Mercurial > repos > abims-sbr > mutcount

changeset 7:f1e24200e5ae draft

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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit b7a3030ea134b5dfad89b1a869db659d72d1145c
author abims-sbr
date Wed, 28 Feb 2018 10:39:41 -0500
parents fe74cf0d4e7a
children 705a7bf4c311
files MutCount.xml scripts/S01b_study_seq_composition_aa.py scripts/S02b_study_seq_composition_nuc.py scripts/functions.py test-data/OUT_aa/AVLIMFYW.csv test-data/OUT_aa/EK_QH.csv test-data/OUT_aa/ERK_DNQTSH.csv test-data/OUT_aa/FYMINK_GARP.csv test-data/OUT_aa/IVYWREL.csv test-data/OUT_aa/PAYRE-MVGDS.csv test-data/OUT_aa/RHKDE.csv test-data/OUT_aa/STNQ.csv test-data/OUT_aa/TotalHydratation.csv test-data/OUT_aa/TotalPartialSpecificVolume.csv test-data/OUT_aa/TotalResidueVolume.csv test-data/OUT_aa/TotalResidueWeight.csv test-data/OUT_aa/prot_compositions_All_AA.csv test-data/sep_aa/locus1_sp8_sp8.fasta
diffstat 18 files changed, 54 insertions(+), 62 deletions(-) [+]
line wrap: on
line diff
--- a/MutCount.xml	Wed Feb 28 06:06:14 2018 -0500
+++ b/MutCount.xml	Wed Feb 28 10:39:41 2018 -0500
@@ -154,7 +154,8 @@
         
     </outputs>
 
-    <tests>        
+    <tests>
+   
         <test>
             <conditional name="method" >
                 <param name="method_run" value="concat" />
@@ -202,7 +203,7 @@
                 </assert_contents>
             </output>
         </test>
-
+        
         <test>
             <conditional name="method" >
                 <param name="method_run" value="separated" />
@@ -212,17 +213,17 @@
             </conditional>            
             <output name="ivywrel">
                 <assert_contents>
-                    <has_line line="locus2_sp6_sp6.fasta,21.00000,0.32812,23.00000,0.35938,NA,NA,23.00000,0.35938,NA,NA,22.00000,0.34375,23.00000,0.35938,NA,NA,NA,NA,22.00000,0.34375" />
+                    <has_line line="locus1_sp8_sp8.fasta,25.00000,0.36765,28.00000,0.36364,NA,NA,NA,NA,27.00000,0.35065,27.00000,0.35065,28.00000,0.36364,0.00000,0.00000,27.00000,0.40909,27.00000,0.35065" />
                 </assert_contents>
             </output>
             <output name="rhkde">
                 <assert_contents>
-                    <has_line line="locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.18182,4.00000,0.05195,10.00000,0.12987,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,16.00000,0.20779,5.00000,0.06494,11.00000,0.14286,15.00000,0.19481,4.00000,0.05195,11.00000,0.14286,14.00000,0.18182,2.00000,0.02597,12.00000,0.15584,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,13.00000,0.19697,2.00000,0.03030,11.00000,0.16667,15.00000,0.19481,4.00000,0.05195,11.00000,0.14286"/>
+                    <has_line line="locus1_sp6_sp6.fasta,28.00000,0.35897,14.00000,0.17949,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949"/>
                 </assert_contents>
             </output>
             <output name="payre_mvgds">
                 <assert_contents>
-                    <has_line line="locus2_sp6_sp6.fasta,18.00000,0.28125,6.00000,0.09375,20.00000,0.31250,0.90000,0.30000,18.00000,0.28125,6.00000,0.09375,21.00000,0.32812,0.85714,0.28571,NA,NA,NA,NA,NA,NA,NA,NA,18.00000,0.28125,6.00000,0.09375,20.00000,0.31250,0.90000,0.30000,NA,NA,NA,NA,NA,NA,NA,NA,17.00000,0.26562,6.00000,0.09375,20.00000,0.31250,0.85000,0.30000,20.00000,0.31250,8.00000,0.12500,19.00000,0.29688,1.05263,0.42105,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,17.00000,0.26562,6.00000,0.09375,20.00000,0.31250,0.85000,0.30000"/>
+                    <has_line line="locus1_sp8_sp8.fasta,16.00000,0.23529,3.00000,0.04412,27.00000,0.39706,0.59259,0.11111,18.00000,0.23377,4.00000,0.05195,29.00000,0.37662,0.62069,0.13793,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,19.00000,0.24675,6.00000,0.07792,30.00000,0.38961,0.63333,0.20000,20.00000,0.25974,7.00000,0.09091,32.00000,0.41558,0.62500,0.21875,20.00000,0.25974,5.00000,0.06494,29.00000,0.37662,0.68966,0.17241,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.21212,2.00000,0.03030,26.00000,0.39394,0.53846,0.07692,19.00000,0.24675,6.00000,0.07792,32.00000,0.41558,0.59375,0.18750"/>
                 </assert_contents>
             </output>
             <output name="avlimfyw">
--- a/scripts/S01b_study_seq_composition_aa.py	Wed Feb 28 06:06:14 2018 -0500
+++ b/scripts/S01b_study_seq_composition_aa.py	Wed Feb 28 10:39:41 2018 -0500
@@ -5,7 +5,7 @@
 ## Last Version : 12/2017 by Victor Mataigne
 ## Object: Test for compositional bias in genome and proteome as marker of thermal adaptation (comparison between 2 "hot" species: Ap and Ps and two "cold" species: Pg, Pp)
 
-import sys,os,shutil,subprocess,string
+import sys,os,shutil,subprocess,string, itertools
 from functions import simplify_fasta_name, dico
 
 script_path = os.path.dirname(sys.argv[0])
--- a/scripts/S02b_study_seq_composition_nuc.py	Wed Feb 28 06:06:14 2018 -0500
