) s.send("a") s.sendall("a") Output: PolySocket init connecting... connected PolySocket sendall As we can see, send method is not overloaded.

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  • Python and sqlite3 - importing and exporting databases

    - by JPC
    I'm trying to write a script to import a database file. I wrote the script to export the file like so: import sqlite3 con = sqlite3.connect('../sqlite.db') with open('../dump.sql', 'w') as f: for line in con.iterdump(): f.write('%s\n' % line) Now I want to be able to import that database. I tried: import sqlite3 con = sqlite3.connect('../sqlite.db') f = open('../dump.sql','r') str = f.read() con.execute(str) but I'm not allowed to execute more than one statement. Is there a way to get it to run a .sql script directly?

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  • python list/dict property best practice

    - by jterrace
    I have a class object that stores some properties that are lists of other objects. Each of the items in the list has an identifier that can be accessed with the id property. I'd like to be able to read and write from these lists but also be able to access a dictionary keyed by their identifier. Let me illustrate with an example: class Child(object): def __init__(self, id, name): self.id = id self.name = name class Teacher(object): def __init__(self, id, name): self.id = id self.name = name class Classroom(object): def __init__(self, children, teachers): self.children = children self.teachers = teachers classroom = Classroom([Child('389','pete')], [Teacher('829','bob')]) This is a silly example, but it illustrates what I'm trying to do. I'd like to be able to interact with the classroom object like this: #access like a list print classroom.children[0] #append like it's a list classroom.children.append(Child('2344','joe')) #delete from like it's a list classroom.children.pop(0) But I'd also like to be able to access it like it's a dictionary, and the dictionary should be automatically updated when I modify the list: #access like a dict print classroom.childrenById['389'] I realize I could just make it a dict, but I want to avoid code like this: classroom.childrendict[child.id] = child I also might have several of these properties, so I don't want to add functions like addChild, which feels very un-pythonic anyway. Is there a way to somehow subclass dict and/or list and provide all of these functions easily with my class's properties? I'd also like to avoid as much code as possible.

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  • Python method to remove iterability

    - by Debilski
    Suppose I have a function which can either take an iterable/iterator or a non-iterable as an argument. Iterability is checked with try: iter(arg). Depending whether the input is an iterable or not, the outcome of the method will be different. Not when I want to pass a non-iterable as iterable input, it is easy to do: I’ll just wrap it with a tuple. What do I do when I want to pass an iterable (a string for example) but want the function to take it as if it’s non-iterable? E.g. make that iter(str) fails.

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  • Python/Django Concatenate a string depending on whether that string exists

    - by Douglas Meehan
    I'm creating a property on a Django model called "address". I want address to consist of the concatenation of a number of fields I have on my model. The problem is that not all instances of this model will have values for all of these fields. So, I want to concatenate only those fields that have values. What is the best/most Pythonic way to do this? Here are the relevant fields from the model: house = models.IntegerField('House Number', null=True, blank=True) suf = models.CharField('House Number Suffix', max_length=1, null=True, blank=True) unit = models.CharField('Address Unit', max_length=7, null=True, blank=True) stex = models.IntegerField('Address Extention', null=True, blank=True) stdir = models.CharField('Street Direction', max_length=254, null=True, blank=True) stnam = models.CharField('Street Name', max_length=30, null=True, blank=True) stdes = models.CharField('Street Designation', max_length=3, null=True, blank=True) stdessuf = models.CharField('Street Designation Suffix',max_length=1, null=True, blank=True) I could just do something like this: def _get_address(self): return "%s %s %s %s %s %s %s %s" % (self.house, self.suf, self.unit, self.stex, self.stdir, self.stname, self.stdes, self.stdessuf) but then there would be extra blank spaces in the result. I could do a series of if statements and concatenate within each, but that seems ugly. What's the best way to handle this situation? Thanks.

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  • How to replace only part of the match with python re.sub

    - by Arty
    I need to match two cases by one reg expression and do replacement 'long.file.name.jpg' - 'long.file.name_suff.jpg' 'long.file.name_a.jpg' - 'long.file.name_suff.jpg' I'm trying to do the following re.sub('(\_a)?\.[^\.]*$' , '_suff.',"long.file.name.jpg") But this is cut the extension '.jpg' and I'm getting long.file.name_suff. instead of long.file.name_suff.jpg I understand that this is because of [^.]*$ part, but I can't exclude it, because I have to find last occurance of '_a' to replace or last '.' Is there a way to replace only part of the match?

