Merge pull request #109 from b-schubert/release_2.0

Release 2.0

Fred2/Core/Generator.py

@@ -366,108 +366,6 @@ def _generate_combinations(tId, vs, seq, usedVs, offset, isReverse=False):
             yield Transcript("".join(varSeq), geneid, tId, vars=varComb)
 
 
-def generate_transcripts_from_tumor_variants(normal, tumor, dbadapter, id_type):
-    """
-    Generates all possible :class:`~Fred2.Core.Transcript.Transcript` variations of the given
-    :class:`~Fred2.Core.Variant.Variant`.
-
-    The result is a generator.
-
-    :param normal: A list of variants of the normal tissue
-    :type normal: list(:class:`~Fred2.Core.Variant.Variant`)
-    :param tumor: A list of variant of the cancer tissue for which transcript should be generated
-    :type tumor: list(:class:`~Fred2.Core.Variant.Variant`)
-    :param dbadapter: a DBAdapter to fetch the transcript sequences
-    :type dbadapter: :class:`~Fred2.IO.ADBAdapter.ADBAdapter`
-    :param id_type: The type of the transcript IDs used in annotation of variants (e.g. REFSEQ, ENSAMBLE)
-    :type id_type: :func:`~Fred2.IO.ADBAdapter.EIdentifierTypes`
-    :return: A generator of transcripts with all possible variations determined by the given variant list
-    :rtype: Generator(:class:`~Fred2.Core.Transcript.Transcript`)
-    """
-    def _generate_combinations(tId, vs, seq, usedVs, offset):
-        """
-        recursive variant combination generator
-        """
-        transOff = generate_transcripts_from_tumor_variants.transOff
-        #print "TransOffset ", transOff, tId,usedVs
-        if vs:
-            flag, v = vs.pop()
-
-            if v.isHomozygous:
-                pos = v.coding[tId].tranPos + offset
-                usedVs[pos] = v
-                offset = _incorp.get(v.type, lambda a, b, c, d, e: e)(seq, v, tId, pos, offset)
-                for s in _generate_combinations(tId, vs, seq, usedVs, offset):
-                    yield s
-            else:
-                vs_tmp = vs[:]
-                tmp_seq = seq[:]
-                tmp_usedVs = usedVs.copy()
-
-                if flag:
-                    for s in _generate_combinations(tId, vs_tmp, tmp_seq, tmp_usedVs, offset):
-                        yield s
-
-                # update the transcript variant id
-                generate_transcripts_from_tumor_variants.transOff += 1
-                pos = v.coding[tId].tranPos + offset
-                usedVs[pos] = v
-
-                offset = _incorp.get(v.type, lambda a, b, c, d, e: e)(seq, v, tId, pos, offset)
-
-                for s in _generate_combinations(tId, vs, seq, usedVs, offset):
-                    yield s
-        else:
-            yield tId+":FRED2_%i"%transOff, seq, usedVs
-
-    #1) get all transcripts and sort the variants to transcripts
-
-    #For a transcript do:
-        #A) get transcript sequences
-        #B) generate all possible combinations of variants
-        #C) apply variants to transcript and generate transcript object
-
-    if not isinstance(dbadapter, ADBAdapter):
-        raise TypeError("The given dbadapter is not of type ADBAdapter")
-
-    transToVar = {}
-    for v in tumor:
-        for trans_id in v.coding.iterkeys():
-            transToVar.setdefault(trans_id, []).append((False, v))
-
-    for v in normal:
-        for trans_id in v.coding.iterkeys():
-            if trans_id in transToVar:
-                transToVar.setdefault(trans_id, []).append((True, v))
-
-    for tId, vs in transToVar.iteritems():
-        query = dbadapter.get_transcript_information(tId, type=id_type)
-        if query is None:
-            warnings.warn("Transcript with ID %s not found in DB"%tId)
-            continue
-
-        tSeq = query[EAdapterFields.SEQ]
-        geneid = query[EAdapterFields.GENE]
-        strand = query[EAdapterFields.STRAND]
-
-        #if its a reverse transcript form the complement of the variants
-        if strand == REVERS:
-            for flag, v in transToVar[tId]:
-                v.ref = v.ref[::-1].translate(COMPLEMENT)
-                v.obs = v.obs[::-1].translate(COMPLEMENT)
-
-        vs.sort(key=lambda (isTumor, v): v.genomePos-1
-                if v.type in [VariationType.FSINS, VariationType.INS]
-                else v.genomePos, reverse=True)
-        if not _check_for_problematic_variants(map(lambda x: x[1],vs)):
-            warnings.warn("Intersecting variants found for Transcript %s"%tId)
-            continue
-
-        generate_transcripts_from_tumor_variants.transOff = 0
-        for tId, varSeq, varComb in _generate_combinations(tId, vs, list(tSeq), {}, 0):
-            yield Transcript("".join(varSeq), geneid, tId, vars=varComb)
-
-
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