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?
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written
by
mdsiddra •
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.
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.
Yeah sure. Thanku for the help.
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Are you just concerned about the file extension or do you also want your program to check the contents?
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.
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
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.
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.
So is there a way I can check the file type using python? Can I get some help? I tried using this also,
but couldn't get successful.
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?
Note: When I use that, it tells me invalid syntax. So what do I do?
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.
Yes, I have given feedback there already.
Great, but you haven't accepted the answer of jrj.healey, although I believe that he solved your issue.
Well, I believed that it was very close and really helpful, but I have accepted it also. Thankyou for guiding me this way. :)
Glad to help and welcome to biostars. Interesting guidelines for posting can be found in the following posts:
Thankyou for this sharing..! Can I also get some help about my question I mentioned above.???