# HG changeset patch
# User abims-sbr
# Date 1549034930 18000
# Node ID acc3674e515bd12fdc95cadf20b1b34c317f0e93
planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
diff -r 000000000000 -r acc3674e515b MutCount.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/MutCount.xml Fri Feb 01 10:28:50 2019 -0500
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+
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+ This tool proceeds to count codons, amino acids on each species of a set of species, and then proceeds to permutation tests.
+
+
+
+ macros.xml
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+ pandas
+ numpy
+ r-optparse
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+
+
+ ${log}
+ #end if
+
+ #if str($method.method_run) == "separated" :
+ mkdir 01_input_files &&
+ ln -s '$__tool_directory__/scripts/S03b_sign_test_binomial.R' . &&
+ #for $input in $method.sep_file
+ ln -s '$input' '01_input_files/$input.element_identifier';
+ #end for
+
+ #if str($method.format_run)== "nucleic" :
+ python '$__tool_directory__/scripts/S01b_extract_variable_nuc.py' ${method.sps_list} &&
+ #end if
+
+ #if str($method.format_run)== "proteic" :
+ cp '$__tool_directory__/scripts/amino_acid_properties.csv' . &&
+ python '$__tool_directory__/scripts/S01b_extract_variable_prot.py' ${method.sps_list} amino_acid_properties.csv &&
+ #end if
+
+ python '$__tool_directory__/scripts/S02b_extreme_2states.py' ${method.sps_gp1} ${method.sps_gp2} ${method.format_run}
+ #end if
+
+ ]]>
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+ (method['method_run']=='concat')
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+ (method['method_run']=='concat')
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+ (method['method_run']=='concat')
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+ (method['method_run']=='concat')
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+ (method['method_run']=='concat')
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+ (method['method_run']=='concat')
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+ (method['method_run']=='concat')
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+ (method['method_run']=='concat')
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+ (method['method_run']=='separated' and method['format_run']== 'nucleic')
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+ (method['method_run']=='separated' and method['format_run']== 'nucleic')
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+ (method['method_run']=='separated' and method['format_run']== 'nucleic')
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+ (method['method_run']=='separated' and method['format_run']== 'nucleic')
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+ (method['method_run']=='separated' and method['format_run']== 'proteic')
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+ (method['method_run']=='separated' and method['format_run']== 'proteic')
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+
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+ (method['method_run']=='separated' and method['format_run']== 'proteic')
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+ (method['method_run']=='separated' and method['format_run']== 'proteic')
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+@HELP_AUTHORS@
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diff -r 000000000000 -r acc3674e515b README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,13 @@
+Changelog
+
+ Version 2.0 - 12/07/2017
+
+ - NEW: Replaced the zip between tools by Dataset Collection
+ - More functional tests
+
+ Version 1.0 - 14/04/2017
+
+ - Added the tools to the suite
+ - Added a functional test with planemo
+ - Planemo test using conda dependencies for python
+ - Scripts renamed + symlinks to the directory 'scripts'
diff -r 000000000000 -r acc3674e515b macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,32 @@
+
+
+
+ python
+
+
+
+.. class:: infomark
+
+**Authors** Eric Fontanillas created the version 1 of this pipeline. Victor Mataigne developped version 2.
+
+.. class:: infomark
+
+**Galaxy integration** Julie Baffard and ABiMS TEAM, Roscoff Marine Station
+
+ | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
+ | Credits : Gildas le Corguillé, Misharl Monsoor
+
+---------------------------------------------------
+
+
+
+
+
+ Credits : ABIMS team, Roscoff Marine Station
+ Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
+ Version 1 : Scripts by Eric Fontanillas -- Galaxy integration by Julie Baffard
+ Version 2 : improvments by Victor Mataigne, Gildas le Corguillé, Misharl Monsoor
+
+
+
+
diff -r 000000000000 -r acc3674e515b scripts/S01a_codons_counting.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/S01a_codons_counting.py Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,937 @@
+#!/usr/bin/env python
+# coding: utf-8
+# Author : Victor Mataigne
+
+import string, os, sys, re, random, itertools, argparse, copy, math
+import pandas as pd
+import numpy as np
+
+def buildDicts(list_codons, content, dict_genetic_code, dict_aa_classif):
+ """ Build dictionaries with values to 0. These dictionaries are used as starting point for each sequence counting
+
+ Args :
+ list_codons (list of str) : all codons except codons-stop
+ content (int or list) : an integer (for coutings and transitions), or an empty list (for resampling)
+ dict_genetic_code (dict) : the genetic code : {'aa1': [codon1, codon2,...], ...}
+ dict_aa_classif (dict) : the types of the amino-acids ( {type: [aa1, aa2, ...], ...}
+
+ Returns :
+ dico_codons, dico_aa, dico_aatypes (dicts) : keys : codons/amico-acids/amico-acids types, values : 0 or []
+ dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions (dicts of dicts) :
+ actually, the three first dictionaries nested as values of keys codons/amico-acids/amico-acids
+ """
+
+ # I could have make sub-routines here.