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  • Python and database

    - by axl456
    hello.. Am working on a personal project, where i need to manipulate values in a database-like format.. Up until now, am using dictionaries, tuples, and list to store and consult those values. Am thinking about starting to use SQL to manipulate those values, but I dont know if its worth the effort, because I dont know anything about SQL, and I dont want to use something that wont bring me any benefits (if I can do it in a simpler way, i dont want to complicate things) if am only storing and consulting values, what would be the benefit of using SQL? PS: the numbers of row goes between 3 and 100 and the number of columns is around 10 (some may have 5 some may have 10 etc)

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  • Python If Statement Defaults to an elif

    - by Brad Carvalho
    Not sure why my code is defaulting to this elif. But it's never getting to the else statement. Even going as far as throwing index out of bound errors in the last elif. Please disregard my non use of regex. It wasn't allowed for this homework assignment. The problem is the last elif before the else statement. Cheers, Brad if item == '': print ("%s\n" % item).rstrip('\n') elif item.startswith('MOVE') and not item.startswith('MOVEI'): print 'Found MOVE' elif item.startswith('MOVEI'): print 'Found MOVEI' elif item.startswith('BGT'): print 'Found BGT' elif item.startswith('ADD'): print 'Found ADD' elif item.startswith('INC'): print 'Found INC' elif item.startswith('SUB'): print 'Found SUB' elif item.startswith('DEC'): print 'Found DEC' elif item.startswith('MUL'): print 'Found MUL' elif item.startswith('DIV'): print 'Found DIV' elif item.startswith('BEQ'): print 'Found BEQ' elif item.startswith('BLT'): print 'Found BLT' elif item.startswith('BR'): print 'Found BR' elif item.startswith('END'): print 'Found END' elif item.find(':') and item[(item.find(':') -1)].isalpha(): print 'Mya have found a label' else: print 'Not sure what I found'

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  • improve my python program to fetch the desire rows by using if condition

    - by user2560507
    unique.txt file contains: 2 columns with columns separated by tab. total.txt file contains: 3 columns each column separated by tab. I take each row from unique.txt file and find that in total.txt file. If present then extract entire row from total.txt and save it in new output file. ###Total.txt column a column b column c interaction1 mitochondria_205000_225000 mitochondria_195000_215000 interaction2 mitochondria_345000_365000 mitochondria_335000_355000 interaction3 mitochondria_345000_365000 mitochondria_5000_25000 interaction4 chloroplast_115000_128207 chloroplast_35000_55000 interaction5 chloroplast_115000_128207 chloroplast_15000_35000 interaction15 2_10515000_10535000 2_10505000_10525000 ###Unique.txt column a column b mitochondria_205000_225000 mitochondria_195000_215000 mitochondria_345000_365000 mitochondria_335000_355000 mitochondria_345000_365000 mitochondria_5000_25000 chloroplast_115000_128207 chloroplast_35000_55000 chloroplast_115000_128207 chloroplast_15000_35000 mitochondria_185000_205000 mitochondria_25000_45000 2_16595000_16615000 2_16585000_16605000 4_2785000_2805000 4_2775000_2795000 4_11395000_11415000 4_11385000_11405000 4_2875000_2895000 4_2865000_2885000 4_13745000_13765000 4_13735000_13755000 My program: file=open('total.txt') file2 = open('unique.txt') all_content=file.readlines() all_content2=file2.readlines() store_id_lines = [] ff = open('match.dat', 'w') for i in range(len(all_content)): line=all_content[i].split('\t') seq=line[1]+'\t'+line[2] for j in range(len(all_content2)): if all_content2[j]==seq: ff.write(seq) break Problem: but istide of giving desire output (values of those 1st column that fulfile the if condition). i nead somthing like if jth of unique.txt == ith of total.txt then write ith row of total.txt into new file.

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  • Plotting a cumulative graph of python datetimes

    - by ventolin
    Say I have a list of datetimes, and we know each datetime to be the recorded time of an event happening. Is it possible in matplotlib to graph the frequency of this event occuring over time, showing this data in a cumulative graph (so that each point is greater or equal to all of the points that went before it), without preprocessing this list? (e.g. passing datetime objects directly to some wonderful matplotlib function) Or do I need to turn this list of datetimes into a list of dictionary items, such as: {"year": 1998, "month": 12, "date": 15, "events": 92} and then generate a graph from this list? Sorry if this seems like a silly question - I'm not all too familiar with matplotlib, and would like to save myself the effort of doing this the latter way if matplotlib can already deal with datetime objects itself.

