def starting_esrna(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_gblocks, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_thread, args_extenddata): '''reconstruct phylogenetic tree by ssu rna extend method''' extend_check = checkFile(args_extenddata) ssu_input = checkSilvaOrganism(in_put) out_retrieve = retrieve16srna(ssu_input, out_put) retrieve_srna_path = os.path.join(out_retrieve, 'rna_sequence.fasta') fw = open(retrieve_srna_path, 'ab') with open(extend_check) as read: for line in read: fw.write(line) fw.close() # set default aligned by muscle if not specify clustalw if args_clustalw: out_alg = doclustalw(out_retrieve, out_put, args_clustalw_p) elif args_muscle: out_alg = domuscle(out_retrieve, out_put, args_muscle_p) # gblocks if args_gblocks is gblockspara_pro: args_gblocks = gblockspara_dna out_gblock = dogblocks(out_alg, args_gblocks) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: args_fasttree_p_add = "-nt " + args_fasttree_p.lstrip() doFastTree(out_f2p, out_put, args_fasttree_p_add, args_thread) elif args_raxml: if args_raxml_p is raxmlpara_pro: args_raxml_p = raxmlpara_dna doraxml(out_f2p, out_put, args_raxml_p, args_thread)
def starting_ehcp(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_gblocks, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_thread, args_extenddata): '''reconstruct phylogenetic tree by ehcp method''' hcp_input = checkKeggOrganism(in_put) out_retrieve = doretrieve(hcp_input, out_put) retrieve_pro = os.listdir(out_retrieve) for reline in retrieve_pro: fw_name = os.path.join(out_retrieve, reline) fr_name = os.path.join(args_extenddata, reline) fw = open(fw_name, 'ab') with open(fr_name) as fr: for line in fr: fw.write(line) fw.close() # set default aligned by muscle if not specify clustalw if args_clustalw: out_alg = doclustalw_file(out_retrieve, out_put, args_clustalw_p) elif args_muscle: out_alg = domuscle_file(out_retrieve, out_put, args_muscle_p) out_concat = cocat_path(out_alg) # gblocks out_gblock = dogblocks(out_concat, args_gblocks) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: doFastTree(out_f2p, out_put, args_fasttree_p, args_thread) elif args_raxml: doraxml(out_f2p, out_put, args_raxml_p, args_thread)
def starting_ehcp(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_mafft, args_mafft_p, args_gblocks, args_gblocks_p, args_trimal, args_trimal_p, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_iqtree, args_iqtree_p, args_thread, args_extenddata, args_db): '''reconstruct phylogenetic tree by ehcp method''' hcp_input, recovery_dic = checkKeggOrganism(in_put) start = time.time() out_retrieve = doretrieve(hcp_input, out_put, args_db) end = time.time() auto_build_log.info( 'Retrieving HCP sequences used time: {} Seconds'.format(end - start)) if not recovery_dic == {}: recovery(out_retrieve, recovery_dic) retrieve_pro = os.listdir(out_retrieve) for reline in retrieve_pro: fw_name = os.path.join(out_retrieve, reline) fr_name = os.path.join(args_extenddata, reline) fw = open(fw_name, 'a') with open(fr_name) as fr: for line in fr: fw.write(line) fw.close() # set default aligned by muscle if not specify clustalw or mafft start2 = time.time() if args_clustalw: out_alg = doclustalw_file(out_retrieve, out_put, args_clustalw_p) elif args_mafft: out_alg = domafft_file(out_retrieve, out_put, args_mafft_p, args_thread) elif args_muscle: out_alg = domuscle_file(out_retrieve, out_put, args_muscle_p, args_thread) out_concat = cocat_path(out_alg) # set default trim by gblocks if not specify trimal if args_trimal: out_f2p = dotrimal(out_concat, args_trimal_p) elif args_gblocks: out_gblock = dogblocks(out_concat, args_gblocks_p) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: doFastTree(out_f2p, out_put, args_fasttree_p, args_thread) elif args_iqtree: doiqtree(out_f2p, out_put, args_iqtree_p, args_thread) elif args_raxml: doraxml(out_f2p, out_put, args_raxml_p, args_thread) end2 = time.time() auto_build_log.info( 'Constructing species tree used time: {} Seconds'.format(end2 - start2))
