trouble about biopython fasta file import

Question

[mendel18221884]

recently, i am leaning biopython for job. However, I got some problem at first step I followed the biopython cookbook and their example did not work.

(python 3.4.2 and version 1.69)

according to cookbook

It contains 94 records, each has a line starting with “>” (greater-than symbol) followed by the sequence on one or more lines. Now try this in Python:

from Bio import SeqIO
for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
    printseq_record.id)
    print(repr(seq_record.seq))
    print(len(seq_record))

You shouldget something like this on your screen:

gi|2765658|emb|Z78533.1|CIZ78533
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG...CGC', SingleLetterAlphabet())
740

...
gi|2765564|emb|Z78439.1|PBZ78439
Seq('CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT...GCC', SingleLetterAlphabet())
592

.

However, after i followed, I got this

from Bio import SeqIO
for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
    printseq_record.id)
    print(repr(seq_record.seq))
    print(len(seq_record))


Traceback (most recent call last):
  File "<pyshell#27>", line 1, in <module>
    for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
  File "C:\Python34\lib\site-packages\Bio\SeqIO\__init__.py", line 590, in parse
    with as_handle(handle, mode) as fp:
  File "C:\Python34\lib\contextlib.py", line 59, in __enter__
    return next(self.gen)
  File "C:\Python34\lib\site-packages\Bio\File.py", line 88, in as_handle
    with open(handleish, mode, **kwargs) as fp:
FileNotFoundError: [Errno 2] No such file or directory: 'ls_orchid.fasta'

Could anyone give some suggestions to solve this problem?

thanks a lot

Answer 1

[lakhujanivijay]

FileNotFoundError: [Errno 2] No such file or directory: 'ls_orchid.fasta'

This error is self explanatory; isn't it? You forgot to have a dummy fasta file with the name "ls_orchid.fasta" in the same directory from where you executed the script.

[mendel18221884]

Can you demonstrate the step or line ?Because, I am just beginner. I need more help.

thank you so much

[lakhujanivijay]

As a beginner, do not jump to Biopython. Learn the basics of Python first! The error is not specific to biopython, but is pointing to a rather very basic stuff i.e for your program to read a file, there must be a file (you must give it); which you forgot.

So your program is screaming loud- buddy, i will read a fasta file for sure but where is that, I can't find it!!

Solution - Your program.py file and the 'ls_orchid.fasta' should be in the same folder from where you are executing the python program.

I hope was able to explain in the most easy way.

[mendel18221884]

https://raw.githubusercontent.com/biopython/biopython/master/Doc/examples/ls_orchid.fasta

[cpad0112]

@mendel

1. Down load the fasta file (https://raw.githubusercontent.com/biopython/biopython/master/Doc/examples/ls_orchid.fasta) onto your computer. Save it on your Desktop or home folder (assuming that you are using linux)
2. Open a terminal and go to the directory wherever you saved the file:ls_orchid.fasta (for eg. home folder/Desktop/downloads)
3. Run biopyhon script.

However, Vijay is right that one should not jump into biopython without knowing python

[thuco.pipe]

thank you! it helps a lot