+ # the copy commands are mandatory, otherwise all dictionaries will reference the same variable(s)
+
+ dico_codons = {}
+ for codon in list_codons:
+ dico_codons[codon] = copy.deepcopy(content)
+
+ dico_aa = {}
+ for aa in dict_genetic_code.keys():
+ dico_aa[aa] = copy.deepcopy(content)
+
+ dico_aatypes = {}
+ for aatype in dict_aa_classif.keys():
+ dico_aatypes[aatype] = copy.deepcopy(content)
+
+ dico_codons_transitions=copy.deepcopy(dico_codons)
+ for key in dico_codons_transitions.keys():
+ dico_codons_transitions[key]=copy.deepcopy(dico_codons)
+
+ dico_aa_transitions = copy.deepcopy(dico_aa)
+ for key in dico_aa_transitions.keys():
+ dico_aa_transitions[key]=copy.deepcopy(dico_aa)
+
+ dico_aatypes_transitions = copy.deepcopy(dico_aatypes)
+ for key in dico_aatypes_transitions.keys():
+ dico_aatypes_transitions[key]=copy.deepcopy(dico_aatypes)
+
+ return dico_codons, dico_aa, dico_aatypes, dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions
+
+def viable(seqs, pos, method):
+ """ Compute if, among a set of sequences, either at least one of the codons at the specified position has not a "-",
+ or not any codon has a "-"
+
+ Args :
+ seqs : a list (the sequences, which must all have the same size)
+ pos : an integer (the positions, <= len(seqs) -3)
+
+ Returns:
+ bool
+ """
+ codons = [seq[pos:pos+3] for seq in seqs]
+ if method == "all":
+ return not all("-" in codon for codon in codons)
+ elif method == "any":
+ return not any("-" in codon for codon in codons)
+
+# # # Function for codons, aa, aatypes Countings -------------------------------------------------------------------------------
+
+def computeAllCountingsAndFreqs(seq, list_codons, init_dict_codons, init_dict_aa, init_dict_classif, dict_genetic_code, dict_aa_classif):
+ """ Call all functions dedicated to the computation of occurences and frequencies of codons, amino-acids, amino-acids types
+
+ Args : see sub-routines
+
+ Returns : 6 dictionaries (occurences and frequencies for codons, amino-acids, amino-acids types). See sub-routines for details.