def starting_esrna(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_mafft, args_mafft_p, args_gblocks, args_gblocks_p, args_trimal, args_trimal_p, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_iqtree, args_iqtree_p, args_thread, args_extenddata, args_db): '''reconstruct phylogenetic tree by ssu rna extend method''' extend_check = checkFile(args_extenddata) ssu_input, recovery_dic = checkSilvaOrganism(in_put) start = time.time() out_retrieve = retrieve16srna(ssu_input, out_put, args_db) end = time.time() auto_build_log.info( 'Retrieving SSU rRNA sequences used time: {} Seconds'.format(end - start)) if not recovery_dic == []: recovery_silva(out_retrieve, recovery_dic, ssu_input) retrieve_srna_path = os.path.join(out_retrieve, 'rna_sequence.fasta') fw = open(retrieve_srna_path, 'a') with open(extend_check) as read: for line in read: fw.write(line) fw.close() # set default aligned by muscle if not specify clustalw start2 = time.time() if args_clustalw: out_alg = doclustalw(out_retrieve, out_put, args_clustalw_p) elif args_mafft: out_alg = domafft(out_retrieve, out_put, args_mafft_p) elif args_muscle: out_alg = domuscle(out_retrieve, out_put, args_muscle_p) # set default trim by gblocks if not specify trimal if args_trimal: out_f2p = dotrimal(out_alg, args_trimal_p) elif args_gblocks: if args_gblocks_p is gblockspara_pro: args_gblocks_p = gblockspara_dna out_gblock = dogblocks(out_alg, args_gblocks_p) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: args_fasttree_p_add = "-nt " + args_fasttree_p.lstrip() doFastTree(out_f2p, out_put, args_fasttree_p_add, args_thread) elif args_iqtree: doiqtree(out_f2p, out_put, args_iqtree_p, args_thread) elif args_raxml: if args_raxml_p is raxmlpara_pro: args_raxml_p = raxmlpara_dna doraxml(out_f2p, out_put, args_raxml_p, args_thread) end2 = time.time() auto_build_log.info( 'Constructing species tree used time: {} Seconds'.format(end2 - start2))
def starting_esrna(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_mafft, args_mafft_p, args_gblocks, args_gblocks_p, args_trimal, args_trimal_p, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_iqtree,args_iqtree_p, args_thread, args_extenddata): '''reconstruct phylogenetic tree by ssu rna extend method''' extend_check = checkFile(args_extenddata) ssu_input,recovery_dic = checkSilvaOrganism(in_put) out_retrieve = retrieve16srna(ssu_input, out_put) if not recovery_dic == {}: recovery(out_retrieve,recovery_dic) retrieve_srna_path = os.path.join(out_retrieve, 'rna_sequence.fasta') fw = open(retrieve_srna_path, 'ab') with open(extend_check) as read: for line in read: fw.write(line) fw.close() # set default aligned by muscle if not specify clustalw if args_clustalw: out_alg = doclustalw(out_retrieve, out_put, args_clustalw_p) elif args_mafft: out_alg = domafft(out_retrieve, out_put, args_mafft_p) elif args_muscle: out_alg = domuscle(out_retrieve, out_put, args_muscle_p) # set default trim by gblocks if not specify trimal if args_trimal: out_f2p = dotrimal(out_alg, args_trimal_p) elif args_gblocks: if args_gblocks_p is gblockspara_pro: args_gblocks_p = gblockspara_dna out_gblock = dogblocks(out_alg, args_gblocks_p) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: args_fasttree_p_add = "-nt " + args_fasttree_p.lstrip() doFastTree(out_f2p, out_put, args_fasttree_p_add, args_thread) elif args_iqtree: doiqtree(out_f2p, out_put, args_iqtree_p, args_thread) elif args_raxml: if args_raxml_p is raxmlpara_pro: args_raxml_p = raxmlpara_dna doraxml(out_f2p, out_put, args_raxml_p, args_thread)
def starting_ehcp(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_mafft, args_mafft_p, args_gblocks, args_gblocks_p, args_trimal, args_trimal_p, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_iqtree,args_iqtree_p, args_thread, args_extenddata): '''reconstruct phylogenetic tree by ehcp method''' hcp_input, recovery_dic = checkKeggOrganism(in_put) out_retrieve = doretrieve(hcp_input, out_put) if not recovery_dic == {}: recovery(out_retrieve,recovery_dic) retrieve_pro = os.listdir(out_retrieve) for reline in retrieve_pro: fw_name = os.path.join(out_retrieve, reline) fr_name = os.path.join(args_extenddata, reline) fw = open(fw_name, 'ab') with open(fr_name) as fr: for line in fr: fw.write(line) fw.close() # set default aligned by muscle if not specify clustalw or mafft if args_clustalw: out_alg = doclustalw_file(out_retrieve, out_put, args_clustalw_p) elif args_mafft: out_alg = domafft_file(out_retrieve, out_put, args_mafft_p) elif args_muscle: out_alg = domuscle_file(out_retrieve, out_put, args_muscle_p) out_concat = cocat_path(out_alg) # set default trim by gblocks if not specify trimal if args_trimal: out_f2p = dotrimal(out_concat, args_trimal_p) elif args_gblocks: out_gblock = dogblocks(out_concat, args_gblocks_p) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: doFastTree(out_f2p, out_put, args_fasttree_p, args_thread) elif args_iqtree: doiqtree(out_f2p, out_put, args_iqtree_p, args_thread) elif args_raxml: doraxml(out_f2p, out_put, args_raxml_p, args_thread)
def build_hcp(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_gblocks, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_thread): '''reconstruct phylogenetic tree by hcp method''' out_retrieve = in_put # set default aligned by muscle if not specify clustalw if args_clustalw: out_alg = doclustalw_file(out_retrieve, out_put, args_clustalw_p) elif args_muscle: out_alg = domuscle_file(out_retrieve, out_put, args_muscle_p) out_concat = cocat_path(out_alg) out_gblock = dogblocks(out_concat, args_gblocks) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: doFastTree(out_f2p, out_put, args_fasttree_p, args_thread) elif args_raxml: doraxml(out_f2p, out_put, args_raxml_p, args_thread)
def starting_hcp(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_mafft, args_mafft_p, args_gblocks, args_gblocks_p, args_trimal, args_trimal_p, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_iqtree, args_iqtree_p, args_thread, args_db): '''reconstruct phylogenetic tree by hcp method''' hcp_input, recovery_dic = checkKeggOrganism(in_put) start = time.time() out_retrieve = doretrieve(hcp_input, out_put, args_db) end = time.time() auto_build_log.info( 'Retrieving HCP sequences used time: {} Seconds'.format(end - start)) if not recovery_dic == {}: recovery(out_retrieve, recovery_dic) # set default aligned by muscle if not specify clustalw start2 = time.time() if args_clustalw: out_alg = doclustalw_file(out_retrieve, out_put, args_clustalw_p) elif args_mafft: out_alg = domafft_file(out_retrieve, out_put, args_mafft_p, args_thread) elif args_muscle: out_alg = domuscle_file(out_retrieve, out_put, args_muscle_p, args_thread) out_concat = cocat_path(out_alg) # set default trim by gblocks if not specify trimal if args_trimal: out_f2p = dotrimal(out_concat, args_trimal_p) elif args_gblocks: out_gblock = dogblocks(out_concat, args_gblocks_p) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: doFastTree(out_f2p, out_put, args_fasttree_p, args_thread) elif args_iqtree: doiqtree(out_f2p, out_put, args_iqtree_p, args_thread) elif args_raxml: doraxml(out_f2p, out_put, args_raxml_p, args_thread) end2 = time.time() auto_build_log.info( 'Contracting species tree used time: {} Seconds'.format(end2 - start2))
def starting_srna(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_mafft, args_mafft_p, args_gblocks, args_gblocks_p, args_trimal, args_trimal_p, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_iqtree,args_iqtree_p, args_thread): '''reconstruct phylogenetic tree by ssu rna method''' ssu_input,recovery_dic = checkSilvaOrganism(in_put) out_retrieve = retrieve16srna(ssu_input, out_put) if not recovery_dic == {}: recovery(out_retrieve,recovery_dic) # set default aligned by muscle if not specify clustalw or mafft if args_clustalw: out_alg = doclustalw(out_retrieve, out_put, args_clustalw_p) elif args_mafft: out_alg = domafft(out_retrieve, out_put, args_mafft_p) elif args_muscle: out_alg = domuscle(out_retrieve, out_put, args_muscle_p) # set default trim by gblocks if not specify trimal if args_trimal: out_f2p = dotrimal(out_alg, args_trimal_p) elif args_gblocks: if args_gblocks_p is gblockspara_pro: args_gblocks_p = gblockspara_dna out_gblock = dogblocks(out_alg, args_gblocks_p) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: args_fasttree_p_add = "-nt " + args_fasttree_p.lstrip() doFastTree(out_f2p, out_put, args_fasttree_p_add, args_thread) elif args_iqtree: doiqtree(out_f2p, out_put, args_iqtree_p, args_thread) elif args_raxml: if args_raxml_p is raxmlpara_pro: args_raxml_p = raxmlpara_dna doraxml(out_f2p, out_put, args_raxml_p, args_thread)
