[BioPython] Random sequence
pan at uchicago.edu
pan at uchicago.edu
Wed Jun 16 21:58:31 EDT 2004
You can make a random seq with one line of python code:
>>> import random
>>> ''.join([random.choice('AGTC') for x in range(10)])
'GGTTTCGGTA'
>>> ''.join([random.choice('AGTC') for x in range(10)])
'GCGGGTCCGT'
>>> ''.join([random.choice('AGTC') for x in range(10)])
'AAAAGCACTG'
Isn't it beautiful?
pan
Quoting ashleigh smythe <absmythe at ucdavis.edu>:
> On Wed, 2004-06-16 at 07:45, Sebastian Bassi wrote:
> > Is there a way to generate a random DNA sequence with biopython?
> > If not, I could submit a function to do it, but before doing it, I'd
> > want to see if its not already done.
>
> Hi Sebastian. I wasn't able to find a random sequence generator in the
> biopython modules so I wrote a simple little one of my own a few months
> ago- it only uses biopython modules to add the sequence to a
> biopython-parsed file. It is quite ugly and brute force as I'm a
> beginner - I'd be curious to see what you come up with. In case you are
> curious, here it is:
>
> #This is designed to generate random DNA sequence data and add
> #it to the end of a biopython-parsed sequence record
> #in fasta format.
> #Modified 2-20 to just make random seq. data for a taxon,
> #rather than adding it onto the existing sequence.
>
> import random
> import string
>
>
>
>
> def generate(n): #generate the dna sequence of n length
> bases=['A', 'T', 'G', 'C']
> dna_in_list=[]
>
>
> while n > 0:
> abase=random.choice(bases)
>
>
> dna_in_list.append(abase)
> n=n-1
>
>
> dnastring=str(dna_in_list) #format the list into a string.
> better_dnastring=string.join(string.split(dnastring),"") #Take
> better2_dnastring=string.strip(better_dnastring) #out
> better3_dnastring=better2_dnastring.replace(',','') #unwanted
> better4_dnastring=better3_dnastring.replace(']','') #characters
> better5_dnastring=better4_dnastring.replace('[','')
> better6_dnastring=better5_dnastring.replace("'",'')
>
> return better6_dnastring
>
>
> def add_seq(n): #this is how start
> import sys #the program:seqgen.add_seq(file, n).
> from Bio import Fasta
> parser=Fasta.RecordParser()
> afile=open(file_to_add_to, 'r')
> iterator=Fasta.Iterator(afile, parser)
>
> out_file=open('randomadded.nex', 'w')
>
> while 1: #loop through each record and add the new
> seq_to_add=generate(n) #sequence
> cur_record=iterator.next()
> if cur_record is None:
> break
> title_and_seq=string.split(cur_record.title)
> title='>' + title_and_seq[0] + '\n'
> new_record=title + 'N' + seq_to_add
> out_file.write(new_record)
> out_file.write('\n')
>
>
> Ashleigh
>
> _______________________________________________
> BioPython mailing list - BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython
>
More information about the BioPython
mailing list