Re: [Tutor] second if
Also, could you explain better what is your doubt? You don't understand what index = 1 means, or why this if at this point, or anything else? Best 2014-02-07 17:14 GMT+01:00 rahmad akbar matbioi...@gmail.com: he guys, i am trying to understand this code: i understand the first if statement (if line.startswith..) in read_fasta function but couldnt understand the next one(if index =...). thanks in advance!! import sys #class declaration with both attributes we need class Fasta: def __init__(self, name, sequence): #this will store the sequence name self.name = name #this will store the sequence itself self.sequence = sequence #this function will receive the list with the file #contents, create instances of the Fasta class as #it scans the list, putting the sequence name on the #first attribute and the sequence itself on the second #attribute def read_fasta(file): #we declare an empty list that will store all #Fasta class instances generated items = [] index = 0 for line in file: #we check to see if the line starts with a sign if line.startswith(): #if so and our counter is large than 1 #we add the created class instance to our list #a counter larger than 1 means we are reading #from sequences 2 and above if index = 1: items.append(aninstance) index+=1 #we add the line contents to a string name = line[:-1] #and initialize the string to store the sequence seq = '' #this creates a class instance and we add the attributes #which are the strings name and seq aninstance = Fasta(name, seq) else: #the line does not start with so it has to be #a sequence line, so we increment the string and #add it to the created instance seq += line[:-1] aninstance = Fasta(name, seq) #the loop before reads everything but the penultimate #sequence is added at the end, so we need to add it #after the loop ends items.append(aninstance) #a list with all read sequences is returned return items fastafile = open(sys.argv[1], 'r').readlines() mysequences = read_fasta(fastafile) print mysequences for i in mysequences: print i.name -- many thanks mat ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] second if
On 07/02/14 16:14, rahmad akbar wrote: he guys, i am trying to understand this code: i understand the first if statement (if line.startswith..) in read_fasta function but couldnt understand the next one(if index =...). thanks in advance!! I'm not sure what you don't understand about it. But so far as I can see its effect is to miss out the first line in the file that starts with '' The logic appears to be, in pseudo code: read the file line buy line if line starts with if not the first time add instance to the collection add one to index create an instance. It has to miss the first one because an instance doesn't exist yet. It seems odd and I'd probably have done it this way: read the file line buy line if line starts with create an instance. add instance to the collection But there may be reasons why the author didn't do that. HTH -- Alan G Author of the Learn to Program web site http://www.alan-g.me.uk/ http://www.flickr.com/photos/alangauldphotos ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] second if
I guess the replies by Alan and Peter precisely answer to your question? Best 2014-02-10 12:46 GMT+01:00 rahmad akbar matbioi...@gmail.com: David, thanks for your reply. i cant figure out why the if at that point and what is the 'if' try to accompolish On Mon, Feb 10, 2014 at 11:52 AM, David Palao dpalao.pyt...@gmail.com wrote: Also, could you explain better what is your doubt? You don't understand what index = 1 means, or why this if at this point, or anything else? Best 2014-02-07 17:14 GMT+01:00 rahmad akbar matbioi...@gmail.com: he guys, i am trying to understand this code: i understand the first if statement (if line.startswith..) in read_fasta function but couldnt understand the next one(if index =...). thanks in advance!! import sys #class declaration with both attributes we need class Fasta: def __init__(self, name, sequence): #this will store the sequence name self.name = name #this will store the sequence itself self.sequence = sequence #this function will receive the list with the file #contents, create instances of the Fasta class as #it scans the list, putting the sequence name on the #first attribute and the sequence itself on the second #attribute def read_fasta(file): #we declare an empty list that will store all #Fasta class instances generated items = [] index = 0 for line in file: #we check to see if the line starts with a sign if line.startswith(): #if so and our counter is large than 1 #we add the created class instance to our list #a counter larger than 1 means we are reading #from sequences 2 and above if index = 1: items.append(aninstance) index+=1 #we add the line contents to a string name = line[:-1] #and initialize the string to store the sequence seq = '' #this creates a class instance and we add the attributes #which are the strings name and seq aninstance = Fasta(name, seq) else: #the line does not start with so it has to be #a sequence line, so we increment the string and #add it to the created instance seq += line[:-1] aninstance = Fasta(name, seq) #the loop before reads everything but the penultimate #sequence is added at the end, so we need to add it #after the loop ends items.append(aninstance) #a list with all read sequences is returned return items fastafile = open(sys.argv[1], 'r').readlines() mysequences = read_fasta(fastafile) print mysequences for i in mysequences: print i.name -- many thanks mat ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor -- many thanks mat ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] second if
By the way, if you are trying to write your own FASTA parser, please reconsider. A good FASTA parser has been written by the folks at BioPython.org. Use that one unless you really know what you're doing. See: http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec12 for example usage. If you are using your own home-grown FASTA parser, consider switching to the biopython one. (As Lincoln Stein of Bioperl fame has observed, reimplementing a FASTA parser should not be a rite of passage. Reference: the talk Bioinformatics: Building a Nation from a Land of City States, mentioned in http://www.oreillynet.com/pub/a/network/2002/01/29/bioday2.html. Sadly, the audio to his keynote speech does not appear to be on Dr. Dobbs Technetcast anymore, as that web site appears to have fallen on hard times.) ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] second if