+++ b/scripts/S02b_study_seq_composition_nuc.py	Wed Feb 28 10:39:41 2018 -0500
@@ -4,7 +4,7 @@
 ## Last Version : 12/2017 by Victor Mataigne
 ## Object: Test for compositional bias in genome and proteome as marker of thermal adaptation (comparison between 2 "hot" species: Ap and Ps and one "cold" species: Pg)
 
-import sys,os,shutil,subprocess, string
+import sys,os,shutil,subprocess, string, itertools
 from functions import simplify_fasta_name, dico
 
 ##################
--- a/scripts/functions.py	Wed Feb 28 06:06:14 2018 -0500
+++ b/scripts/functions.py	Wed Feb 28 10:39:41 2018 -0500
@@ -1,3 +1,5 @@
+import itertools
+
 def simplify_fasta_name(fasta_name,LT):
     for abbreviation in LT:
         if abbreviation in fasta_name:
@@ -7,35 +9,25 @@
 
 ## Generates bash, with key = fasta name; value = sequence (WITH GAP, IF ANY, REMOVED IN THIS FUNCTION)
 def dico(fasta_file,LT):
-
-    count_fastaName=0
-    F1 = open(fasta_file, "r")
-    
+    #count_fastaName = 0
     bash1 = {}
-    while 1:
-        nextline = F1.readline()
-        #print nextline
-        if not nextline :
-            break
-        
-        if nextline[0] == ">":
-            count_fastaName = count_fastaName + 1
-            fasta_name = nextline[1:-1]
-            nextline = F1.readline()
-            sequence = nextline[:-1]
-            
-            if fasta_name not in bash1.keys():
-                fasta_name = simplify_fasta_name(fasta_name,LT)  ### DEF 0 ###
-                bash1[fasta_name] = sequence
-            else:
-                print fasta_name
+    with open(fasta_file, "r") as file:
+        for name, query in itertools.izip_longest(*[file]*2):
+            if not name:
+                break
+            if name[0] == ">":
+                #count_fastaName += 1
+                fasta_name = name[1:-1]
+                sequence = query[:-1]
+                if fasta_name not in bash1.keys():
+                    fasta_name = simplify_fasta_name(fasta_name, LT)
+                    bash1[fasta_name] = sequence
+                else :
+                    print fasta_name
 
-    # Find alignment length
     kk = bash1.keys()
     key0 = kk[0]
     seq0 = bash1[key0]
     ln_seq = len(seq0)
-
-    F1.close()
     
-    return(bash1)
+    return(bash1)
\ No newline at end of file
--- a/test-data/OUT_aa/AVLIMFYW.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/AVLIMFYW.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_count_AVLIMFYW,Ac_prop_AVLIMFYW,Ac_count_AVLIM,Ac_prop_AVLIM,Ac_count_FYW,Ac_prop_FYW,Pu_count_AVLIMFYW,Pu_prop_AVLIMFYW,Pu_count_AVLIM,Pu_prop_AVLIM,Pu_count_FYW,Pu_prop_FYW,Am_count_AVLIMFYW,Am_prop_AVLIMFYW,Am_count_AVLIM,Am_prop_AVLIM,Am_count_FYW,Am_prop_FYW,Ap_count_AVLIMFYW,Ap_prop_AVLIMFYW,Ap_count_AVLIM,Ap_prop_AVLIM,Ap_count_FYW,Ap_prop_FYW,Pf_count_AVLIMFYW,Pf_prop_AVLIMFYW,Pf_count_AVLIM,Pf_prop_AVLIM,Pf_count_FYW,Pf_prop_FYW,Pg_count_AVLIMFYW,Pg_prop_AVLIMFYW,Pg_count_AVLIM,Pg_prop_AVLIM,Pg_count_FYW,Pg_prop_FYW,Ph_count_AVLIMFYW,Ph_prop_AVLIMFYW,Ph_count_AVLIM,Ph_prop_AVLIM,Ph_count_FYW,Ph_prop_FYW,Ps_count_AVLIMFYW,Ps_prop_AVLIMFYW,Ps_count_AVLIM,Ps_prop_AVLIM,Ps_count_FYW,Ps_prop_FYW,Pp_count_AVLIMFYW,Pp_prop_AVLIMFYW,Pp_count_AVLIM,Pp_prop_AVLIM,Pp_count_FYW,Pp_prop_FYW,Pa_count_AVLIMFYW,Pa_prop_AVLIMFYW,Pa_count_AVLIM,Pa_prop_AVLIM,Pa_count_FYW,Pa_prop_FYW
-locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,28.00000,0.36364,25.00000,0.32468,3.00000,0.03896,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,29.00000,0.37662,26.00000,0.33766,3.00000,0.03896,30.00000,0.38961,27.00000,0.35065,3.00000,0.03896,28.00000,0.36364,25.00000,0.32468,3.00000,0.03896,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,24.00000,0.36364,22.00000,0.33333,2.00000,0.03030,29.00000,0.37662,26.00000,0.33766,3.00000,0.03896
+locus2_sp6_sp6.fasta,27.00000,0.42188,21.00000,0.32812,6.00000,0.09375,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,30.00000,0.46875,24.00000,0.37500,6.00000,0.09375,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375
 locus1_sp6_sp6.fasta,25.00000,0.32051,22.00000,0.28205,3.00000,0.03846,25.00000,0.32051,23.00000,0.29487,2.00000,0.02564,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,25.00000,0.32051,23.00000,0.29487,2.00000,0.02564,24.00000,0.30769,22.00000,0.28205,2.00000,0.02564,24.00000,0.30769,22.00000,0.28205,2.00000,0.02564,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,24.00000,0.30769,22.00000,0.28205,2.00000,0.02564
-locus2_sp6_sp6.fasta,27.00000,0.42188,21.00000,0.32812,6.00000,0.09375,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,30.00000,0.46875,24.00000,0.37500,6.00000,0.09375,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375
+locus1_sp8_sp8.fasta,23.00000,0.33824,21.00000,0.30882,2.00000,0.02941,28.00000,0.36364,25.00000,0.32468,3.00000,0.03896,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,29.00000,0.37662,26.00000,0.33766,3.00000,0.03896,30.00000,0.38961,27.00000,0.35065,3.00000,0.03896,28.00000,0.36364,25.00000,0.32468,3.00000,0.03896,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,24.00000,0.36364,22.00000,0.33333,2.00000,0.03030,29.00000,0.37662,26.00000,0.33766,3.00000,0.03896
