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src/c/o/cogent-1.5.3/cogent/app/muscle_v38.py   cogent(Download)
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
 
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
    seqs_collection = SequenceCollection(seqs)
    #Create mapping between abbreviated IDs and full IDs
    seqs_int_map, seqs_int_keys = seqs_collection.getIntMap(prefix='seq_')
    #Create SequenceCollection from int_map.
    seqs_int_map = SequenceCollection(seqs_int_map)
 
    #create SequenceCollection object from aln
    aln_collection = SequenceCollection(aln)
    #Create mapping between abbreviated IDs and full IDs
    aln_int_map, aln_int_keys = aln_collection.getIntMap(prefix='aln_')
    aln1_collection = SequenceCollection(aln1)
    #Create mapping between abbreviated IDs and full IDs
    aln1_int_map, aln1_int_keys = aln1_collection.getIntMap(prefix='aln1_')
    #Create SequenceCollection from int_map.
    aln1_int_map = SequenceCollection(aln1_int_map)

src/c/o/cogent-1.5.3/cogent/app/muscle.py   cogent(Download)
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
 
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
    seqs_collection = SequenceCollection(seqs)
    #Create mapping between abbreviated IDs and full IDs
    seqs_int_map, seqs_int_keys = seqs_collection.getIntMap(prefix='seq_')
    #Create SequenceCollection from int_map.
    seqs_int_map = SequenceCollection(seqs_int_map)
 
    #create SequenceCollection object from aln
    aln_collection = SequenceCollection(aln)
    #Create mapping between abbreviated IDs and full IDs
    aln_int_map, aln_int_keys = aln_collection.getIntMap(prefix='aln_')
    aln1_collection = SequenceCollection(aln1)
    #Create mapping between abbreviated IDs and full IDs
    aln1_int_map, aln1_int_keys = aln1_collection.getIntMap(prefix='aln1_')
    #Create SequenceCollection from int_map.
    aln1_int_map = SequenceCollection(aln1_int_map)

src/p/y/pycogent-HEAD/cogent/app/muscle_v38.py   pycogent(Download)
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
 
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
    seqs_collection = SequenceCollection(seqs)
    #Create mapping between abbreviated IDs and full IDs
    seqs_int_map, seqs_int_keys = seqs_collection.getIntMap(prefix='seq_')
    #Create SequenceCollection from int_map.
    seqs_int_map = SequenceCollection(seqs_int_map)
 
    #create SequenceCollection object from aln
    aln_collection = SequenceCollection(aln)
    #Create mapping between abbreviated IDs and full IDs
    aln_int_map, aln_int_keys = aln_collection.getIntMap(prefix='aln_')
    aln1_collection = SequenceCollection(aln1)
    #Create mapping between abbreviated IDs and full IDs
    aln1_int_map, aln1_int_keys = aln1_collection.getIntMap(prefix='aln1_')
    #Create SequenceCollection from int_map.
    aln1_int_map = SequenceCollection(aln1_int_map)

src/p/y/pycogent-HEAD/cogent/app/muscle.py   pycogent(Download)
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
 
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
    seqs_collection = SequenceCollection(seqs)
    #Create mapping between abbreviated IDs and full IDs
    seqs_int_map, seqs_int_keys = seqs_collection.getIntMap(prefix='seq_')
    #Create SequenceCollection from int_map.
    seqs_int_map = SequenceCollection(seqs_int_map)
 
    #create SequenceCollection object from aln
    aln_collection = SequenceCollection(aln)
    #Create mapping between abbreviated IDs and full IDs
    aln_int_map, aln_int_keys = aln_collection.getIntMap(prefix='aln_')
    aln1_collection = SequenceCollection(aln1)
    #Create mapping between abbreviated IDs and full IDs
    aln1_int_map, aln1_int_keys = aln1_collection.getIntMap(prefix='aln1_')
    #Create SequenceCollection from int_map.
    aln1_int_map = SequenceCollection(aln1_int_map)

src/q/i/qiime-1.8.0/qiime/align_seqs.py   qiime(Download)
        #Need to make separate mapping for unaligned sequences
        unaligned = SequenceCollection(candidate_sequences,MolType=moltype)
        int_map, int_keys = unaligned.getIntMap(prefix='unaligned_')
        int_map = SequenceCollection(int_map,MolType=moltype)
 

src/c/o/cogent-1.5.3/cogent/app/clustalw.py   cogent(Download)
    # Setup mapping. Clustalw clips identifiers. We will need to remap them.
    seq_collection = SequenceCollection(aln)
    int_map, int_keys = seq_collection.getIntMap()
    int_map = SequenceCollection(int_map)
 
    # Setup mapping. Clustalw clips identifiers. We will need to remap them.
    seq_collection = SequenceCollection(aln)
    int_map, int_keys = seq_collection.getIntMap()
    int_map = SequenceCollection(int_map)
 
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    seq_int_map, seq_int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    seq_int_map = SequenceCollection(seq_int_map,MolType=moltype)

src/p/y/pycogent-HEAD/cogent/app/clustalw.py   pycogent(Download)
    # Setup mapping. Clustalw clips identifiers. We will need to remap them.
    seq_collection = SequenceCollection(aln)
    int_map, int_keys = seq_collection.getIntMap()
    int_map = SequenceCollection(int_map)
 
    # Setup mapping. Clustalw clips identifiers. We will need to remap them.
    seq_collection = SequenceCollection(aln)
    int_map, int_keys = seq_collection.getIntMap()
    int_map = SequenceCollection(int_map)
 
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    seq_int_map, seq_int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    seq_int_map = SequenceCollection(seq_int_map,MolType=moltype)

src/c/o/cogent-1.5.3/cogent/app/mafft.py   cogent(Download)
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    seq_int_map, seq_int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    seq_int_map = SequenceCollection(seq_int_map,MolType=moltype)

src/p/y/pycogent-HEAD/cogent/app/mafft.py   pycogent(Download)
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    seq_int_map, seq_int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    seq_int_map = SequenceCollection(seq_int_map,MolType=moltype)

src/c/o/cogent-1.5.3/cogent/app/cd_hit.py   cogent(Download)
    seqs = SequenceCollection(seqs, MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seqs.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)

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