Hi,
I'm trying to concatenate hundreds of .fasta files into a single, large fasta file containing all of the sequences. I haven't found a specific method to accomplish this in the forums. I did come across this code from, which I have adapted a bit.
Fasta.py contains the following code:
class fasta: def __init__(self, name, sequence): self.name = name self.sequence = sequence def read_fasta(file): items = [] index = 0 for line in file: if line.startswith(">"): if index >= 1: items.append(aninstance) index+=1 name = line[:-1] seq = '' aninstance = fasta(name, seq) else: seq += line[:-1] aninstance = fasta(name, seq) items.append(aninstance) return items
And here is the adapted script to concatenate .fasta files:
import sys import glob import fasta #obtain directory containing single fasta files for query filepattern = input('Filename pattern to match: ') #obtain output directory outfile = input('Filename of output file: ') #create new output file output = open(outfile, 'w') #initialize lists names = [] seqs = [] #glob.glob returns a list of files that match the pattern for file in glob.glob(filepattern): print ("file: " + file) #we read the contents and an instance of the class is returned contents = fasta.read_fasta(open(file).readlines()) #a file can contain more than one sequence so we read them in a loop for item in contents: names.appenditem.name) seqs.append(item.sequence) #we print the output for i in range(len(names)): output.write(names[i] + '\n' + seqs[i] + '\n\n') output.close() print("done")
It is able to read the fasta files but the newly created output file contains no sequences. The error I receive is due to the fasta.py, which is beyond my capability to mess with:
Traceback (most recent call last): File "C:\Python32\myfiles\test\3\Fasta_Concatenate.py", line 28, in <module> contents = fasta.read_fasta(open(file).readlines()) File "C:\Python32\lib\fasta.py", line 18, in read_fasta seq += line[:-1] UnboundLocalError: local variable 'seq' referenced before assignment
Any suggestions? Thanks!
why don't simply use 'cat *fasta > largenewfasta'?
It looks like he's on windows...
wow, MS-Windows, I have years without touching one except for presentations. In that case, you can use DOS: copy /a *.fasta newfasta.txt
Thanks for the help, easier than i was thinking ;)
cat doesn't seem to work for a ~5000 genomes (protein fasta files). I get the following error: /bin/cat: Argument list too long. Any suggestions?
It looks like you need to look at line 18. Here you assume that seq has been initialised to '' already, but for some reason it is not (eg there are spaces between entries), so it is 'referenced before assignment'. Learning to read tracebacks is tricky but very important and useful.
This is the very literal answer, but you should check out Biopython. This is the kind of common task that doesn't need to be repeatedly implemented. See the SeqIO module:
I actually use Biopython, and have thought of using the SeqIO module to read through the sequence and add it to a file but am unsure how to do so.
You really should just concatenate the files together like the other commentors have recommended. Answering your question though, in case you want to do anything else with the files like verify their integrity/format is correct, you can use SeqIO:
Thank you for your help!