--- a/test-data/OUT_aa/EK_QH.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/EK_QH.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_count_EK,Ac_prop_EK,Ac_count_QH,Ac_prop_QH,Ac_ratio_EK_vs_QH,Pu_count_EK,Pu_prop_EK,Pu_count_QH,Pu_prop_QH,Pu_ratio_EK_vs_QH,Am_count_EK,Am_prop_EK,Am_count_QH,Am_prop_QH,Am_ratio_EK_vs_QH,Ap_count_EK,Ap_prop_EK,Ap_count_QH,Ap_prop_QH,Ap_ratio_EK_vs_QH,Pf_count_EK,Pf_prop_EK,Pf_count_QH,Pf_prop_QH,Pf_ratio_EK_vs_QH,Pg_count_EK,Pg_prop_EK,Pg_count_QH,Pg_prop_QH,Pg_ratio_EK_vs_QH,Ph_count_EK,Ph_prop_EK,Ph_count_QH,Ph_prop_QH,Ph_ratio_EK_vs_QH,Ps_count_EK,Ps_prop_EK,Ps_count_QH,Ps_prop_QH,Ps_ratio_EK_vs_QH,Pp_count_EK,Pp_prop_EK,Pp_count_QH,Pp_prop_QH,Pp_ratio_EK_vs_QH,Pa_count_EK,Pa_prop_EK,Pa_count_QH,Pa_prop_QH,Pa_ratio_EK_vs_QH
-locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,10.00000,0.12987,5.00000,0.06494,2.00000,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,9.00000,0.11688,4.00000,0.05195,2.25000,9.00000,0.11688,5.00000,0.06494,1.80000,10.00000,0.12987,4.00000,0.05195,2.50000,0.00000,0.00000,0.00000,0.00000,0.00000,9.00000,0.13636,4.00000,0.06061,2.25000,9.00000,0.11688,5.00000,0.06494,1.80000
+locus2_sp6_sp6.fasta,13.00000,0.20312,2.00000,0.03125,6.50000,13.00000,0.20312,2.00000,0.03125,6.50000,NA,NA,NA,NA,NA,13.00000,0.20312,2.00000,0.03125,6.50000,NA,NA,NA,NA,NA,14.00000,0.21875,2.00000,0.03125,7.00000,13.00000,0.20312,2.00000,0.03125,6.50000,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,14.00000,0.21875,2.00000,0.03125,7.00000
 locus1_sp6_sp6.fasta,10.00000,0.12821,11.00000,0.14103,0.90909,11.00000,0.14103,11.00000,0.14103,1.00000,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,10.00000,0.12821,11.00000,0.14103,0.90909,10.00000,0.12821,11.00000,0.14103,0.90909,10.00000,0.12821,11.00000,0.14103,0.90909,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,10.00000,0.12821,11.00000,0.14103,0.90909
-locus2_sp6_sp6.fasta,13.00000,0.20312,2.00000,0.03125,6.50000,13.00000,0.20312,2.00000,0.03125,6.50000,NA,NA,NA,NA,NA,13.00000,0.20312,2.00000,0.03125,6.50000,NA,NA,NA,NA,NA,14.00000,0.21875,2.00000,0.03125,7.00000,13.00000,0.20312,2.00000,0.03125,6.50000,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,14.00000,0.21875,2.00000,0.03125,7.00000
+locus1_sp8_sp8.fasta,8.00000,0.11765,4.00000,0.05882,2.00000,10.00000,0.12987,5.00000,0.06494,2.00000,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,9.00000,0.11688,4.00000,0.05195,2.25000,9.00000,0.11688,5.00000,0.06494,1.80000,10.00000,0.12987,4.00000,0.05195,2.50000,0.00000,0.00000,0.00000,0.00000,0.00000,9.00000,0.13636,4.00000,0.06061,2.25000,9.00000,0.11688,5.00000,0.06494,1.80000
--- a/test-data/OUT_aa/ERK_DNQTSH.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/ERK_DNQTSH.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_count_ERK,Ac_prop_ERK,Ac_count_DNQTSH,Ac_prop_DNQTSH,Ac_ratio_ERK_vs_DNQTSH,Pu_count_ERK,Pu_prop_ERK,Pu_count_DNQTSH,Pu_prop_DNQTSH,Pu_ratio_ERK_vs_DNQTSH,Am_count_ERK,Am_prop_ERK,Am_count_DNQTSH,Am_prop_DNQTSH,Am_ratio_ERK_vs_DNQTSH,Ap_count_ERK,Ap_prop_ERK,Ap_count_DNQTSH,Ap_prop_DNQTSH,Ap_ratio_ERK_vs_DNQTSH,Pf_count_ERK,Pf_prop_ERK,Pf_count_DNQTSH,Pf_prop_DNQTSH,Pf_ratio_ERK_vs_DNQTSH,Pg_count_ERK,Pg_prop_ERK,Pg_count_DNQTSH,Pg_prop_DNQTSH,Pg_ratio_ERK_vs_DNQTSH,Ph_count_ERK,Ph_prop_ERK,Ph_count_DNQTSH,Ph_prop_DNQTSH,Ph_ratio_ERK_vs_DNQTSH,Ps_count_ERK,Ps_prop_ERK,Ps_count_DNQTSH,Ps_prop_DNQTSH,Ps_ratio_ERK_vs_DNQTSH,Pp_count_ERK,Pp_prop_ERK,Pp_count_DNQTSH,Pp_prop_DNQTSH,Pp_ratio_ERK_vs_DNQTSH,Pa_count_ERK,Pa_prop_ERK,Pa_count_DNQTSH,Pa_prop_DNQTSH,Pa_ratio_ERK_vs_DNQTSH
-locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,11.00000,0.14286,31.00000,0.40260,0.35484,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,11.00000,0.14286,32.00000,0.41558,0.34375,10.00000,0.12987,30.00000,0.38961,0.33333,11.00000,0.14286,30.00000,0.38961,0.36667,0.00000,0.00000,0.00000,0.00000,0.00000,10.00000,0.15152,27.00000,0.40909,0.37037,10.00000,0.12987,31.00000,0.40260,0.32258
+locus2_sp6_sp6.fasta,13.00000,0.20312,14.00000,0.21875,0.92857,13.00000,0.20312,14.00000,0.21875,0.92857,NA,NA,NA,NA,NA,13.00000,0.20312,13.00000,0.20312,1.00000,NA,NA,NA,NA,NA,14.00000,0.21875,13.00000,0.20312,1.07692,13.00000,0.20312,14.00000,0.21875,0.92857,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,14.00000,0.21875,13.00000,0.20312,1.07692
 locus1_sp6_sp6.fasta,16.00000,0.20513,31.00000,0.39744,0.51613,18.00000,0.23077,27.00000,0.34615,0.66667,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,18.00000,0.23077,30.00000,0.38462,0.60000,17.00000,0.21795,31.00000,0.39744,0.54839,17.00000,0.21795,31.00000,0.39744,0.54839,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,17.00000,0.21795,31.00000,0.39744,0.54839
