Merge pull request #80 from McTavishLab/dev

Dev

bin/physcraper_run.py

@@ -3,7 +3,7 @@
 import os
 import sys
 import physcraper
-from physcraper.opentree_helpers import get_tree_from_study, scraper_from_opentree, get_max_match_aln, count_match_tree_to_aln
+from physcraper.opentree_helpers import get_tree_from_study, scraper_from_opentree, get_max_match_aln, count_match_tree_to_aln, generate_ATT_from_phylesystem
 from physcraper.aligntreetax import generate_ATT_from_run
 
 parser = argparse.ArgumentParser()
@@ -15,32 +15,42 @@
 parser.add_argument("-db", "--blast_db", help="local download of blast database")
 parser.add_argument("-o","--output", help="path to output directory")
 parser.add_argument("-tx","--taxonomy", help="path to taxonomy")
-parser.add_argument("-c","--config_file", help="path to config file")
+parser.add_argument("-c","--configfile", help="path to config file")
 parser.add_argument("-e","--email", help="email address for ncbi balst searches")
 parser.add_argument("-re","--reload_files",  help="reload files and configureation from dir")
 parser.add_argument("-tag","--tag", help="gene name or other specifier")
 parser.add_argument("-tb","--treebase", action="store_true", help="download alignment from treebase")
 parser.add_argument("-no_est","--no_estimate_tree", action='store_true', help="run blast search and estimate tree")
+parser.add_argument("-ev","--eval", help="blast evalue cutoff")
+parser.add_argument("-hl","--hitlist_len", help="number of blast searches to save per taxon")
+parser.add_argument("-tp","--trim_perc", help="minimum percentage of seqs end of alignemnts")
+parser.add_argument("-rl","--relative_length", help="max relative length of added seqs, compared to input aln len")
+parser.add_argument("-spn","--species_number", help="max number of seqs to include per species")
+parser.add_argument("-nt","--num_threads", help="number of threads to use in processing")
+parser.add_argument("-de","--delay", help="how long to wait before blasting the same sequence again")
+parser.add_argument("-st","--search_taxon", help="taxonomic id to constrain blast search. format ott:123 or ncbi:123. Deafult will use ingroup of tree on OpenTree, or MRCA of input tips ")
+
+
 
 
 
 #Not yet implemented
-parser.add_argument("-bl","--blast_sequence", action='store_true', help="run blast search, and align but do not estimate tree")
-parser.add_argument("-d","--download_data", action='store_true', help="write out tree and alignment, without blasting")
-parser.add_argument("-bs","--bootstrap", help="number of bootstrap reps")
-parser.add_argument("-gt","--get_tree", action='store_true', help="get tree from opentree")
-parser.add_argument("-ga","--get_aln", action='store_true', help="get alignment from opentree")
-parser.add_argument("-tf", "--tree_file", help="path to your tree")
-parser.add_argument("-l","--linker_file", help="path to .csv linking tip labels to taxon names")
+#parser.add_argument("-bl","--blast_sequence", action='store_true', help="run blast search, and align but do not estimate tree")
+#parser.add_argument("-d","--download_data", action='store_true', help="write out tree and alignment, without blasting")
+#parser.add_argument("-bs","--bootstrap", help="number of bootstrap reps")
+#parser.add_argument("-gt","--get_tree", action='store_true', help="get tree from opentree")
+#parser.add_argument("-ga","--get_aln", action='store_true', help="get alignment from opentree")
+#parser.add_argument("-tf", "--tree_file", help="path to your tree")
+#parser.add_argument("-l","--linker_file", help="path to .csv linking tip labels to taxon names")
 
 
 args = parser.parse_args()
 
 assert(args.output), "Output directory (-o) is required."
 workdir = args.output
 
-
-if args.config_file:
+#set configuration
+if args.configfile:
     conf = physcraper.ConfigObj(args.configfile)
 elif args.reload_files:
     configfile = "{}/run.config".format(args.reload_files)
@@ -52,22 +62,45 @@
 if args.taxonomy:
     conf.taxonomy_dir = args.taxonomy
 
-
 if args.blast_db:
     conf.blast_loc = "local"
     conf.blastdb = args.blast_db
     conf.set_local()
 
+if args.eval:
+    conf.e_value_thresh = args.eval
+
+if args.hitlist_len:
+    conf.hitlist_size = args.hitlist_len
+
+if args.trim_perc:
+    conf.trim_perc = args.trim_perc
+
+if args.relative_length:
+    conf.maxlen = args.relative_length
+
+if args.species_number:
+    conf.spp_threshold = int(args.species_number)
+
+if args.num_threads:
+   conf.num_threads = args.num_threads
+
+if args.delay:
+    conf.delay = args.delay
+
+if args.email:
+    conf.email = args.email
+
+sys.stdout.write("Configuration Settings\n")
+sys.stdout.write(conf.config_str())
+
 study_id =  None
 if args.tree_link:
     linkl = args.tree_link.split("/")
     assert(linkl[4]=="view")
     study_id == linkl[5]
     tree_id = linkl[-1].split("=")[1]
 
-if args.email:
-    conf.email = args.email
-
 if args.study_id:
     study_id = args.study_id
     tree_id = args.tree_id
@@ -95,15 +128,33 @@
         sys.stdout.write("Using alignment file found at {}.\n".format(alnfile))
 
 if study_id:
-    scraper = scraper_from_opentree(study_id =study_id, 
-                                    tree_id = tree_id, 
-                                    alnfile = alnfile, 
-                                    aln_schema = aln_schema,
-                                    workdir = workdir,
-                                    configfile = conf)
+    if args.search_taxon:
+        ids = physcraper.IdDicts(conf)
+        if args.search_taxon.startswith('ott'):
+            ott_id = args.search_taxon.split(':')[1]
+        elif args.search_taxon.startswith('ncbi'):
+            ncbi_id = inst(args.search_taxon.split(':')[1])
+            ott_id = ids.ncbi_ott[ncbi_id]
+        else:
+            sys.stderr.write("search taxon id must be in format ott:123 or ncbi:123\n")
+        data_obj = generate_ATT_from_phylesystem(study_id =study_id, 
+                                                tree_id = tree_id, 
+                                                alnfile = alnfile, 
+                                                aln_schema = aln_schema,
+                                                workdir = workdir,
+                                                configfile = conf,
+                                                ingroup_mrca = ott_id)
+        scraper = physcraper.PhyscraperScrape(data_obj, ids)
+    else:
+        scraper = scraper_from_opentree(study_id =study_id, 
+                                        tree_id = tree_id, 
+                                        alnfile = alnfile, 
+                                        aln_schema = aln_schema,
+                                        workdir = workdir,
+                                        configfile = conf)
     sys.stdout.write("{} taxa in alignment and tree\n".format(len(scraper.data.aln)))
-
     scraper.data.write_files()
+    scraper.data.write_labelled(filename="before_labelled_{}".format(scraper.data.tag), label='^ot:ottTaxonName')
     scraper.data.write_otus(schema="json")
 
 if args.reload_files: