memory load does not exceed 1GB for phy/nex output

dereneaton · Sep 11, 2015 · 0303332 · 0303332
1 parent 6619406
commit 0303332
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Showing 2 changed files with 18 additions and 9 deletions.
diff --git a/pyrad/alignable.py b/pyrad/alignable.py
@@ -2,6 +2,7 @@
 
 import numpy as np
 import os
+import shutil
 import sys
 import glob
 import subprocess
@@ -798,12 +799,19 @@ def main(outgroup, minspecies, outname,
     formats = outform.split(",")
 
     " make phy, nex, SNP, uSNP, structure"
-    if any([i in formats for i in ['n','p']]):
-        if 'n' in formats:
-            print "\twriting nexus file"
-        if 'p' in formats:
-            print "\twriting phylip file"
-        loci2phynex.make(WORK,outname,names,longname, formats)
+    try:
+        os.mkdir(os.path.join(WORK, "tmp"))
+        if any([i in formats for i in ['n','p']]):
+            if 'p' in formats:
+                print "\tfiltering & writing to phylip file"
+            if 'n' in formats:
+                print "\twriting nexus file"
+            loci2phynex.make(WORK,outname,names,longname, formats)
+    finally:
+        print 'done'
+        if os.path.exists(os.path.join(WORK, "tmp")):
+            shutil.rmtree(os.path.join(WORK, "tmp"))
+
 
     if 'f' in formats:
         print "\tWriting gphocs file"
@@ -813,7 +821,7 @@ def main(outgroup, minspecies, outname,
         if 's' in formats:
             print "\t  + writing full SNPs file"
         if 'u' in formats:
-            print "\t  + writing unlinked SNPs file"
+            print "\t  + writing unlinked bi-allelic SNPs file"
         if 'k' in formats:
             print "\t  + writing STRUCTURE file"            
         if 'g' in formats:

diff --git a/pyrad/loci2SNP.py b/pyrad/loci2SNP.py
@@ -77,20 +77,21 @@ def make(WORK, outname, names, formats, seed, ploidy):
             rando = bisnps[np.random.randint(len(bisnps))]
         elif maxlist:
             rando = maxlist[np.random.randint(len(maxlist))]
+        tbi = 0
         for tax in S:
             if tax in ns:
                 if pis:
                     " if none are bi-allelic "
                     if not bisnps:
-                        bis += 1
+                        tbi += 1
                     Si[tax].append(ss[ns.index(tax)][rando])
             if pis:
                 " add spacer between loci "                
                 S[tax].append(" ")
             else:
                 " invariable locus "
                 S[tax].append("_ ")
-
+        bis += tbi
     " names "
     SF = list(S.keys())
     SF.sort()