rahmad akbar matbioi...@gmail.com Wrote in message: Between invisible colors and a tiny font, your message is totally incomprehensible to me. This is a text list, please post in text, not html. -- DaveA ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
[Tutor] Second follow up
How would I go from one def statement to another? I am developing a text based rpg. Sent from my iPod ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Second follow up
On 02/26/2013 09:23 AM, Jack Little wrote: How would I go from one def statement to another? I am developing a text based rpg. Sent from my iPod ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor For your next thread, please try to pick a subject line that has something to do with what you're asking, or what you're trying to learn about. A def statement defines a function (or method). Once it's defined, the compiler goes on to the next line, and if that's a def statement, it defines that function. So all you need is a text editor. Just understand that code that will call those functions from the top-level needs to be *after* the definition is complete. Code that calls functions from inside a function does not need to be in any particular order. If this isn't what you want, then try composing a ten-line sample, tell us what environment you're running it in, and what you hoped for, and what it did instead. On the other hand, perhaps you're asking how to make indirect calls to functions. A function object can be stored in a 'variable', simply by assigning it without using parentheses. You can then later call that function by naming the object, and following the object with the parentheses. Simple example follows; def func1(name): print function1, running with, name def func2(name): print function2, running with, name funclist = [] funclist.append(func1) funclist.append(func2) funclist.append(func1) funclist[1](Sam) will call func2, and pass it Sam as an argument. Normally, if you're doing this type of thing, you'd be using methods, not functions, but I'm not going to introduce classes unless you're already familiar with them. -- DaveA ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Second follow up
On 26/02/13 14:23, Jack Little wrote: How would I go from one def statement to another? Type it in. Based on your message that's all I can suggest. Can you explain what you mean? What do you have in mind by a def statement? def foo(): print 'foo' def bar(): print 'bar' Those are two def statements. You can add as many more as you like? But I suspect that's not really what you mean? I am developing a text based rpg. I don't see whether/how that makes any difference to anything. Telling us which OS and Python version you are using and what programming tools might help though. -- Alan G Author of the Learn to Program web site http://www.alan-g.me.uk/ ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Second follow up
On 26/02/2013 14:23, Jack Little wrote: How would I go from one def statement to another? I am developing a text based rpg. Sent from my iPod ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor I'd like to see your project when it's finished as a text based rocket propelled grenade seems very interesting, or are we talking cross purposes owing to a major lack of data? -- Cheers. Mark Lawrence ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Second follow up
On 27/02/13 01:23, Jack Little wrote: How would I go from one def statement to another? I am developing a text based rpg. def first_function(): # write your code here, indented by FOUR spaces or ONE tab def second_function(): # NO INDENT # write your code here, indented by FOUR spaces or ONE tab Does that help? -- Steven ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Second follow up
On 27/02/13 02:12, Mark Lawrence wrote: On 26/02/2013 14:23, Jack Little wrote: How would I go from one def statement to another? I am developing a text based rpg. I'd like to see your project when it's finished as a text based rocket propelled grenade seems very interesting, or are we talking cross purposes owing to a major lack of data? RPG: Role Playing Game. -- Steven ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Second follow up
On 26/02/2013 16:01, Steven D'Aprano wrote: On 27/02/13 01:23, Jack Little wrote: How would I go from one def statement to another? I am developing a text based rpg. def first_function(): # write your code here, indented by FOUR spaces or ONE tab def second_function(): # NO INDENT # write your code here, indented by FOUR spaces or ONE tab Does that help? Get thee behind me Satan/Steven, tabs indeed :) -- Cheers. Mark Lawrence ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
[Tutor] Second attempt convert DateTimeTyep to datetime.datetime
Hi, I'm using FreeTDS (MS SQL database access lib) and for datetime fields it returns a type 'DateTimeType'. I need it in type 'datetime.datetime'. There is very little in the form of a tutorial that explains what I need to do. Can someone help me with this issue. John ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Second attempt convert DateTimeTyep to datetime.datetime
johnf wrote: Hi, I'm using FreeTDS (MS SQL database access lib) and for datetime fields it returns a type 'DateTimeType'. I need it in type 'datetime.datetime'. There is very little in the form of a tutorial that explains what I need to do. if a datetimetype object has a __str__ or __repr__ method, you can probably just use datetime.datetime's parsing system to convert it from a string into a datetime.datetime object. Can someone help me with this issue. John ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor ___ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
