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
