Update Xander to speedup graph building, update gene references in Xa…

…nder_assembler
rdpstaff · Mar 15, 2015 · 96770fa · 96770fa
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diff --git a/Xander-HMMgs b/Xander-HMMgs
diff --git a/Xander_assembler b/Xander_assembler
+271 −2		src/edu/msu/cme/rdp/graph/filter/BloomFilter.java
+43 −17		src/edu/msu/cme/rdp/graph/filter/MultiBitArray.java
+5 −1		src/edu/msu/cme/rdp/graph/utils/BloomFilterStats.java
+45 −44		README.md
+0 −1		bin/get_OTUabundance.sh
+2 −2		bin/prepare_gene_ref.sh
+29 −25		bin/qsub_run_xander_skel.sh
+33 −28		bin/run_xander_skel.sh
+0 −0		gene_resource/amoA_AOA/for_enone.hmm
+0 −0		gene_resource/amoA_AOA/originaldata/amoA_AOA.aln
+0 −0		gene_resource/amoA_AOA/originaldata/amoA_AOA.hmm
+0 −0		gene_resource/amoA_AOA/originaldata/amoA_AOA.seeds
+158 −158		gene_resource/amoA_AOA/originaldata/framebot.fa
+0 −0		gene_resource/amoA_AOA/originaldata/nucl.fa
+0 −0		gene_resource/amoA_AOA/ref_aligned.faa
+0 −0		gene_resource/amoA_AOA/rev_enone.hmm
+0 −0		gene_resource/amoA_AOB/for_enone.hmm
+0 −0		gene_resource/amoA_AOB/originaldata/amoA_AOB.aln
+0 −0		gene_resource/amoA_AOB/originaldata/amoA_AOB.hmm
+0 −0		gene_resource/amoA_AOB/originaldata/amoA_AOB.seeds
+85 −85		gene_resource/amoA_AOB/originaldata/framebot.fa
+0 −0		gene_resource/amoA_AOB/originaldata/nucl.fa
+0 −0		gene_resource/amoA_AOB/ref_aligned.faa
+0 −0		gene_resource/amoA_AOB/rev_enone.hmm
+0 −0		gene_resource/nifH/for_enone.hmm
+11 −11		gene_resource/nifH/originaldata/framebot.fa
+0 −0		gene_resource/nifH/originaldata/nifH.hmm
+0 −0		gene_resource/nifH/originaldata/nifH.seeds
+0 −0		gene_resource/nifH/originaldata/nucl.fa
+0 −0		gene_resource/nifH/ref_aligned.faa
+0 −0		gene_resource/nifH/rev_enone.hmm
+0 −0		gene_resource/nirK/for_enone.hmm
+3 −3		gene_resource/nirK/originaldata/framebot.fa
+0 −0		gene_resource/nirK/originaldata/nirK.hmm
+0 −0		gene_resource/nirK/originaldata/nirK.seeds
+0 −0		gene_resource/nirK/originaldata/nucl.fa
+0 −0		gene_resource/nirK/ref_aligned.faa
+0 −0		gene_resource/nirK/rev_enone.hmm
+0 −0		gene_resource/nirS/for_enone.hmm
+0 −0		gene_resource/nirS/originaldata/framebot.fa
+0 −0		gene_resource/nirS/originaldata/nirS.hmm
+0 −0		gene_resource/nirS/originaldata/nirS.seeds
+0 −0		gene_resource/nirS/originaldata/nucl.fa
+0 −0		gene_resource/nirS/ref_aligned.faa
+0 −0		gene_resource/nirS/rev_enone.hmm
+0 −0		gene_resource/norB_cNor/for_enone.hmm
+0 −0		gene_resource/norB_cNor/originaldata/framebot.fa
+0 −0		gene_resource/norB_cNor/originaldata/norB_cNor.hmm
+0 −0		gene_resource/norB_cNor/originaldata/norB_cNor.seeds
+0 −0		gene_resource/norB_cNor/originaldata/nucl.fa
+0 −0		gene_resource/norB_cNor/ref_aligned.faa
+0 −0		gene_resource/norB_cNor/rev_enone.hmm
+0 −0		gene_resource/norB_qNor/for_enone.hmm
+26 −26		gene_resource/norB_qNor/originaldata/framebot.fa
+0 −0		gene_resource/norB_qNor/originaldata/norB_qNor.aln
+0 −0		gene_resource/norB_qNor/originaldata/norB_qNor.hmm
+0 −0		gene_resource/norB_qNor/originaldata/norB_qNor.seeds
+0 −0		gene_resource/norB_qNor/originaldata/nucl.fa
+0 −0		gene_resource/norB_qNor/ref_aligned.faa
+0 −0		gene_resource/norB_qNor/rev_enone.hmm
+0 −0		gene_resource/nosZ/for_enone.hmm
+0 −0		gene_resource/nosZ/originaldata/framebot.fa
+0 −0		gene_resource/nosZ/originaldata/nosZ.aln
+0 −0		gene_resource/nosZ/originaldata/nosZ.hmm
+0 −0		gene_resource/nosZ/originaldata/nosZ.seeds
+0 −0		gene_resource/nosZ/originaldata/nucl.fa
+0 −0		gene_resource/nosZ/ref_aligned.faa
+0 −0		gene_resource/nosZ/rev_enone.hmm
+0 −0		gene_resource/rplB/for_enone.hmm
+31 −31		gene_resource/rplB/originaldata/framebot.fa
+0 −0		gene_resource/rplB/originaldata/nucl.fa
+0 −0		gene_resource/rplB/originaldata/rplB.hmm
+0 −0		gene_resource/rplB/originaldata/rplB.seeds
+0 −0		gene_resource/rplB/ref_aligned.faa
+0 −0		gene_resource/rplB/rev_enone.hmm
+2 −0		pythonscripts/fetch_ncbi_xml.py
+60 −0		pythonscripts/mergeNearstmatchAbund.py
+69 −0		pythonscripts/mergeTaxonAbund.py
+7 −4		testdata/test_reads.fa