+ """
+
+ # ------ Sub-routines ------ #
+
+ def codonsCountings(seq, list_codons, init_dict_codons):
+ """ Count occurences of each codon in a sequence
+ First reading frame only : input sequence is supposed to be an ORF
+
+ Args :
+ seq (str) : the sequence
+ list_codons (list of str) : all codons except codons-stop
+ init_dict_codons (dict) : {codon1 : 0, codon2: 0, ...}
+
+ Return :
+ codon (dict) : codons (keys) and their occurences (values) in the sequence
+ """
+
+ codons = copy.deepcopy(init_dict_codons)
+
+ l = len(seq)
+
+ if l%3 == 0: max_indice = l-3
+ if l%3 == 1: max_indice = l-4
+ if l%3 == 2: max_indice = l-5
+
+ for codon in range(0,max_indice+1,3):
+ if "-" not in seq[codon:codon+3] :
+ codons[seq[codon:codon+3]] += 1
+
+ return codons
+
+ def codonsFreqs(dict_codons_counts):
+ """ Computes frequencies of each codon in a sequence
+
+ Args :
+ dict_codons (dict) : the output of codonsCounting()
+
+ Return :
+ codons_freqs (dict) : codons (keys) and their frequencies (values)
+ """
+
+ codons_freqs = {}
+
+ for key in dict_codons_counts.keys():
+ freq = float(dict_codons_counts[key])/sum(dict_codons_counts.values())
+ codons_freqs[key] = freq
+
+ return codons_freqs
+
+ def aaCountings(dict_codons, dict_genetic_code, init_dict_aa):
+ """ Count occurences of each amino-acid in a sequence, based on the countings of codons (1st ORF)
+
+ Args :
+ dict_codons (dict) : the output of codonsCounting()
+ dict_genetic_code (dict) : the genetic code : {'aa1': [codon1, codon2,...], ...}
+ init_dict_aa (dict) : {aa1 : 0, aa2: 0, ...}
+
+ Return :
+ dict_aa (dict) : amino-acids (keys) and their occurences (values)
+ """
+ dict_aa = copy.deepcopy(init_dict_aa)
+
+ for key in dict_codons.keys():
+ for value in dict_genetic_code.values():
+ if key in value:
+ dict_aa[dict_genetic_code.keys()[dict_genetic_code.values().index(value)]] += dict_codons[key]
+
+ return dict_aa
+
+ def aaFreqs(dict_aa_counts):
+ """ Computes frequencies of each amino-acid in a sequence, based on the countings of codons (1st ORF)
+
+ Args :
+ dict_aa_counts (dict) : the output of aaCountings()
+
+ Return :
+ dict_aa_freqs (dict) : amino-acids (keys) and their frequencies (values)
+ """
+
+ dict_aa_freqs = {}
+
+ for key in dict_aa_counts.keys():
+ freq = float(dict_aa_counts[key])/sum(dict_aa_counts.values())
+ dict_aa_freqs[key] = freq
+
+ return dict_aa_freqs
+
+ def aatypesCountings(dict_aa, dict_aa_classif, init_dict_classif):
+ """ Computes frequencies of each amino-acid type in a sequence, based on the countings of amino-acids (1st ORF)
+
+ Args :
+ - dict_aa (dict) : the output of aaCountings()
+ - dict_aa_classif (dict) : the types of the amino-acids ( {type: [aa1, aa2, ...], ...} )
+ - init_dict_classif (dict) : {'polar': 0, 'apolar': 0, ...}
+
+ Return :
+ dict_aatypes (dict) : amino-acids types (keys) and their occurences (values)
+ """
+ dict_aatypes = copy.deepcopy(init_dict_classif)
+
+ for key_classif in dict_aa_classif.keys():
+ for key_aa in dict_aa.keys():
+ if key_aa in dict_aa_classif[key_classif]:
+ dict_aatypes[key_classif] += dict_aa[key_aa]
+
+ return dict_aatypes
+
+ def aatypesFreqs(dict_aatypes):
+ """ Computes frequencies of each amino-acid type in a sequence, based on the countings of amino-acids (1st ORF)
+
+ Args :
+ dict_aatypes (dict) : the output of aatypesCountings()
+
+ Return :
+ dict_aatypes_freqs : amino-acids types (keys) and their frequencies (values)
+ """
+ dict_aatypes_freqs = {}
+
+ for key in dict_aatypes.keys():
+ freq = float(dict_aatypes[key])/sum(dict_aatypes.values())
+ dict_aatypes_freqs[key] = freq
+
+ return dict_aatypes_freqs
+
+ # ------ The function ------ #
+
+ codons_c = codonsCountings(seq, list_codons, init_dict_codons)
+ codons_f = codonsFreqs(codons_c)
+ aa_c = aaCountings(codons_c, dict_genetic_code, init_dict_aa)
+ aa_f = aaFreqs(aa_c)
+ aat_c = aatypesCountings(aa_c, dict_aa_classif, init_dict_classif)
+ aat_f = aatypesFreqs(aat_c)
+
+ return codons_c, codons_f, aa_c, aa_f, aat_c, aat_f
+
+# # # Functions for various measures (ivywrel, ekqh...) -------------------------------------------------------------------------
+
+def computeVarious(seq, dict_aa_counts, dict_aa_types):
+ """ Call al the functions for nucleic and amino-acids sequences description
+
+ Args : See sub-routines for details.
