Checking for a specific file type

Question

[mdsiddra]

I am using python to take a file (protein sequence file) from user. I want to know how can I keep a check if a user specifies a specific file /typeformat.

for example, the function is :

def user_file():
    file_var = input("Enter your file name: ")

    with open(file_var, 'r') as obj:
        print (obj.read())

As I am working with protein sequence files, so I want to check if user has entered a "input.phy" (a sequences file in phylip format) then a block of statements are printed / calculated and if user has entered a "input.aln" (A sequence file in clustalw format) , then another conditional block of statements are printed and if user has entered a "input.fa" (a sequence file in FASTA format), then a 3rd block of statements are printed.

I am confused about how the specific file type will be checked?

[Pierre Lindenbaum]

input("Enter your file name: ")

please don't. every-time someone write such interactive program, god kills a kitten,

just parse the cmd-line arguments https://docs.python.org/2/howto/argparse.html

I want to check if user has entered a "input.phy"

just check the extension of the file ?

but anyway, you should never trust a user: parse the input and throw an exception if the file is badly formatted.

[mdsiddra]

Yes, you are right. I would prefer to check both the file type (extension) and the format of the file and also throw an exception if the file is badly formatted.

[mdsiddra]

So is there a way I can check the file type using python? Can I get some help? I tried using this also,

https://stackoverflow.com/questions/5899497/checking-file-extension

but couldn't get successful.

[mdsiddra]

I'm working on a certain program and I need to have it do different things if the file in question is a "phy" (phylip file), or a "aln" (clustal file) or "fa"(fasta file). Could I just use this?

if m == *.phy
   ....
elif m == *.aln

elif m== *.fa

Note: When I use that, it tells me invalid syntax. So what do I do?

[lakhujanivijay]

Are you just concerned about the file extension or do you also want your program to check the contents?

[mdsiddra]

I am preferably concerned with the extension of the file but I would check both the file type (extension) and the format of the file and also throw an exception if the file is badly formatted.

[WouterDeCoster]

Hi mdsiddra,

Please give feedback on your previous thread: Text file to Phylip format

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

[mdsiddra]

Yes, I have given feedback there already.

[WouterDeCoster]

Great, but you haven't accepted the answer of jrj.healey, although I believe that he solved your issue.

[mdsiddra]

Well, I believed that it was very close and really helpful, but I have accepted it also. Thankyou for guiding me this way. :)

[WouterDeCoster]

Glad to help and welcome to biostars. Interesting guidelines for posting can be found in the following posts:

• How To Ask Good Questions On Technical And Scientific Forums
• How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
• How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking

[mdsiddra]

Thankyou for this sharing..! Can I also get some help about my question I mentioned above.???

Answer 1

[Joe]

Here is a brute force approach to testing file types based on my script at:

https://github.com/jrjhealey/bioinfo-tools/blob/master/x2y.py#L91-L115

def guessExt(infile, verbose):
    """If no input type was specified, guess it from the extension name or emit a warning"""
    extension = os.path.splitext(infile)[1]
    if verbose > 0: print("Extension is " + extension)
    # Figure out what extension to return
    if extension in (".abi",".ab1"):
        type = "abi"
    elif extension in (".embl"):
        type = "embl"
    elif extension in (".clust", ".cw", ".clustal"):
        type = "clustal"
    elif extension in (".fa", ".fasta", ".fas", ".fna", ".faa", ".afasta"):
        type = "fasta"
    elif extension in (".fastq", ".fq"):
        type = "fastq"
    elif extension in (".gbk", ".genbank", ".gb"):
        type = "genbank"
    elif extension in (".paup", ".nexus"):
        type = "nexus"
    else:
        print("Couldn't determine the file type from the extension. Reattempt with the -j|--intype option specified.")
        sys.exit(1)

    if verbose > 0: print("Your file looks like a " + type)
    return type

The rest of the script used BioPython which handles the vast, vast majority of file parsing an exception handling if it fails. I would suggest you use it unless you have a very, very good reason not to. Predicting all the ways users will break your tool with dodgy input files is an NP-hard problem. This set of switches exists purely to identify the file format by extension and return a string to pass to BioPython which does the rest.

[mdsiddra]

Alright, Thanku for the help. Let me try this with my script. But it would have helped if I could throw exceptions for the dodgy input files by users.

[Joe]

You can. Just wrap any section you like in a try and except block, then raise whatever error you wish, some pseudo-code for example:

try:
    ext = os.path.splitext(infile)[1]
except:
     sys.stderr.write("Your file doesn't have an extension")

[mdsiddra]

Yeah sure. Thanku for the help.