How can I convert a genbank file to a FASTA file? IOError

Question

[albamaria.muniesa]

Hello,

I am trying to convert a genbank file to a FASTA file. I have a problem, it seems like python can't recognizes the genbank codes, I don't know how to solve the problem

To prove that I search for an example found in some website, the script and terminal are below... Thanks for your answers

SCRIPT

from Bio import GenBank

gbk_filename = "NC_005213.gbk"
faa_filename = "NC_005213_converted.faa"

input_handle  = open(gbk_filename, "r")
output_handle = open(faa_filename, "w")

for seq_record in SeqIO.parse(input_handle, "genbank") :
    print "Dealing with GenBank record %s" % seq_record.id
    for seq_feature in seq_record.features :
        if seq_feature.type=="CDS" :
            assert len(seq_feature.qualifiers['translation'])==1
            output_handle.write(">%s from %s\n%s\n" % (
                   seq_feature.qualifiers['locus_tag'][0],
                   seq_record.name,
                   seq_feature.qualifiers['translation'][0]))

output_handle.close()
input_handle.close()
print "Done"

TERMINAL

albam@albam-TravelMate-P253:~/Desktop$ python gbk_to_faa.py
Traceback (most recent call last):
  File "gbk_to_faa.py", line 6, in <module>
    input_handle  = open(gbk_filename, "r")
IOError: [Errno 2] No such file or directory: 'NC_005213.gbk'

[pld]

A few suggestions for your script that make use of some better practices:

• Do not hard code things, in the module sys, you can specify command line arguments to your scripts!
• Instead of individual calls to file.open and file.close you should use the with open()... syntax. It makes file operations a bit safer since the file will be closed automatically after completion of the with open statement.
• Always read the error messages, they contain useful information. For example, the IOError exception provided you with a very useful error message.
• In general exceptions in programming are used to notify the programmer that the function raising the exception received some value or values not in the domain of that function. In other words, they're there to provide the programmer/user with (usually) useful information about why the program crashed. Generally speaking, you the programmer/user is the one who provided this invalid input. In your case, you provided a path to file that does not exist.
• You said: "Python does not understand genbank", you're correct, but not in the way you think. Python has no idea of what a genbank file is! BioPython provides several functions that allow you to take the data in a genbank file and format it into another type. You can think of the BioPython code as being the list of python instructions required to convert information in genbank format to information in python values (strings, etc).

[albamaria.muniesa]

I am trying to work with a cDNA sequence from genbank, but the problem is that I don't know which function is the correct to open the sequence directly, from python, this sequence is not saved in my computer that's why I need to open it directly, whitout download it.

I don't know if yo understand me...

Thank you

[pld]

You can't open a file that you do not have. You're telling python to find a file under ~/Desktop, but there is no file there. You have to have the file and tell the script where to get it, you can't just pull files out of no where.

[aproposdiver]

Can you explain this a little more? I am trying to get the same script to work but don't like the hard coding of NC_005213.gbk. I want to be able to read many files and have each of them parsed to a new file. Can you explain how this can be done?

Answer 1

[Neilfws]

Error suggests the file NC_005213.gbk is not in the directory ~/Desktop.