+
+ Returns : 6 integer or floats. See sub-routines for details.
+ """
+
+ # ------ Sub-routines ------ #
+
+ def nbCodons(seq):
+ """ Compute the number of full codons in a sequence
+ Arg : seq (str): the sequence
+ Return: nb_codons (int)
+ """
+ l = len(seq)
+ if l%3 == 0: nb_codons = l/3
+ if l%3 == 1: nb_codons = (l-1)/3
+ if l%3 == 2: nb_codons = (l-2)/3
+ return nb_codons
+
+ def maxIndice(seq):
+ """ Compute the highest indice for parsing a sequence
+ Arg : seq (str): the sequence
+ Return : max_indice (int)
+ """
+ l = len(seq)
+ if l%3 == 0: max_indice = l-3
+ if l%3 == 1: max_indice = l-4
+ if l%3 == 2: max_indice = l-5
+ return max_indice
+
+ def gc12Andgc3Count(seq, nb_codons, max_indice):
+ """ Compute the frequency of gc12 in a sequence
+ Arg : seq (str) : the sequence
+ Return : (float)
+ """
+
+ # TO IMPROVE ? : make this computation in the codonCountigns() function to avoid parsing twice the sequence ?
+ # But : involves a less readable code
+
+ gc12 = 0
+ gc3 = 0
+
+ for i in range(0, max_indice+1,3):
+ if seq[i] in ["c","g"]: gc12 += 1
+ if seq[i+1] in ["c","g"]: gc12 += 1
+ if seq[i+2] in ["c","g"] or seq[i+2] in ["c","g"]: gc3 += 1
+
+ return float(gc3)/nb_codons, float(gc12)/(2*nb_codons)
+
+ def ivywrelCount(nb_codons, dict_aa_counts):
+ """ Compute the sum of occurences of amino-acids IVYWREL divided by the number of codons
+
+ Args :
+ nb_codons (int) : the number of codons in the sequence
+ dict_aa_counts (dict) : the output of aaCountings()
+
+ return : (float)
+ """
+
+ IVYWREL = 0
+
+ for aa in ["I","V","Y","W","R","E","L"]: # Impossible to make a simple sum, in case one the aa is not in the dict keys
+ if aa in dict_aa_counts.keys():
+ IVYWREL += dict_aa_counts[aa]
+
+ return float(IVYWREL)/nb_codons
+
+ def ekqhCount(dict_aa_counts):
+ """ Compute the ratio of amino-acids EK/QH
+ Arg : dict_aa_counts (dict) : the output of aaCountings()
+ Return : (float)
+ """
+ ek = 0
+ qh = 0
+
+ ek = dict_aa_counts["E"] + dict_aa_counts["K"]
+ qh = dict_aa_counts["Q"] + dict_aa_counts["H"]
+
+ if qh != 0:
+ return float(ek)/qh
+ else : return ek
+
+ def payresdgmCount(dict_aa_counts):
+ """ Compute the ratio of amino-acids PASRE/SDGM
+ Arg : dict_aa_counts (dict) : the output of aaCountings()
+ Return : (float)
+ """
+ payre = 0
+ sdgm = 0
+
+ for aa in ["P","A","Y","R","E"]:
+ payre += dict_aa_counts[aa]
+ for aa in ["S","D","G","M"]:
+ sdgm += dict_aa_counts[aa]
+
+ if sdgm != 0:
+ return float(payre)/sdgm
+ else : return payre
+
+ def purineLoad(seq, nb_codons):
+ """ Compute the purine load indice of a sequence
+ Args :
+ seq (str) : the sequence
+ nb_codons (int) : the number of codons in the sequence
+
+ Return (float)
+ """
+
+ # TO IMPROVE ? : make this computation in the codonCountigns() function to avoid parsing twice the sequence ?
