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applied-bioinformatics / An-Introduction-To-Applied-Bioinformatics

Interactive lessons in bioinformatics.
http://readIAB.org
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error Sequence mapping and clustering #320

Open theokirkland opened 4 years ago

theokirkland commented 4 years ago

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.