Source code for bsPlugins.Table2Tracks

from bsPlugins import *
from bbcflib.track import track
from bbcflib import genrep
import os, tarfile


class Table2TracksForm(BaseForm):
    table = twb.BsFileField(label='Table: ',
        help_text='Select table',
        validator=twb.BsFileFieldValidator(required=True))
    id_columns = twf.TextField(label='columns id: ',
        validator=twc.Validator(required=True),
        value='',
        help_text='comma separated list of columns id for which signal tracks will be generated (e.g. 3,5)')
    format = twf.SingleSelectField(label='Output format: ',
        options=["sql","bedgraph","bigwig","wig"],
        validator=twc.Validator(required=False),
        help_text='Output file(s) format (default: bedGraph)')
    assembly = twf.SingleSelectField(label='Assembly: ',
        options=genrep.GenRep().assemblies_available(),
        help_text='Reference genome')
    submit = twf.SubmitButton(id="submit", value="Submit")


meta = {'version': "1.0.0",
        'author': "BBCF",
        'contact': "webmaster-bbcf@epfl.ch"}

in_parameters = [{'id': 'table', 'type': 'txt', 'required': True},
                {'id': 'id_columns', 'type': 'text', 'required': True},
                {'id': 'assembly', 'type': 'assembly', 'required': True},
                {'id': 'format', 'type': 'format'}
]

out_parameters = [{'id': 'output_tar', 'type': 'file'},
                {'id': 'output', 'type':'track'}]


class Table2TracksPlugin(BasePlugin):
    """Generates signal tracks from a tab-delimited table."""
    info = {
        'title': 'Genome tracks from scores table',
        'description': __doc__,
        'path': ['Files', 'Table2Tracks'],
        'output': Table2TracksForm,
        'in': in_parameters,
        'out': out_parameters,
        'meta': meta,
        }
    def __call__(self, **kw):
        assembly = genrep.Assembly(kw.get('assembly'))
        chrmeta = assembly.chrmeta or "guess"

        with open(kw['table'],"rb") as f:
            h=f.readline().strip().replace('#','').split('\t')

        colnames=[]
        for i in kw['id_columns'].split(','):
            indice = int(i)-1
            if indice <= len(h) and indice > 2: #columns 0,1,2 are for chr,start,end
                colnames.append(h[indice])

        t=track(kw['table'],chrmeta=chrmeta, fields=h)
        (filepath, filename) = os.path.split(kw['table'])
        (shortname, extension) = os.path.splitext(filename)

        outfiles=[]
        for _f in colnames:
            output_name = self.temporary_path(fname=shortname+'_'+_f,ext=kw.get('format',"bedGraph"))
            out_track = track(output_name,chrmeta=chrmeta)
            s = t.read(fields=['chr','start','end',_f])
            s.fields[3] = "score"
            out_track.write(s, mode='write')
            out_track.close()
            outfiles.append(output_name)

#        print outfiles
        if len(outfiles) > 1:
            tar_name = self.temporary_path(fname=shortname+"_out.tgz")
            tar = tarfile.open(tar_name, "w:gz")
            [tar.add(f,arcname=os.path.basename(f)) for f in outfiles]
            tar.close()
            self.new_file(tar_name, 'output_tar')
        else:
            self.new_file(outfiles[0], 'output')

        return self.display_time()