def starting_hcp(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_mafft, args_mafft_p, args_gblocks, args_gblocks_p, args_trimal, args_trimal_p, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_iqtree,args_iqtree_p, args_thread): '''reconstruct phylogenetic tree by hcp method''' hcp_input, recovery_dic = checkKeggOrganism(in_put) out_retrieve = doretrieve(hcp_input, out_put) if not recovery_dic == {}: recovery(out_retrieve,recovery_dic) # set default aligned by muscle if not specify clustalw if args_clustalw: out_alg = doclustalw_file(out_retrieve, out_put, args_clustalw_p) elif args_mafft: out_alg = domafft_file(out_retrieve, out_put, args_mafft_p) elif args_muscle: out_alg = domuscle_file(out_retrieve, out_put, args_muscle_p) out_concat = cocat_path(out_alg) # set default trim by gblocks if not specify trimal if args_trimal: out_f2p = dotrimal(out_concat, args_trimal_p) elif args_gblocks: out_gblock = dogblocks(out_concat, args_gblocks_p) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: doFastTree(out_f2p, out_put, args_fasttree_p, args_thread) elif args_iqtree: doiqtree(out_f2p, out_put, args_iqtree_p, args_thread) elif args_raxml: doraxml(out_f2p, out_put, args_raxml_p, args_thread)
def build_srna(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_gblocks, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_thread): '''reconstruct phylogenetic tree by ssu rna method''' out_retrieve = in_put # set default aligned by muscle if not specify clustalw if args_clustalw: out_alg = doclustalw(out_retrieve, out_put, args_clustalw_p) elif args_muscle: out_alg = domuscle(out_retrieve, out_put, args_muscle_p) if args_gblocks == gblockspara_pro: args_gblocks = gblockspara_dna out_gblock = dogblocks(out_alg, args_gblocks) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: args_fasttree_p_add = "-nt " + args_fasttree_p.lstrip() doFastTree(out_f2p, out_put, args_fasttree_p_add, args_thread) elif args_raxml: if args_raxml_p == raxmlpara_pro: args_raxml_p = raxmlpara_dna doraxml(out_f2p, out_put, args_raxml_p, args_thread)
def build_srna(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_mafft, args_mafft_p, args_gblocks, args_gblocks_p, args_trimal, args_trimal_p, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_iqtree,args_iqtree_p, args_thread): '''reconstruct phylogenetic tree by ssu rna method''' out_retrieve = in_put # set default aligned by muscle if not specify clustalw or mafft if args_clustalw: out_alg = doclustalw(out_retrieve, out_put, args_clustalw_p) elif args_mafft: out_alg = domafft(out_retrieve, out_put, args_mafft_p) elif args_muscle: out_alg = domuscle(out_retrieve, out_put, args_muscle_p) # set default trim by gblocks if not specify trimal if args_trimal: out_f2p = dotrimal(out_alg, args_trimal_p) elif args_gblocks: if args_gblocks_p == gblockspara_pro: args_gblocks_p = gblockspara_dna out_gblock = dogblocks(out_alg, args_gblocks_p) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: args_fasttree_p_add = "-nt " + args_fasttree_p.lstrip() doFastTree(out_f2p, out_put, args_fasttree_p_add, args_thread) elif args_iqtree: doiqtree(out_f2p, out_put, args_iqtree_p, args_thread) elif args_raxml: if args_raxml_p == raxmlpara_pro: args_raxml_p = raxmlpara_dna doraxml(out_f2p, out_put, args_raxml_p, args_thread)
def build_srna(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_mafft, args_mafft_p, args_gblocks, args_gblocks_p, args_trimal, args_trimal_p, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_iqtree, args_iqtree_p, args_thread): '''reconstruct phylogenetic tree by ssu rna method''' start = time.time() out_retrieve = in_put # set default aligned by muscle if not specify clustalw or mafft if args_clustalw: out_alg = doclustalw(out_retrieve, out_put, args_clustalw_p) elif args_mafft: out_alg = domafft(out_retrieve, out_put, args_mafft_p) elif args_muscle: out_alg = domuscle(out_retrieve, out_put, args_muscle_p) # set default trim by gblocks if not specify trimal if args_trimal: out_f2p = dotrimal(out_alg, args_trimal_p) elif args_gblocks: if args_gblocks_p == gblockspara_pro: args_gblocks_p = gblockspara_dna out_gblock = dogblocks(out_alg, args_gblocks_p) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: args_fasttree_p_add = "-nt " + args_fasttree_p.lstrip() doFastTree(out_f2p, out_put, args_fasttree_p_add, args_thread) elif args_iqtree: doiqtree(out_f2p, out_put, args_iqtree_p, args_thread) elif args_raxml: if args_raxml_p == raxmlpara_pro: args_raxml_p = raxmlpara_dna doraxml(out_f2p, out_put, args_raxml_p, args_thread) end = time.time() build_log.info( 'Constructing species tree used time: {} Seconds'.format(end - start))