-locus2_sp6_sp6.fasta,13.00000,0.20312,14.00000,0.21875,0.92857,13.00000,0.20312,14.00000,0.21875,0.92857,NA,NA,NA,NA,NA,13.00000,0.20312,13.00000,0.20312,1.00000,NA,NA,NA,NA,NA,14.00000,0.21875,13.00000,0.20312,1.07692,13.00000,0.20312,14.00000,0.21875,0.92857,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,14.00000,0.21875,13.00000,0.20312,1.07692
+locus1_sp8_sp8.fasta,11.00000,0.16176,24.00000,0.35294,0.45833,11.00000,0.14286,31.00000,0.40260,0.35484,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,11.00000,0.14286,32.00000,0.41558,0.34375,10.00000,0.12987,30.00000,0.38961,0.33333,11.00000,0.14286,30.00000,0.38961,0.36667,0.00000,0.00000,0.00000,0.00000,0.00000,10.00000,0.15152,27.00000,0.40909,0.37037,10.00000,0.12987,31.00000,0.40260,0.32258
--- a/test-data/OUT_aa/FYMINK_GARP.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/FYMINK_GARP.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_count_FYMINK,Ac_prop_FYMINK,Ac_count_GARP,Ac_prop_GARP,Pu_count_FYMINK,Pu_prop_FYMINK,Pu_count_GARP,Pu_prop_GARP,Am_count_FYMINK,Am_prop_FYMINK,Am_count_GARP,Am_prop_GARP,Ap_count_FYMINK,Ap_prop_FYMINK,Ap_count_GARP,Ap_prop_GARP,Pf_count_FYMINK,Pf_prop_FYMINK,Pf_count_GARP,Pf_prop_GARP,Pg_count_FYMINK,Pg_prop_FYMINK,Pg_count_GARP,Pg_prop_GARP,Ph_count_FYMINK,Ph_prop_FYMINK,Ph_count_GARP,Ph_prop_GARP,Ps_count_FYMINK,Ps_prop_FYMINK,Ps_count_GARP,Ps_prop_GARP,Pp_count_FYMINK,Pp_prop_FYMINK,Pp_count_GARP,Pp_prop_GARP,Pa_count_FYMINK,Pa_prop_FYMINK,Pa_count_GARP,Pa_prop_GARP
-locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,16.00000,0.20779,12.00000,0.15584,NA,NA,NA,NA,NA,NA,NA,NA,15.00000,0.19481,13.00000,0.16883,12.00000,0.15584,15.00000,0.19481,17.00000,0.22078,14.00000,0.18182,0.00000,0.00000,0.00000,0.00000,12.00000,0.18182,8.00000,0.12121,12.00000,0.15584,14.00000,0.18182
+locus2_sp6_sp6.fasta,21.00000,0.32812,16.00000,0.25000,20.00000,0.31250,15.00000,0.23438,NA,NA,NA,NA,21.00000,0.32812,16.00000,0.25000,NA,NA,NA,NA,21.00000,0.32812,15.00000,0.23438,20.00000,0.31250,15.00000,0.23438,NA,NA,NA,NA,NA,NA,NA,NA,21.00000,0.32812,15.00000,0.23438
 locus1_sp6_sp6.fasta,15.00000,0.19231,17.00000,0.21795,12.00000,0.15385,20.00000,0.25641,NA,NA,NA,NA,NA,NA,NA,NA,13.00000,0.16667,19.00000,0.24359,13.00000,0.16667,18.00000,0.23077,12.00000,0.15385,18.00000,0.23077,NA,NA,NA,NA,NA,NA,NA,NA,13.00000,0.16667,18.00000,0.23077
-locus2_sp6_sp6.fasta,21.00000,0.32812,16.00000,0.25000,20.00000,0.31250,15.00000,0.23438,NA,NA,NA,NA,21.00000,0.32812,16.00000,0.25000,NA,NA,NA,NA,21.00000,0.32812,15.00000,0.23438,20.00000,0.31250,15.00000,0.23438,NA,NA,NA,NA,NA,NA,NA,NA,21.00000,0.32812,15.00000,0.23438
+locus1_sp8_sp8.fasta,14.00000,0.20588,16.00000,0.23529,16.00000,0.20779,12.00000,0.15584,NA,NA,NA,NA,NA,NA,NA,NA,15.00000,0.19481,13.00000,0.16883,12.00000,0.15584,15.00000,0.19481,17.00000,0.22078,14.00000,0.18182,0.00000,0.00000,0.00000,0.00000,12.00000,0.18182,8.00000,0.12121,12.00000,0.15584,14.00000,0.18182
--- a/test-data/OUT_aa/IVYWREL.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/IVYWREL.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_count_IVYWREL,Ac_prop_IVYWREL,Pu_count_IVYWREL,Pu_prop_IVYWREL,Am_count_IVYWREL,Am_prop_IVYWREL,Ap_count_IVYWREL,Ap_prop_IVYWREL,Pf_count_IVYWREL,Pf_prop_IVYWREL,Pg_count_IVYWREL,Pg_prop_IVYWREL,Ph_count_IVYWREL,Ph_prop_IVYWREL,Ps_count_IVYWREL,Ps_prop_IVYWREL,Pp_count_IVYWREL,Pp_prop_IVYWREL,Pa_count_IVYWREL,Pa_prop_IVYWREL
-locus1_sp8_sp8.fasta,0.00000,0.00000,28.00000,0.36364,NA,NA,NA,NA,27.00000,0.35065,27.00000,0.35065,28.00000,0.36364,0.00000,0.00000,27.00000,0.40909,27.00000,0.35065
+locus2_sp6_sp6.fasta,21.00000,0.32812,23.00000,0.35938,NA,NA,23.00000,0.35938,NA,NA,22.00000,0.34375,23.00000,0.35938,NA,NA,NA,NA,22.00000,0.34375
 locus1_sp6_sp6.fasta,29.00000,0.37179,31.00000,0.39744,NA,NA,NA,NA,29.00000,0.37179,28.00000,0.35897,29.00000,0.37179,NA,NA,NA,NA,28.00000,0.35897
-locus2_sp6_sp6.fasta,21.00000,0.32812,23.00000,0.35938,NA,NA,23.00000,0.35938,NA,NA,22.00000,0.34375,23.00000,0.35938,NA,NA,NA,NA,22.00000,0.34375
+locus1_sp8_sp8.fasta,25.00000,0.36765,28.00000,0.36364,NA,NA,NA,NA,27.00000,0.35065,27.00000,0.35065,28.00000,0.36364,0.00000,0.00000,27.00000,0.40909,27.00000,0.35065
--- a/test-data/OUT_aa/PAYRE-MVGDS.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/PAYRE-MVGDS.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_count_PAYRE,Ac_prop_PAYRE,Ac_count_AC,Ac_prop_AC,Ac_count_MVGDS,Ac_prop_MVGDS,Ac_ratio_PAYRE_vs_MVGDS,Ac_ratio_AC_vs_MVGDS,Pu_count_PAYRE,Pu_prop_PAYRE,Pu_count_AC,Pu_prop_AC,Pu_count_MVGDS,Pu_prop_MVGDS,Pu_ratio_PAYRE_vs_MVGDS,Pu_ratio_AC_vs_MVGDS,Am_count_PAYRE,Am_prop_PAYRE,Am_count_AC,Am_prop_AC,Am_count_MVGDS,Am_prop_MVGDS,Am_ratio_PAYRE_vs_MVGDS,Am_ratio_AC_vs_MVGDS,Ap_count_PAYRE,Ap_prop_PAYRE,Ap_count_AC,Ap_prop_AC,Ap_count_MVGDS,Ap_prop_MVGDS,Ap_ratio_PAYRE_vs_MVGDS,Ap_ratio_AC_vs_MVGDS,Pf_count_PAYRE,Pf_prop_PAYRE,Pf_count_AC,Pf_prop_AC,Pf_count_MVGDS,Pf_prop_MVGDS,Pf_ratio_PAYRE_vs_MVGDS,Pf_ratio_AC_vs_MVGDS,Pg_count_PAYRE,Pg_prop_PAYRE,Pg_count_AC,Pg_prop_AC,Pg_count_MVGDS,Pg_prop_MVGDS,Pg_ratio_PAYRE_vs_MVGDS,Pg_ratio_AC_vs_MVGDS,Ph_count_PAYRE,Ph_prop_PAYRE,Ph_count_AC,Ph_prop_AC,Ph_count_MVGDS,Ph_prop_MVGDS,Ph_ratio_PAYRE_vs_MVGDS,Ph_ratio_AC_vs_MVGDS,Ps_count_PAYRE,Ps_prop_PAYRE,Ps_count_AC,Ps_prop_AC,Ps_count_MVGDS,Ps_prop_MVGDS,Ps_ratio_PAYRE_vs_MVGDS,Ps_ratio_AC_vs_MVGDS,Pp_count_PAYRE,Pp_prop_PAYRE,Pp_count_AC,Pp_prop_AC,Pp_count_MVGDS,Pp_prop_MVGDS,Pp_ratio_PAYRE_vs_MVGDS,Pp_ratio_AC_vs_MVGDS,Pa_count_PAYRE,Pa_prop_PAYRE,Pa_count_AC,Pa_prop_AC,Pa_count_MVGDS,Pa_prop_MVGDS,Pa_ratio_PAYRE_vs_MVGDS,Pa_ratio_AC_vs_MVGDS
-locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,18.00000,0.23377,4.00000,0.05195,29.00000,0.37662,0.62069,0.13793,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,19.00000,0.24675,6.00000,0.07792,30.00000,0.38961,0.63333,0.20000,20.00000,0.25974,7.00000,0.09091,32.00000,0.41558,0.62500,0.21875,20.00000,0.25974,5.00000,0.06494,29.00000,0.37662,0.68966,0.17241,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.21212,2.00000,0.03030,26.00000,0.39394,0.53846,0.07692,19.00000,0.24675,6.00000,0.07792,32.00000,0.41558,0.59375,0.18750
+locus2_sp6_sp6.fasta,18.00000,0.28125,6.00000,0.09375,20.00000,0.31250,0.90000,0.30000,18.00000,0.28125,6.00000,0.09375,21.00000,0.32812,0.85714,0.28571,NA,NA,NA,NA,NA,NA,NA,NA,18.00000,0.28125,6.00000,0.09375,20.00000,0.31250,0.90000,0.30000,NA,NA,NA,NA,NA,NA,NA,NA,17.00000,0.26562,6.00000,0.09375,20.00000,0.31250,0.85000,0.30000,20.00000,0.31250,8.00000,0.12500,19.00000,0.29688,1.05263,0.42105,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,17.00000,0.26562,6.00000,0.09375,20.00000,0.31250,0.85000,0.30000
 locus1_sp6_sp6.fasta,24.00000,0.30769,7.00000,0.08974,20.00000,0.25641,1.20000,0.35000,25.00000,0.32051,7.00000,0.08974,20.00000,0.25641,1.25000,0.35000,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,25.00000,0.32051,8.00000,0.10256,21.00000,0.26923,1.19048,0.38095,24.00000,0.30769,7.00000,0.08974,22.00000,0.28205,1.09091,0.31818,24.00000,0.30769,7.00000,0.08974,20.00000,0.25641,1.20000,0.35000,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,24.00000,0.30769,7.00000,0.08974,22.00000,0.28205,1.09091,0.31818
-locus2_sp6_sp6.fasta,18.00000,0.28125,6.00000,0.09375,20.00000,0.31250,0.90000,0.30000,18.00000,0.28125,6.00000,0.09375,21.00000,0.32812,0.85714,0.28571,NA,NA,NA,NA,NA,NA,NA,NA,18.00000,0.28125,6.00000,0.09375,20.00000,0.31250,0.90000,0.30000,NA,NA,NA,NA,NA,NA,NA,NA,17.00000,0.26562,6.00000,0.09375,20.00000,0.31250,0.85000,0.30000,20.00000,0.31250,8.00000,0.12500,19.00000,0.29688,1.05263,0.42105,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,17.00000,0.26562,6.00000,0.09375,20.00000,0.31250,0.85000,0.30000
+locus1_sp8_sp8.fasta,16.00000,0.23529,3.00000,0.04412,27.00000,0.39706,0.59259,0.11111,18.00000,0.23377,4.00000,0.05195,29.00000,0.37662,0.62069,0.13793,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,19.00000,0.24675,6.00000,0.07792,30.00000,0.38961,0.63333,0.20000,20.00000,0.25974,7.00000,0.09091,32.00000,0.41558,0.62500,0.21875,20.00000,0.25974,5.00000,0.06494,29.00000,0.37662,0.68966,0.17241,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.21212,2.00000,0.03030,26.00000,0.39394,0.53846,0.07692,19.00000,0.24675,6.00000,0.07792,32.00000,0.41558,0.59375,0.18750
--- a/test-data/OUT_aa/RHKDE.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/RHKDE.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_count_RHKDE,Ac_prop_RHKDE,Ac_count_RHK,Ac_prop_RHK,Ac_count_DE,Ac_prop_DE,Pu_count_RHKDE,Pu_prop_RHKDE,Pu_count_RHK,Pu_prop_RHK,Pu_count_DE,Pu_prop_DE,Am_count_RHKDE,Am_prop_RHKDE,Am_count_RHK,Am_prop_RHK,Am_count_DE,Am_prop_DE,Ap_count_RHKDE,Ap_prop_RHKDE,Ap_count_RHK,Ap_prop_RHK,Ap_count_DE,Ap_prop_DE,Pf_count_RHKDE,Pf_prop_RHKDE,Pf_count_RHK,Pf_prop_RHK,Pf_count_DE,Pf_prop_DE,Pg_count_RHKDE,Pg_prop_RHKDE,Pg_count_RHK,Pg_prop_RHK,Pg_count_DE,Pg_prop_DE,Ph_count_RHKDE,Ph_prop_RHKDE,Ph_count_RHK,Ph_prop_RHK,Ph_count_DE,Ph_prop_DE,Ps_count_RHKDE,Ps_prop_RHKDE,Ps_count_RHK,Ps_prop_RHK,Ps_count_DE,Ps_prop_DE,Pp_count_RHKDE,Pp_prop_RHKDE,Pp_count_RHK,Pp_prop_RHK,Pp_count_DE,Pp_prop_DE,Pa_count_RHKDE,Pa_prop_RHKDE,Pa_count_RHK,Pa_prop_RHK,Pa_count_DE,Pa_prop_DE
-locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.18182,4.00000,0.05195,10.00000,0.12987,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,16.00000,0.20779,5.00000,0.06494,11.00000,0.14286,15.00000,0.19481,4.00000,0.05195,11.00000,0.14286,14.00000,0.18182,2.00000,0.02597,12.00000,0.15584,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,13.00000,0.19697,2.00000,0.03030,11.00000,0.16667,15.00000,0.19481,4.00000,0.05195,11.00000,0.14286
+locus2_sp6_sp6.fasta,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,NA,NA,NA,NA,NA,NA,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,NA,NA,NA,NA,NA,NA,20.00000,0.31250,10.00000,0.15625,10.00000,0.15625,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,20.00000,0.31250,10.00000,0.15625,10.00000,0.15625
