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github.io.sublime-workspace
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"contents": "\"\"\"\nFilter the aligned and cleaned ortholog matrices by number of taxa and characters\nWrite out name of matrices that passed the filter\nAlso write out supermatrix stats\n\"\"\"\nfrom seq import read_fasta_file\nfrom tree_utils import get_name\nimport sys,os\n\ndef concatenate(clnDIR,numofsitesFilter,numoftaxaFilter,seqtype,outname):\n \"\"\"filter cleaned alignments and concatenate\"\"\"\n if clnDIR[-1] != \"/\": clnDIR += \"/\"\n sites_filter = int(numofsitesFilter)\n taxa_filter = int(numoftaxaFilter)\n assert seqtype == \"aa\" or seqtype == \"dna\",\"Input data type: dna or aa\"\n model = \"AUTO\" if seqtype == \"aa\" else \"DNA\"\n \n print \"Filtering ortholog matrixes\"\n selected = [] # list of alignment file names that pass the filters\n for i in os.listdir(clnDIR):\n if i.endswith(\".aln-cln\"):\n seqlist = read_fasta_file(clnDIR+i)\n num_seq = len(seqlist)\n num_col = len(seqlist[0].seq)\n if num_seq >= taxa_filter and num_col >= sites_filter:\n selected.append(i)\n print len(selected),\"matrices passed the filter\"\n\n print \"Getting matrix occupancy stats\"\n taxon_occupancy = {}\n #key is taxon name, value is [times present in a matrix,total length for this taxon]\n total_aligned_len = 0 #record how long the final concatenated matrix is\n if seqtype == \"aa\":\n cmd = \"phyutility -concat -aa -out \"+outname+\".nex -in \"\n else: cmd = \"phyutility -concat -out \"+outname+\".nex -in \"\n for i in selected:\n cmd += clnDIR+i+\" \"\n seqlist = read_fasta_file(clnDIR+i)\n total_aligned_len += len(seqlist[0].seq)\n for s in seqlist:\n taxonid = get_name(s.name)\n if taxonid not in taxon_occupancy:\n taxon_occupancy[taxonid] = [0,0]\n taxon_occupancy[taxonid][0] += 1\n taxon_occupancy[taxonid][1] += len((s.seq.replace(\"-\",\"\")).replace(\"?\",\"\"))\n cmd += \"\\n\"\n \n total_ortho = len(selected)\n with open(outname+\"_taxon_occupancy_stats\",\"w\") as outfile:\n outfile.write(\"taxon\\t#orthologs\\t#total_charactors\\tperc_orthologs\\tperc_charactors\\n\")\n sum_char = 0\n for taxon in taxon_occupancy:\n times,chars = taxon_occupancy[taxon][0],taxon_occupancy[taxon][1]\n sum_char += chars\n out = taxon+\"\\t\"+str(times)+\"\\t\"+str(chars)+\"\\t\"\n out += str(times/float(total_ortho))+\"\\t\"+str(chars/float(total_aligned_len))+\"\\n\"\n outfile.write(out)\n total_taxa = len(taxon_occupancy)\n out = \"\\nSupermatrix dimension \"+str(total_taxa)+\" taxa, \"\n out += str(total_ortho)+\" loci and \"+str(total_aligned_len)+\" aligned columns\\n\"\n out += \"Overall matrix occupancy \"+str(sum_char/float(total_taxa*total_aligned_len))+\"\\n\"\n outfile.write(out)\n\n print \"Supermatrix taxon occupancy stats written to\",outname+\"_taxon_occupancy_stats\"\n print \"Waiting for concatenation to finish. This may take several minutes...\"\n with open(outname+\".temp.sh\",\"w\") as f: f.write(cmd)\n os.system(cmd)\n \n #convert the .nex file to .fasta and .model files for raxml\n infile = open(outname+\".nex\",\"r\")\n outfile = open(outname+\".phy\",\"w\")\n for line in infile: \n line = line.strip()\n if len(line) < 10: continue\n if line[0]==\"#\" or line[:5]==\"BEGIN\" or line[:6]==\"MATRIX\" or line==\"END;\" or line[:6]==\"FORMAT\":\n continue\n if line[0] == \"[\":\n line = line.replace(\"[\",model+\",\")\n line = line.replace(\" ]\",\"\")\n line = line.replace(\" cluster\",\"\\n\"+model+\",cluster\")\n #line = line.replace(\" homolog\",\"\\n\"+model+\",homolog\")\n line = line.replace(\" \",\"=\")\n with open(outname+\".model\",\"w\") as outfile2:\n outfile2.write(line.strip()+\"\\n\")\n #make sure that wc -l will get how many partitions\n elif line[:10]==\"DIMENSIONS\":\n ntax = (line.split(\"NTAX=\")[1]).split(\" \")[0]\n nchar = (line.split(\"NCHAR=\")[1]).replace(\";\",\"\")\n outfile.write(ntax+\" \"+nchar+\"\\n\")\n else:\n spls=line.split(\"\\t\")\n outfile.write(spls[0]+\" \"+spls[1]+\"\\n\")\n infile.close()\n outfile.close()\n assert os.path.exists(outname+\".phy\"), \"error concatenate\"\n os.system(\"rm \"+outname+\".temp.sh\")\n print \"outfiles written\",outname+\".phy\",outname+\".model\"\n os.system(\"rm \"+outname+\".nex\") #remove intermediate .nex file\n\nif __name__ == \"__main__\":\n if len(sys.argv) != 6:\n print \"usage: python concatenate_matrices.py aln-clnDIR numofsitesFilter numoftaxaFilter dna/aa outname\"\n sys.exit()\n \n clnDIR,numofsitesFilter,numoftaxaFilter,seqtype,outname = sys.argv[1:]\n concatenate(clnDIR,numofsitesFilter,numoftaxaFilter,seqtype,outname)\n",
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