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  • Sympy python circumference

    - by Mattia Villani
    I need to display a circumference. In order to do that I thought I could calculata for a lot of x the two values of y, so I did: import sympy as sy from sympy.abc import x,y f = x**2 + y**2 - 1 a = x - 0.5 sy.solve([f,a],[x,y]) and this is what I get: Traceback (most recent call last): File "<input>", line 1, in <module> File "/usr/lib/python2.7/dist-packages/sympy/solvers/solvers.py", line 484, in solve solution = _solve(f, *symbols, **flags) File "/usr/lib/python2.7/dist-packages/sympy/solvers/solvers.py", line 749, in _solve result = solve_poly_system(polys) File "/usr/lib/python2.7/dist-packages/sympy/solvers/polysys.py", line 40, in solve_poly_system return solve_biquadratic(f, g, opt) File "/usr/lib/python2.7/dist-packages/sympy/solvers/polysys.py", line 48, in solve_biquadratic G = groebner([f, g]) File "/usr/lib/python2.7/dist-packages/sympy/polys/polytools.py", line 5308, i n groebner raise DomainError("can't compute a Groebner basis over %s" % domain) DomainError: can't compute a Groebner basis over RR How can I calculate the y's values ?

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  • importing classes python

    - by Richard
    Just wondering why import sys exit(0) gives me this error: Traceback (most recent call last): File "<pyshell#1>", line 1, in ? exit(0) TypeError: 'str' object is not callable but from sys import exit exit(0) works fine?

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  • Sorting and aligning the contents of a text file in Python

    - by Emily Price
    In my program I have a text file that I read from and write to. However, I would like to display the contents of the text file in an aligned and sorted manner. The contents currently read: name, score name, score This is my code where the text file in read and printed: elif userCommand == 'V': print "High Scores:" scoresFile = open("scores1.txt", 'r') scores = scoresFile.read().split("\n") for score in scores: print score scoresFile.close() Would I have to convert this information into lists in order to be able to do this? If so, how do I go about doing this? Thank you

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  • How to find links and modify an Html using BeautifulSoup in Python

    - by systempuntoout
    Starting from an Html input like this: <p> <a href="http://www.foo.com">this if foo</a> <a href="http://www.bar.com">this if bar</a> </p> using BeautifulSoup, i would like to change this Html in: <p> <a href="http://www.foo.com">this if foo[1]</a> <a href="http://www.bar.com">this if bar[2]</a> </p> saving parsed links in a dictionary with a result like this: links_dict = {"1":"http://www.foo.com","2":"http://www.bar.com"} Is it possible to do this using BeautifulSoup? Any valid alternative?

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  • tkinter python entry not being displayed

    - by user1050619
    I have created a Form with labels and entries..but for some reason the entries are not being created, peoplegui.py from tkinter import * from tkinter.messagebox import showerror import shelve shelvename = 'class-shelve' fieldnames = ('name','age','job','pay') def makewidgets(): global entries window = Tk() window.title('People Shelve') form = Frame(window) form.pack() entries = {} for (ix, label) in enumerate(('key',) + fieldnames): lab = Label(form, text=label) ent = Entry(form) lab.grid(row=ix, column=0) lab.grid(row=ix, column=1) entries[label] = ent Button(window, text="Fetch", command=fetchRecord).pack(side=LEFT) Button(window, text="Update", command=updateRecord).pack(side=LEFT) Button(window, text="Quit", command=window.quit).pack(side=RIGHT) return window def fetchRecord(): print('In fetch') def updateRecord(): print('In update') if __name__ == '__main__': window = makewidgets() window.mainloop() When I run it the labels are created but not the entries.

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  • Easy Python input question

    - by Josh K
    I'd like to have something similar to the following pseudo code: while input is not None and timer < 5: input = getChar() timer = time.time() - start if timer >= 5: print "took too long" else: print input Anyway to do this without threading? I would like an input method that returns whatever has been entered since the last time it was called, or None (null) if nothing was entered.

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