def build_hcp(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_mafft, args_mafft_p, args_gblocks, args_gblocks_p, args_trimal, args_trimal_p, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_iqtree, args_iqtree_p, args_thread): '''reconstruct phylogenetic tree by hcp method''' start = time.time() out_retrieve = in_put # set default aligned by muscle if not specify clustalw or mafft if args_clustalw: out_alg = doclustalw_file(out_retrieve, out_put, args_clustalw_p) elif args_mafft: out_alg = domafft_file(out_retrieve, out_put, args_mafft_p, args_thread) elif args_muscle: out_alg = domuscle_file(out_retrieve, out_put, args_muscle_p, args_thread) out_concat = cocat_path(out_alg) # set default trim by gblocks if not specify trimal if args_trimal: out_f2p = dotrimal(out_concat, args_trimal_p) elif args_gblocks: out_gblock = dogblocks(out_concat, args_gblocks_p) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: doFastTree(out_f2p, out_put, args_fasttree_p, args_thread) elif args_iqtree: doiqtree(out_f2p, out_put, args_iqtree_p, args_thread) elif args_raxml: doraxml(out_f2p, out_put, args_raxml_p, args_thread) end = time.time() build_log.info( 'Constructing species tree used time: {} Seconds'.format(end - start))
def build_hcp(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_mafft, args_mafft_p, args_gblocks, args_gblocks_p, args_trimal, args_trimal_p, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_iqtree,args_iqtree_p, args_thread): '''reconstruct phylogenetic tree by hcp method''' out_retrieve = in_put # set default aligned by muscle if not specify clustalw or mafft if args_clustalw: out_alg = doclustalw_file(out_retrieve, out_put, args_clustalw_p) elif args_mafft: out_alg = domafft_file(out_retrieve, out_put, args_mafft_p) elif args_muscle: out_alg = domuscle_file(out_retrieve, out_put, args_muscle_p) out_concat = cocat_path(out_alg) # set default trim by gblocks if not specify trimal if args_trimal: out_f2p = dotrimal(out_concat, args_trimal_p) elif args_gblocks: out_gblock = dogblocks(out_concat, args_gblocks_p) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: doFastTree(out_f2p, out_put, args_fasttree_p, args_thread) elif args_iqtree: doiqtree(out_f2p, out_put, args_iqtree_p, args_thread) elif args_raxml: doraxml(out_f2p, out_put, args_raxml_p, args_thread)
def starting_srna(in_put, out_put, args_muscle, args_muscle_p, args_clustalw, args_clustalw_p, args_gblocks, args_raxml, args_raxml_p, args_fasttree, args_fasttree_p, args_thread): '''reconstruct phylogenetic tree by ssu rna method''' ssu_input = checkSilvaOrganism(in_put) out_retrieve = retrieve16srna(ssu_input, out_put) # set default aligned by muscle if not specify clustalw if args_clustalw: out_alg = doclustalw(out_retrieve, out_put, args_clustalw_p) elif args_muscle: out_alg = domuscle(out_retrieve, out_put, args_muscle_p) # gblocks if args_gblocks is gblockspara_pro: args_gblocks = gblockspara_dna out_gblock = dogblocks(out_alg, args_gblocks) out_f2p = fasta2phy(out_gblock) # reconstruct tree if args_fasttree: args_fasttree_p_add = "-nt " + args_fasttree_p.lstrip() doFastTree(out_f2p, out_put, args_fasttree_p_add, args_thread) elif args_raxml: if args_raxml_p is raxmlpara_pro: args_raxml_p = raxmlpara_dna doraxml(out_f2p, out_put, args_raxml_p, args_thread)
from physpetool.convert.fasta2phy import fasta2phy fr = '/home/yangfang/physpetools/testdata/muscle_alignment/protein.fastq.alg-gb1' fasta2phy(fr)
from physpetool.convert.fasta2phy import fasta2phy fr ='/home/yangfang/physpetools/testdata/muscle_alignment/protein.fastq.alg-gb1' fasta2phy(fr)