Merge pull request #93 from McTavishLab/re-org

Re org

docs/examples/minimal.py

@@ -9,7 +9,7 @@
 from physcraper.opentree_helpers import scraper_from_opentree
 
 configfi = "tests/data/test.config"
-workdir ="physcraper_example_minimal"
+workdir ="example_minimal"
 aln_fi = "tests/data/tiny_test_example/test.fas"
 blast_dir = "tests/data/precooked/fixed/tte_blast_files"
 # mattype="fasta"
@@ -61,8 +61,7 @@
 sys.stdout.write("Running align_query_seqs()...\n")
 scraper.align_new_seqs()
 scraper.est_full_tree()
-scraper.data.write_labelled(label="^ot:ottTaxonName", filename="updated_taxon_name", norepeats=True)
-scraper.data.write_labelled(label="^ncbi:taxon", filename="updated_ncbi_id", norepeats=False)
+scraper.data.write_labelled(label="^ncbi:taxon", filename="updated_ncbi_id", norepeats=False, direc = scraper.outputsdir)
 
 
 # sys.stdout.write("estimating tree...")

physcraper/aligntreetax.py

@@ -192,7 +192,7 @@ def __init__(self, tree, otu_dict, alignment, ingroup_mrca, workdir, configfile=
         elif isinstance(configfile, str):
             self.config = ConfigObj(configfile)
             if not os.path.exists("{}/run.config".format(self.workdir)):
-                shutil.copyfile(self.config.configfi, "{}/run.config".format(self.workdir))
+                shutil.copyfile(self.config.configfi, "{}/copy.config".format(self.workdir))
         else:
             assert(isinstance(configfile, ConfigObj)),type(configfile)
             self.config = configfile
@@ -557,10 +557,14 @@ def write_papara_files(self, treefilename="random_resolve.tre", alnfilename="aln
         self.aln.write(path="{}/{}".format(self.workdir, alnfilename), schema="phylip")
 
 
-    def write_random_resolve_tre(self, treefilename='random_resolve.tre'):
+    def write_random_resolve_tre(self, treefilename='random_resolve.tre', direc='workdir'):
         self.tre.resolve_polytomies()
         self.tre.deroot()
-        treepath= "{}/{}".format(self.workdir, treefilename)
+        if direc == 'workdir':
+            direc = self.workdir
+        else:
+            assert(os.path.exists(direc))
+        treepath= "{}/{}".format(direc, treefilename)
         tmptre = self.tre.as_string(schema="newick",
                                     unquoted_underscores=True,
                                     suppress_rooting=True)
@@ -571,30 +575,39 @@ def write_random_resolve_tre(self, treefilename='random_resolve.tre'):
         fi.close()
         return treepath
 
-    def write_aln(self, filename=None, alnschema="fasta"):
+    def write_aln(self, filename=None, alnschema="fasta", direc='workdir'):
+        if direc == 'workdir':
+            direc = self.workdir
+        else:
+            assert(os.path.exists(direc))
         if filename == None:
             filename = "physcraper_{}.fas".format(self.tag)
-        alnpath = "{}/{}".format(self.workdir, filename)
+        alnpath = "{}/{}".format(direc, filename)
         self.aln.write(path=alnpath,
                        schema=alnschema)
         return os.path.abspath(alnpath)
 
-    def write_files(self, treefilename=None, treeschema="newick", alnfilename=None, alnschema="fasta"):
+    def write_files(self, treefilename=None, treeschema="newick", alnfilename=None, alnschema="fasta", direc='workdir'):
         """Outputs both the streaming files, labeled with OTU ids.
         Can be mapped to original labels using otu_dict.json or otu_seq_info.csv"""
         #debug("write_files")
+        if direc == 'workdir':
+            direc = self.workdir
+        else:
+            assert(os.path.exists(direc))
         if treefilename == None:
-            treepath = "physcraper_{}.tre".format(self.tag)
+            treepath = "{}/physcraper_{}.tre".format(direc, self.tag)
         else:
-            treepath = "{}/{}".format(self.workdir, treefilename)
+            treepath = "{}/{}".format(direc, treefilename)
         if alnfilename == None:
-            alnpath = "physcraper_{}.fas".format(self.tag)
+            alnpath = "{}/physcraper_{}.fas".format(direc, self.tag)
         else:
-            alnpath = "{}/{}".format(self.workdir, alnfilename)
+            alnpath = "{}/{}".format(direc, alnfilename)
         self.tre.write(path=treepath,
                        schema=treeschema, unquoted_underscores=True)
         self.aln.write(path=alnpath,
                        schema=alnschema)
+
         return(treepath, alnpath)
 
 
@@ -665,17 +678,20 @@ def write_labelled(self, label, filename = "labelled", direc='workdir', norepeat
         tmp_aln.write(path=alnpath,
                       schema="fasta")
 
-    def write_otus(self, filename = "otu_info", schema="table"):
+    def write_otus(self, filename = "otu_info", schema="table", direc='workdir'):
         """Writes out OTU dict as json or table.
 
         :param filename: filename
         :param schema: either table or json format
         :return: writes out otu_dict to file
         """
-
+        if direc == 'workdir':
+            direc = self.workdir
+        else:
+            assert(os.path.exists(direc))
         assert schema in ["table", "json"]
         if schema == "json":
-            with open("{}/{}_{}.json".format(self.workdir, filename, self.tag), "w") as outfile:
+            with open("{}/{}_{}.json".format(direc, filename, self.tag), "w") as outfile:
                 json.dump(self.otu_dict, outfile)
         if schema == "table":
             #all_keys =  set()
@@ -685,7 +701,7 @@ def write_otus(self, filename = "otu_info", schema="table"):
             #keys.sort()
             keys = ['^ot:ottTaxonName','^ot:ottId','^ncbi:taxon','^ncbi:accession','^ncbi:gi','^physcraper:last_blasted','^physcraper:status','^ot:originalLabel','^ncbi:title']
             header = ["otu_id"] + keys
-            with open("{}/{}_{}.csv".format(self.workdir, filename, self.tag), "w") as outfile:
+            with open("{}/{}_{}.csv".format(direc, filename, self.tag), "w") as outfile:
                 outfile.write("\t".join(header)+"\n")
                 for otu in self.otu_dict:
                     vals = [str(self.otu_dict[otu].get(key, "-")) for key in keys]

physcraper/configobj.py

@@ -119,9 +119,9 @@ def config_str(self):
                                     maxlen=self.maxlen,
                                     taxonomy = self.taxonomy_dir)
         return(config_text)
-    def write_file(self, workdir, filename = "run.config"):
+    def write_file(self, direc, filename = "run.config"):
         config_text = self.config_str()
-        fi = open("{}/{}".format(workdir, filename),"w")
+        fi = open("{}/{}".format(direc, filename),"w")
         fi.write(config_text)
         fi.close()
     def read_config(self, configfi, interactive):

physcraper/ids.py

@@ -103,7 +103,7 @@ def __init__(self, configfile = None, workdir=None):
             self.ncbi_parser = ncbi_data_parser.Parser(names_file=self.config.ncbi_names,
                                                        nodes_file=self.config.ncbi_nodes)
         self.acc_tax_seq_dict = {}
-        self.full_seq_path = "{}/full_seqs".format(self.config.taxonomy_dir)
+        self.full_seq_path = "{}/downloaded_ncbi_sequences".format(self.config.taxonomy_dir)
 
 
     def get_ncbiid_from_acc(self, acc):