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
>
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