error Sequence mapping and clustering

[theokirkland]

Describe the environment

What version of IAB are you reading (e.g. v0.0.1)? Not sure - just downloaded 1/1/19

from iab import __version__ as iab_version
print(iab_version)

Describe the problem

command line 8
clusters, num_alignments = cluster([s1, s2], 0.70,
furthest_neighbor, aligner=global_pairwise_align_nucleotide, verbose=True) gave an error

s1
Created OTU
s2
OTU 1

---

AttributeError Traceback (most recent call last)
in
1 clusters, num_alignments = cluster([s1, s2], 0.70,
----> 2 furthest_neighbor, aligner=global_pairwise_align_nucleotide, verbose=True)
3 show_clusters(clusters, plot_labels=True)

in cluster(seqs, similarity_threshold, cluster_fn, aligner, verbose)
11 if verbose: print(" OTU %d" % i)
12 clustered, alignment_results = cluster_fn(
---> 13 query_seq, cluster, similarity_threshold, aligner, verbose=verbose)
14 num_alignments += len(alignment_results)
15 if clustered:

in furthest_neighbor(seq, cluster, similarity_threshold, aligner, verbose)
40 alignment_results = []
41 for node in cluster.nodes():
---> 42 aln, _, _ = aligner(seq, cluster.node[node]['seq'])
43 percent_similarity = 1. - aln[0].distance(aln[1])
44 alignment_results.append((node, percent_similarity))

AttributeError: 'Graph' object has no attribute 'node'

show_clusters(clusters, plot_labels=True)

Steps to reproduce

Followed steps 1-7 in Furthest Neighbor Clustering
command 8 clusters, num_alignments = cluster([s1, s2], 0.70,
furthest_neighbor, aligner=global_pairwise_align_nucleotide, verbose=True)

Observed Results

s1
Created OTU
s2
OTU 1

---

AttributeError Traceback (most recent call last)
in
1 clusters, num_alignments = cluster([s1, s2], 0.70,
----> 2 furthest_neighbor, aligner=global_pairwise_align_nucleotide, verbose=True)
3 show_clusters(clusters, plot_labels=True)

in cluster(seqs, similarity_threshold, cluster_fn, aligner, verbose)
11 if verbose: print(" OTU %d" % i)
12 clustered, alignment_results = cluster_fn(
---> 13 query_seq, cluster, similarity_threshold, aligner, verbose=verbose)
14 num_alignments += len(alignment_results)
15 if clustered:

in furthest_neighbor(seq, cluster, similarity_threshold, aligner, verbose)
40 alignment_results = []
41 for node in cluster.nodes():
---> 42 aln, _, _ = aligner(seq, cluster.node[node]['seq'])
43 percent_similarity = 1. - aln[0].distance(aln[1])
44 alignment_results.append((node, percent_similarity))

AttributeError: 'Graph' object has no attribute 'node'

Expected Results

• What did you expect to happen? Get a graph as well as the text.