 locus1_sp6_sp6.fasta,28.00000,0.35897,14.00000,0.17949,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949
-locus2_sp6_sp6.fasta,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,NA,NA,NA,NA,NA,NA,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,NA,NA,NA,NA,NA,NA,20.00000,0.31250,10.00000,0.15625,10.00000,0.15625,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,20.00000,0.31250,10.00000,0.15625,10.00000,0.15625
+locus1_sp8_sp8.fasta,14.00000,0.20588,4.00000,0.05882,10.00000,0.14706,14.00000,0.18182,4.00000,0.05195,10.00000,0.12987,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,16.00000,0.20779,5.00000,0.06494,11.00000,0.14286,15.00000,0.19481,4.00000,0.05195,11.00000,0.14286,14.00000,0.18182,2.00000,0.02597,12.00000,0.15584,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,13.00000,0.19697,2.00000,0.03030,11.00000,0.16667,15.00000,0.19481,4.00000,0.05195,11.00000,0.14286
--- a/test-data/OUT_aa/STNQ.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/STNQ.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_count_STNQ,Ac_prop_STNQ,Pu_count_STNQ,Pu_prop_STNQ,Am_count_STNQ,Am_prop_STNQ,Ap_count_STNQ,Ap_prop_STNQ,Pf_count_STNQ,Pf_prop_STNQ,Pg_count_STNQ,Pg_prop_STNQ,Ph_count_STNQ,Ph_prop_STNQ,Ps_count_STNQ,Ps_prop_STNQ,Pp_count_STNQ,Pp_prop_STNQ,Pa_count_STNQ,Pa_prop_STNQ
-locus1_sp8_sp8.fasta,0.00000,0.00000,28.00000,0.36364,NA,NA,NA,NA,27.00000,0.35065,25.00000,0.32468,27.00000,0.35065,0.00000,0.00000,24.00000,0.36364,26.00000,0.33766
+locus2_sp6_sp6.fasta,8.00000,0.12500,8.00000,0.12500,NA,NA,7.00000,0.10938,NA,NA,7.00000,0.10938,8.00000,0.12500,NA,NA,NA,NA,7.00000,0.10938
 locus1_sp6_sp6.fasta,19.00000,0.24359,15.00000,0.19231,NA,NA,NA,NA,18.00000,0.23077,18.00000,0.23077,18.00000,0.23077,NA,NA,NA,NA,18.00000,0.23077
-locus2_sp6_sp6.fasta,8.00000,0.12500,8.00000,0.12500,NA,NA,7.00000,0.10938,NA,NA,7.00000,0.10938,8.00000,0.12500,NA,NA,NA,NA,7.00000,0.10938
+locus1_sp8_sp8.fasta,21.00000,0.30882,28.00000,0.36364,NA,NA,NA,NA,27.00000,0.35065,25.00000,0.32468,27.00000,0.35065,0.00000,0.00000,24.00000,0.36364,26.00000,0.33766
--- a/test-data/OUT_aa/TotalHydratation.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/TotalHydratation.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_Total_Hydratation,Pu_Total_Hydratation,Am_Total_Hydratation,Ap_Total_Hydratation,Pf_Total_Hydratation,Pg_Total_Hydratation,Ph_Total_Hydratation,Ps_Total_Hydratation,Pp_Total_Hydratation,Pa_Total_Hydratation
-locus1_sp8_sp8.fasta,0.00000,188.00000,NA,NA,190.50000,188.50000,192.00000,0.00000,167.50000,189.50000
+locus2_sp6_sp6.fasta,171.50000,171.50000,NA,170.50000,NA,171.00000,171.50000,NA,NA,171.00000
 locus1_sp6_sp6.fasta,224.00000,224.50000,NA,NA,223.00000,226.00000,226.00000,NA,NA,226.00000
-locus2_sp6_sp6.fasta,171.50000,171.50000,NA,170.50000,NA,171.00000,171.50000,NA,NA,171.00000
+locus1_sp8_sp8.fasta,163.00000,188.00000,NA,NA,190.50000,188.50000,192.00000,0.00000,167.50000,189.50000
--- a/test-data/OUT_aa/TotalPartialSpecificVolume.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/TotalPartialSpecificVolume.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_Total_Partial_Specific_Volume,Pu_Total_Partial_Specific_Volume,Am_Total_Partial_Specific_Volume,Ap_Total_Partial_Specific_Volume,Pf_Total_Partial_Specific_Volume,Pg_Total_Partial_Specific_Volume,Ph_Total_Partial_Specific_Volume,Ps_Total_Partial_Specific_Volume,Pp_Total_Partial_Specific_Volume,Pa_Total_Partial_Specific_Volume
-locus1_sp8_sp8.fasta,0.00000,56.86000,NA,NA,56.93000,57.09000,56.25000,0.00000,49.09000,57.05000
+locus2_sp6_sp6.fasta,47.40000,47.77000,NA,47.71000,NA,48.17000,47.97000,NA,NA,48.17000
 locus1_sp6_sp6.fasta,56.53000,56.56000,NA,NA,56.37000,56.43000,56.54000,NA,NA,56.43000
-locus2_sp6_sp6.fasta,47.40000,47.77000,NA,47.71000,NA,48.17000,47.97000,NA,NA,48.17000
+locus1_sp8_sp8.fasta,49.95000,56.86000,NA,NA,56.93000,57.09000,56.25000,0.00000,49.09000,57.05000
--- a/test-data/OUT_aa/TotalResidueVolume.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/TotalResidueVolume.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_Total_Residue_Volume,Pu_Total_Residue_Volume,Am_Total_Residue_Volume,Ap_Total_Residue_Volume,Pf_Total_Residue_Volume,Pg_Total_Residue_Volume,Ph_Total_Residue_Volume,Ps_Total_Residue_Volume,Pp_Total_Residue_Volume,Pa_Total_Residue_Volume
-locus1_sp8_sp8.fasta,0.00000,7671.00000,NA,NA,7642.00000,7493.00000,7561.00000,0.00000,6633.00000,7519.00000
+locus2_sp6_sp6.fasta,6575.00000,6593.00000,NA,6587.00000,NA,6645.00000,6631.00000,NA,NA,6645.00000
 locus1_sp6_sp6.fasta,8265.00000,8257.00000,NA,NA,8305.00000,8257.00000,8277.00000,NA,NA,8257.00000
-locus2_sp6_sp6.fasta,6575.00000,6593.00000,NA,6587.00000,NA,6645.00000,6631.00000,NA,NA,6645.00000
+locus1_sp8_sp8.fasta,6699.00000,7671.00000,NA,NA,7642.00000,7493.00000,7561.00000,0.00000,6633.00000,7519.00000
