Compiling of the scripts for the SSN filtering:
cd scripts/Cluster_validation/compositional/
gcc is_connected.c -I${HOME}.linuxbrew/Cellar/igraph/0.7.1_6/include -L${HOME}/.linuxbrew/Cellar/igraph/0.7.1_6/lib/ -ligraph -o is_connected
gcc -O3 filter_graph.c -I${HOME}/.linuxbrew/Cellar/igraph/0.7.1_6/include -L${HOME}/.linuxbrew/Cellar/igraph/0.7.1_6/lib/ -ligraph -o filter_graph
Running the evaluation script using ffindex in mpi mode (ffindex)
/bioinf/software/openmpi/openmpi-1.8.1/bin/mpirun -np 32 ~/opt/ffindex_mg_updt/bin/ffindex_apply_mpi \
data/mmseqs_clustering/marine_hmp_db_03112017_clu_fa \
data/mmseqs_clustering/marine_hmp_db_03112017_clu_fa.index \
-- scripts/Cluster_validation/compositional/compos_val.sh
- output: tab-separated file with 24 fields:
- <cl_name>
- <new_representative>
- <cl_size>
- <n_vertices> info about the Sequence Similarity Network
- <n_edges> as above
- as above
- <cut_w> as above
- as above
- <n_compon> as above
- <tr_min_id> min intra-cluster identity (trimmed)
- <tr_mean_id> mean intra-cluster identity (trimmed)
- <tr_median_id> median intra-cluster identity (trimmed)
- <tr_max_id> max intra-cluster identity (trimmed)
- <raw_min_id> min intra-cluster identity (original graph)
- <raw_mean_id> mean intra-cluster identity (original graph)
- <raw_median_id> median intra-cluster identity (original graph)
- <raw_max_id> max intra-cluster identity (original graph)
- <min_len> min ORF length in the cluster
- <mean_len> mean ORF length in the cluster
- <median_len> median ORF length in the cluster
- <max_len> max ORF length in the cluster
- number of bad aligned sequences
- number of good sequences
- <prop_rejected> proportion of bad aligned sequences per cluster