+ # But : involves a less readable code
+
+ g12, g3, A, c12, c3, T = 0.0,0.0,seq.count("a"),0.0,0.0,seq.count("t")
+
+ # g3 and c3 : g and c in 3rd position of a codon
+ s = ""
+ for i in range(2, len(seq), 3):
+ s += seq[i]
+ g3 = s.count("g")
+ c3 = s.count("c")
+
+ # g12 and c12 : g and c in 1st and 2d positions of a codon
+ s = ""
+ for i in range(0, len(seq), 3):
+ s += seq[i]
+ g12 = s.count("g")
+ c12 = s.count("c")
+ s = ""
+ for i in range(1, len(seq), 3):
+ s += seq[i]
+ g12 += s.count("g")
+ c12 += s.count("c")
+
+ return float(1000*(g12+g3+A-c12-c3-T))/(3*nb_codons)
+
+ def cvp(dict_aatypes):
+ """ Compute the difference nb_charged_aamino_acids - nb_polar_amino_acids
+ Return: (int)
+ """
+ return dict_aatypes["charged"] - dict_aatypes["polar"]
+
+ # ------ The function ------ #
+
+ nb_codons = nbCodons(seq)
+ max_indice = maxIndice(seq)
+ GC3, GC12 = gc12Andgc3Count(seq, nb_codons, max_indice)
+ IVYWREL, EKQH, PAYRESDGM = ivywrelCount(nb_codons, dict_aa_counts), ekqhCount(dict_aa_counts), payresdgmCount(dict_aa_counts)
+ purineload, CvP = purineLoad(seq, nb_codons), cvp(dict_aa_types)
+ return GC3, GC12, IVYWREL, EKQH, PAYRESDGM, purineload, CvP
+
+# # # Function for codons, aa, aatypes Transitions -----------------------------------------------------------------------------
+
+def computeAllBiases(seq1, seq2, dico_codons_transi, dico_aa_transi, dico_aatypes_transi, reversecode, reverseclassif) :
+ """ Compute all biases (transisitions codon->codon, aa->-aa, aa_type->aa_type) between two sequences
+
+ Args : See sub-routines for details
+
+ Returns 3 dictionaries of dictionaries. See sub-routines for details
+ """
+
+ # ------ Sub-routines ------ #
+
+ def codons_transitions(seq1, seq2, dico_codons_transi):
+ """ Compute the number of transitions from a codon of a sequence to the codon of a second sequence
+
+ Args :
+ seq1 (str) : the first sequence
+ seq2 (str) : the second sequence
+ dico_codons_transi (dict of dicts) : { codon1 : {codon1: 0, codon2 : 0, ...}, ..}
+
+ Return :
+ codons_transi (dict of dicts) : the occurences of each codon to codon transition
+ """
+
+ codons_transi = copy.deepcopy(dico_codons_transi)
+
+ for i in range(0, len(seq1), 3):
+ # check if no indel and if len seq[i:i+3] is really 3 (check for the last codon)
+ if viable([seq1, seq2], i, "any") and len(seq1[i:i+3]) == 3 and len(seq2[i:i+3]) == 3 :
+ codons_transi[seq1[i:i+3]][seq2[i:i+3]] += 1
+
+ return codons_transi
+
+ def codons_transitions_freqs(codons_transitions_counts):
+ """ Computes frequencies of codon transitions between two sequences
+
+ Arg :
+ codons_transitions_counts (dict) : the output of codons_transitions()
+
+ Return :
+ codons_transi_freqs (dict of dicts) : the frequencies of each codon to codon transition
+ """
+
+ codons_transi_freqs = {}
+
+ for key in codons_transitions_counts.keys():
+ codons_transi_freqs[key] = {}
+ for key2 in codons_transitions_counts[key].keys():
+ if sum(codons_transitions_counts[key].values()) != 0:
+ freq = float(codons_transitions_counts[key][key2])/sum(codons_transitions_counts[key].values())
+ codons_transi_freqs[key][key2] = freq
+ else :
+ codons_transi_freqs[key][key2] = 0
+ return codons_transi_freqs
+
+ def aa_transitions(dico_codons_transi, dico_aa_transi, reversecode):
+ """ Compute the number of transitions from an amino-acid of a sequence to the amino-acid of a second sequence
+
+ Args :
+ dico_codons_transi (dict of dicts) : the codons transitions computed by codons_transitions()