--- a/test-data/OUT_aa/TotalResidueWeight.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/TotalResidueWeight.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_Total_Residue_Weight,Pu_Total_Residue_Weight,Am_Total_Residue_Weight,Ap_Total_Residue_Weight,Pf_Total_Residue_Weight,Pg_Total_Residue_Weight,Ph_Total_Residue_Weight,Ps_Total_Residue_Weight,Pp_Total_Residue_Weight,Pa_Total_Residue_Weight
-locus1_sp8_sp8.fasta,0.00000,8270.91000,NA,NA,8248.86000,8082.66000,8213.63000,0.00000,7124.55000,8112.69000
+locus2_sp6_sp6.fasta,6981.51000,6977.50000,NA,6961.51000,NA,6990.69000,7005.54000,NA,NA,6990.69000
 locus1_sp6_sp6.fasta,8981.54000,8937.66000,NA,NA,9023.69000,8989.64000,8985.64000,NA,NA,8989.64000
-locus2_sp6_sp6.fasta,6981.51000,6977.50000,NA,6961.51000,NA,6990.69000,7005.54000,NA,NA,6990.69000
+locus1_sp8_sp8.fasta,7216.76000,8270.91000,NA,NA,8248.86000,8082.66000,8213.63000,0.00000,7124.55000,8112.69000
--- a/test-data/OUT_aa/prot_compositions_All_AA.csv	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/OUT_aa/prot_compositions_All_AA.csv	Wed Feb 28 10:39:41 2018 -0500
@@ -1,4 +1,4 @@
 LOCUS,Ac_prop_K,Ac_prop_R,Ac_prop_A,Ac_prop_F,Ac_prop_I,Ac_prop_L,Ac_prop_M,Ac_prop_V,Ac_prop_W,Ac_prop_N,Ac_prop_Q,Ac_prop_S,Ac_prop_T,Ac_prop_H,Ac_prop_Y,Ac_prop_C,Ac_prop_D,Ac_prop_E,Ac_prop_P,Ac_prop_G,Pu_prop_K,Pu_prop_R,Pu_prop_A,Pu_prop_F,Pu_prop_I,Pu_prop_L,Pu_prop_M,Pu_prop_V,Pu_prop_W,Pu_prop_N,Pu_prop_Q,Pu_prop_S,Pu_prop_T,Pu_prop_H,Pu_prop_Y,Pu_prop_C,Pu_prop_D,Pu_prop_E,Pu_prop_P,Pu_prop_G,Am_prop_K,Am_prop_R,Am_prop_A,Am_prop_F,Am_prop_I,Am_prop_L,Am_prop_M,Am_prop_V,Am_prop_W,Am_prop_N,Am_prop_Q,Am_prop_S,Am_prop_T,Am_prop_H,Am_prop_Y,Am_prop_C,Am_prop_D,Am_prop_E,Am_prop_P,Am_prop_G,Ap_prop_K,Ap_prop_R,Ap_prop_A,Ap_prop_F,Ap_prop_I,Ap_prop_L,Ap_prop_M,Ap_prop_V,Ap_prop_W,Ap_prop_N,Ap_prop_Q,Ap_prop_S,Ap_prop_T,Ap_prop_H,Ap_prop_Y,Ap_prop_C,Ap_prop_D,Ap_prop_E,Ap_prop_P,Ap_prop_G,Pf_prop_K,Pf_prop_R,Pf_prop_A,Pf_prop_F,Pf_prop_I,Pf_prop_L,Pf_prop_M,Pf_prop_V,Pf_prop_W,Pf_prop_N,Pf_prop_Q,Pf_prop_S,Pf_prop_T,Pf_prop_H,Pf_prop_Y,Pf_prop_C,Pf_prop_D,Pf_prop_E,Pf_prop_P,Pf_prop_G,Pg_prop_K,Pg_prop_R,Pg_prop_A,Pg_prop_F,Pg_prop_I,Pg_prop_L,Pg_prop_M,Pg_prop_V,Pg_prop_W,Pg_prop_N,Pg_prop_Q,Pg_prop_S,Pg_prop_T,Pg_prop_H,Pg_prop_Y,Pg_prop_C,Pg_prop_D,Pg_prop_E,Pg_prop_P,Pg_prop_G,Ph_prop_K,Ph_prop_R,Ph_prop_A,Ph_prop_F,Ph_prop_I,Ph_prop_L,Ph_prop_M,Ph_prop_V,Ph_prop_W,Ph_prop_N,Ph_prop_Q,Ph_prop_S,Ph_prop_T,Ph_prop_H,Ph_prop_Y,Ph_prop_C,Ph_prop_D,Ph_prop_E,Ph_prop_P,Ph_prop_G,Ps_prop_K,Ps_prop_R,Ps_prop_A,Ps_prop_F,Ps_prop_I,Ps_prop_L,Ps_prop_M,Ps_prop_V,Ps_prop_W,Ps_prop_N,Ps_prop_Q,Ps_prop_S,Ps_prop_T,Ps_prop_H,Ps_prop_Y,Ps_prop_C,Ps_prop_D,Ps_prop_E,Ps_prop_P,Ps_prop_G,Pp_prop_K,Pp_prop_R,Pp_prop_A,Pp_prop_F,Pp_prop_I,Pp_prop_L,Pp_prop_M,Pp_prop_V,Pp_prop_W,Pp_prop_N,Pp_prop_Q,Pp_prop_S,Pp_prop_T,Pp_prop_H,Pp_prop_Y,Pp_prop_C,Pp_prop_D,Pp_prop_E,Pp_prop_P,Pp_prop_G,Pa_prop_K,Pa_prop_R,Pa_prop_A,Pa_prop_F,Pa_prop_I,Pa_prop_L,Pa_prop_M,Pa_prop_V,Pa_prop_W,Pa_prop_N,Pa_prop_Q,Pa_prop_S,Pa_prop_T,Pa_prop_H,Pa_prop_Y,Pa_prop_C,Pa_prop_D,Pa_prop_E,Pa_prop_P,Pa_prop_G
-locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.02597,0.01299,0.05195,0.01299,0.02597,0.10390,0.05195,0.09091,0.00000,0.06494,0.05195,0.15584,0.09091,0.01299,0.02597,0.00000,0.02597,0.10390,0.03896,0.05195,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.02597,0.02597,0.07792,0.01299,0.03896,0.10390,0.05195,0.06494,0.00000,0.03896,0.03896,0.18182,0.09091,0.01299,0.02597,0.00000,0.05195,0.09091,0.02597,0.03896,0.02597,0.01299,0.09091,0.01299,0.02597,0.10390,0.03896,0.09091,0.00000,0.02597,0.05195,0.18182,0.06494,0.01299,0.02597,0.00000,0.05195,0.09091,0.03896,0.05195,0.01299,0.01299,0.06494,0.01299,0.02597,0.10390,0.05195,0.07792,0.00000,0.09091,0.05195,0.14286,0.06494,0.00000,0.02597,0.00000,0.03896,0.11688,0.03896,0.06494,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.01515,0.01515,0.03030,0.01515,0.04545,0.12121,0.04545,0.09091,0.00000,0.04545,0.06061,0.16667,0.09091,0.00000,0.01515,0.00000,0.04545,0.12121,0.03030,0.04545,0.02597,0.01299,0.07792,0.01299,0.02597,0.10390,0.03896,0.09091,0.00000,0.02597,0.05195,0.18182,0.07792,0.01299,0.02597,0.00000,0.05195,0.09091,0.03896,0.05195
+locus2_sp6_sp6.fasta,0.12500,0.00000,0.09375,0.04688,0.03125,0.09375,0.03125,0.07812,0.00000,0.04688,0.01562,0.03125,0.03125,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.09375,0.12500,0.00000,0.09375,0.04688,0.03125,0.09375,0.01562,0.10938,0.00000,0.04688,0.01562,0.04688,0.01562,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.07812,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.12500,0.00000,0.09375,0.04688,0.04688,0.09375,0.01562,0.09375,0.00000,0.04688,0.01562,0.03125,0.01562,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.09375,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.14062,0.00000,0.09375,0.06250,0.04688,0.09375,0.01562,0.09375,0.00000,0.03125,0.01562,0.04688,0.01562,0.01562,0.03125,0.00000,0.07812,0.07812,0.06250,0.07812,0.12500,0.00000,0.12500,0.04688,0.03125,0.09375,0.01562,0.10938,0.00000,0.04688,0.01562,0.04688,0.01562,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.04688,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.14062,0.00000,0.09375,0.06250,0.04688,0.09375,0.01562,0.09375,0.00000,0.03125,0.01562,0.04688,0.01562,0.01562,0.03125,0.00000,0.07812,0.07812,0.06250,0.07812
