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dmnfarrell / epitopepredict

Python package and command line tool for epitope prediction
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missing module #1

Closed ever4cyth closed 9 years ago

ever4cyth commented 9 years ago

from mhcpredict import base,genome,analysis

is genome.py not included in the package?

Thanks!

dmnfarrell commented 9 years ago

The import was written wrong. It should be 

from mhcpredict import base,sequtils,analysis

You might find a few more bugs. I will add a few unit tests to check basic things are working.

ever4cyth commented 9 years ago

Thnaks for your reply, Damien!

What is this line about? Appreciate if you can show me how to get the data.

get data

df = Genome.genbank2Dataframe(genbankfile, cds=True)

On Mon, Sep 7, 2015 at 7:10 AM, Damien Farrell notifications@github.com wrote:

The import was written wrong. It should be

from mhcpredict import base,sequtils,analysis

You might find a few more bugs. I will add a few unit tests to check basic things are working.

— Reply to this email directly or view it on GitHub https://github.com/dmnfarrell/mhcpredict/issues/1#issuecomment-138272329 .

dmnfarrell commented 9 years ago

Yes the examples are probably a bit incomplete but I have updated them. I have added some unit tests in tests.py and they can also serve as examples. You can run the tests from the package directory using python tests.py

The line df = sequtils.genbank2Dataframe(genbankfile) loads protiens from a genbank file into a dataframe format. You can also use fasta files with df = sequtils.fasta2Dataframe(fastafile)

There are sample files in the testing folder. genbank is more reliable than fasta because they use locus_tags for identifiers.

ever4cyth commented 9 years ago

thanks, works great now.

On Tue, Sep 8, 2015 at 9:39 AM, Damien Farrell notifications@github.com wrote:

Yes the examples are probably a bit incomplete but I have updated them. I have added some unit tests in tests.py and they can also serve as examples. You can run the tests from the package directory using python tests.py

The line df = sequtils.genbank2Dataframe(genbankfile) loads protiens from a genbank file into a dataframe format. You can also use fasta files with df = sequtils.fasta2Dataframe(fastafile)

There are sample files in the testing folder. genbank is more reliable than fasta because they use locus_tags for identifiers.

— Reply to this email directly or view it on GitHub https://github.com/dmnfarrell/mhcpredict/issues/1#issuecomment-138561348 .