+ dico_aa_transi (dict of dicts) : { aa1 : {aa1: 0, aa2 : 0, ...}, ..}
+ reversecode (dict) : the reversed genetic code {aa1 : [codons],...} -> {codon1: aa1, codon2: aa2, ...}
+
+ Return :
+ aa_transi (dict of dicts) : the occurences of each aa to aa transition
+ """
+
+ aa_transi = copy.deepcopy(dico_aa_transi)
+
+ for k in dico_codons_transi.keys():
+ newk = reversecode[k]
+ for k2 in dico_codons_transi[k].keys():
+ newk2 = reversecode[k2]
+ aa_transi[newk][newk2] += dico_codons_transi[k][k2]
+
+ return aa_transi
+
+ def aa_transitions_freqs(aa_transitions_counts):
+ """ Computes frequencies of amico-acids transitions between two sequences
+ Arg : aa_transitions_counts (dict of dicts): the output of aa_transitions()
+ Return : aa_transi_freqs (dict of dicts) : the frequencies of each aa to aa transition
+ """
+
+ aa_transi_freqs = {}
+
+ for key in aa_transitions_counts.keys():
+ aa_transi_freqs[key] = {}
+ for key2 in aa_transitions_counts[key].keys():
+ if sum(aa_transitions_counts[key].values()) != 0:
+ freq = float(aa_transitions_counts[key][key2])/sum(aa_transitions_counts[key].values())
+ aa_transi_freqs[key][key2] = freq
+ else :
+ aa_transi_freqs[key][key2] = 0
+ return aa_transi_freqs
+
+ def aatypes_transitions(dico_aa_transi, dico_aatypes_transi, reverseclassif):
+ """ Compute the number of transitions from an amino-acid type of a sequence to the amino-acid type of a second sequence
+
+ Args :
+ dico_aa_transi (dict of dicts) : the output of aa_transitions()
+ dico_aatypes_transi (dict of dicts) : { type1 : {type1: 0, type2 : 0, ...}, ..}
+ reverseclassif (dict) : the reversed amino-acid clasification {aa1: type, aa2: type, ...}
+
+ Return :
+ aatypes_transi (dict of dicts) : the occurences of each aatype to aatype transition
+ """
+
+ aatypes_transi = copy.deepcopy(dico_aatypes_transi)
+ for k in dico_aa_transi.keys():
+ newk = reverseclassif[k]
+ for k2 in dico_aa_transi[k].keys():
+ newk2 = reverseclassif[k2]
+ aatypes_transi[newk][newk2] += dico_aa_transi[k][k2]
+
+ return aatypes_transi
+
+ def aatypes_transitions_freqs(aatypes_transitions_counts):
+ """ Computes frequencies of amico-acids types transitions between two sequences
+ Args : aatypes_transitions_counts (dict of dicts) : the output of aatypes_transitions()
+ Return : aatypes_transi_freqs (dict of dicts) : the frequencies of each aatype to aatype transition
+ """
+
+ aatypes_transi_freqs = {}
+
+ for key in aatypes_transitions_counts.keys():
+ aatypes_transi_freqs[key] = {}
+ for key2 in aatypes_transitions_counts[key].keys():
+ if sum(aatypes_transitions_counts[key].values()) != 0:
+ freq = float(aatypes_transitions_counts[key][key2])/sum(aatypes_transitions_counts[key].values())
+ aatypes_transi_freqs[key][key2] = freq
+ else :
+ aatypes_transi_freqs[key][key2] = 0
+ return aatypes_transi_freqs
+
+
+
+
+ # ------ The function ------ #
+
+ codons_transitions = codons_transitions(seq1, seq2, dico_codons_transi)
+ codons_transitions_freqs = codons_transitions_freqs(codons_transitions)
+ aa_transitions = aa_transitions(codons_transitions, dico_aa_transi, reversecode)
+ aa_transitions_freqs = aa_transitions_freqs(aa_transitions)
+ aatypes_transitions = aatypes_transitions(aa_transitions, dico_aatypes_transi, reverseclassif)
+ aatypes_transitions_freqs = aatypes_transitions_freqs(aatypes_transitions)
+
+ return codons_transitions, codons_transitions_freqs, aa_transitions, aa_transitions_freqs, aatypes_transitions, aatypes_transitions_freqs