 locus1_sp6_sp6.fasta,0.03846,0.07692,0.07692,0.01282,0.03846,0.11538,0.02564,0.02564,0.00000,0.05128,0.07692,0.08974,0.02564,0.06410,0.02564,0.01282,0.08974,0.08974,0.03846,0.02564,0.03846,0.08974,0.07692,0.01282,0.01282,0.12821,0.02564,0.05128,0.00000,0.05128,0.06410,0.05128,0.02564,0.07692,0.01282,0.01282,0.07692,0.10256,0.03846,0.05128,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.03846,0.10256,0.08974,0.01282,0.01282,0.11538,0.03846,0.03846,0.00000,0.05128,0.07692,0.07692,0.02564,0.06410,0.01282,0.01282,0.08974,0.08974,0.02564,0.02564,0.03846,0.08974,0.07692,0.01282,0.01282,0.11538,0.03846,0.03846,0.00000,0.05128,0.06410,0.08974,0.02564,0.07692,0.01282,0.01282,0.08974,0.08974,0.03846,0.02564,0.03846,0.08974,0.07692,0.01282,0.01282,0.12821,0.02564,0.03846,0.00000,0.05128,0.06410,0.07692,0.03846,0.07692,0.01282,0.01282,0.08974,0.08974,0.03846,0.02564,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.03846,0.08974,0.07692,0.01282,0.01282,0.11538,0.03846,0.03846,0.00000,0.05128,0.06410,0.08974,0.02564,0.07692,0.01282,0.01282,0.08974,0.08974,0.03846,0.02564
-locus2_sp6_sp6.fasta,0.12500,0.00000,0.09375,0.04688,0.03125,0.09375,0.03125,0.07812,0.00000,0.04688,0.01562,0.03125,0.03125,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.09375,0.12500,0.00000,0.09375,0.04688,0.03125,0.09375,0.01562,0.10938,0.00000,0.04688,0.01562,0.04688,0.01562,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.07812,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.12500,0.00000,0.09375,0.04688,0.04688,0.09375,0.01562,0.09375,0.00000,0.04688,0.01562,0.03125,0.01562,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.09375,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.14062,0.00000,0.09375,0.06250,0.04688,0.09375,0.01562,0.09375,0.00000,0.03125,0.01562,0.04688,0.01562,0.01562,0.03125,0.00000,0.07812,0.07812,0.06250,0.07812,0.12500,0.00000,0.12500,0.04688,0.03125,0.09375,0.01562,0.10938,0.00000,0.04688,0.01562,0.04688,0.01562,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.04688,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.14062,0.00000,0.09375,0.06250,0.04688,0.09375,0.01562,0.09375,0.00000,0.03125,0.01562,0.04688,0.01562,0.01562,0.03125,0.00000,0.07812,0.07812,0.06250,0.07812
+locus1_sp8_sp8.fasta,0.01471,0.04412,0.04412,0.02941,0.05882,0.07353,0.04412,0.08824,0.00000,0.05882,0.05882,0.11765,0.07353,0.00000,0.00000,0.00000,0.04412,0.10294,0.04412,0.10294,0.02597,0.01299,0.05195,0.01299,0.02597,0.10390,0.05195,0.09091,0.00000,0.06494,0.05195,0.15584,0.09091,0.01299,0.02597,0.00000,0.02597,0.10390,0.03896,0.05195,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.02597,0.02597,0.07792,0.01299,0.03896,0.10390,0.05195,0.06494,0.00000,0.03896,0.03896,0.18182,0.09091,0.01299,0.02597,0.00000,0.05195,0.09091,0.02597,0.03896,0.02597,0.01299,0.09091,0.01299,0.02597,0.10390,0.03896,0.09091,0.00000,0.02597,0.05195,0.18182,0.06494,0.01299,0.02597,0.00000,0.05195,0.09091,0.03896,0.05195,0.01299,0.01299,0.06494,0.01299,0.02597,0.10390,0.05195,0.07792,0.00000,0.09091,0.05195,0.14286,0.06494,0.00000,0.02597,0.00000,0.03896,0.11688,0.03896,0.06494,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.01515,0.01515,0.03030,0.01515,0.04545,0.12121,0.04545,0.09091,0.00000,0.04545,0.06061,0.16667,0.09091,0.00000,0.01515,0.00000,0.04545,0.12121,0.03030,0.04545,0.02597,0.01299,0.07792,0.01299,0.02597,0.10390,0.03896,0.09091,0.00000,0.02597,0.05195,0.18182,0.07792,0.01299,0.02597,0.00000,0.05195,0.09091,0.03896,0.05195
--- a/test-data/sep_aa/locus1_sp8_sp8.fasta	Wed Feb 28 06:06:14 2018 -0500
+++ b/test-data/sep_aa/locus1_sp8_sp8.fasta	Wed Feb 28 10:39:41 2018 -0500
@@ -1,5 +1,5 @@
 >PsContigII15300
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+-----------------------------------------------------------------------------
 >Pg1Pg2Pg2115381
 YSVLSTSSLHGENIMLTSEAVTADGGRSGPLFVVSQATLDQIKSEKNVVSEQTAMMDSALLESEDPSAPALVQYSES
 >Pal3389Transcri
@@ -9,9 +9,8 @@
 >Ph35190g1i1
 YSVLSTNSLNGENIMLTSEAVTADGGRNGPLFVVSQATLDQIKSEENMVSEQNAMMGSSLLESEDPNAETLVQYPES
 >Pp13976c0seq1
-YSVLSTSSLQGENIMLTSEAVTEDGSRNGPLFVVSQATLDQIKSELNIVSEQTVMMDSTLLESEEP---------------------------------
+YSVLSTSSLQGENIMLTSEAVTEDGSRNGPLFVVSQATLDQIKSELNIVSEQTVMMDSTLLESEEP------------
 >Ac100631/110004
----------------------------------
-ENIMLTSEAVTGDGGRSGPLFVVSQATLDQIKSERNIVSEQPSMMDNTLLDSEDPNTAALVQYSEA
+---------QGENIMLTSEAVTEDGSRNGPLFVENIMLTSEAVTGDGGRSGPLFVVSQATLDQIKSERNIVSEQPSM
 >Pfi19278Transcr
 YSVLSTSSLHGENIMLTSEAVTADGTRSGPLFVMSRAALDQIKSEKNIVSEQSAMMDSTLLESEDPNATTLVQYSES