+
+def all_sed(codons_c, aa_c, aat_c, codons_transitions, aa_transitions, aatypes_transitions, dico_codons_transi, dico_aa_transi, dico_aatypes_transi):
+
+ def compute_sed(transi, counts, dico):
+ """ Compute the substitution exchangeability disequilibrium (SED) from one species A to another B between codons/aa//aatypes couples
+
+ Args:
+ transi ; dict - dictionaries of all counts of transition from codon/aa/aatype X to Y from sp A to sp B
+ counts : dict - dictionaries of codons/aa/aatypes counts in species A
+ dico : dict - a dictionary (nested) with all values to 0
+
+ """
+ dict_sed = copy.deepcopy(dico)
+
+ for key in transi.keys():
+ for key2 in transi.keys():
+ if counts[key] != 0 and float(transi[key2][key])/counts[key] != 0.0:
+ x = (float(transi[key][key2])/counts[key]) / (float(transi[key2][key])/counts[key])
+ dict_sed[key][key2] = - pow(2,1-x)+1
+ else :
+ dict_sed[key][key2] = 'NA'
+
+ return dict_sed
+
+ codons_sed = compute_sed(codons_transitions, codons_c, dico_codons_transi)
+ aa_sed = compute_sed(aa_transitions, aa_c, dico_aa_transi)
+ aatypes_sed = compute_sed(aatypes_transitions, aat_c, dico_aatypes_transi)
+
+ return codons_sed, aa_sed, aatypes_sed
+
+# # # Function for random resampling --------------------------------------------------------------------------------------------
+
+def sampling (dict_seq, nb_iter, len_sample, list_codons, genetic_code, aa_classif, reversecode, reverseclassif):
+ """ Resample randomly codons from sequences (sort of bootsrap)
+
+ Args :
+ dict_seq (dict) : contains the species name and sequences used ( { 'sp1': seq1, 'sp2': seq2, ...}) without '-' removal
+ nb_iter (int) : number of resampling iterations (better >= 1000)
+ len_sample (int) : length (in codons) of a resampled sequence (better >= 1000)
+ list_codons (list of str): all codons except codons-stop
+ genetic_code (dict) : the genetic code : {'aa1': [codon1, codon2,...], ...}
+ aa_classif (dict) : the types of the amino-acids : {type: [aa1, aa2, ...], ...}
+ reversecode (dict) : the reversed genetic code : {codon1: aa1, codon2: aa2, ...}
+ reverseclassif (dict) : the reversed amino-acid : clasification {aa1: type, aa2: type, ...}
+
+ Returns :
+ codons_lst, aa_lst, classif_lst (dicts) : keys : codons/aa/aatypes, values : []
+ codons_transitions_lst, aa_transitions_lst, classif_transitions_lst (dict of dicts) : keys : codons/aa/aatypes, values : the 3 previous dicts
+ """
+
+ # Initialize empty dictionaries for countings and transitions. It's also possible to isntanciate these ones in the main() but it would make a function with ~14 parameters
+ codons_0, aa_0, classif_0, codons_transitions_0, aa_transitions_0, classif_transitions_0 = buildDicts(list_codons, 0, genetic_code, aa_classif)
+ codons_lst, aa_lst, classif_lst, codons_transitions_lst, aa_transitions_lst, classif_transitions_lst = buildDicts(list_codons, [], genetic_code, aa_classif)
+
+ # determine the max position where sampling is possible
+ l = len(dict_seq.values()[1])
+ if l%3 == 0: max_indice = l-3
+ if l%3 == 1: max_indice = l-4
+ if l%3 == 2: max_indice = l-5
+
+ # List of positions to resample
+ viable_positions = [pos for pos in range(0,max_indice,3) if viable(dict_seq.values(), pos, "all")]
+ sample_positions = np.random.choice(viable_positions, len_sample)
+
+ # nb_iter resampled sequences
+ for i in range(nb_iter):
+ if (i+1)%(nb_iter/10) == 0:
+ print " "+str( (i+1)*100/nb_iter)+"%"
+
+ seqa, seqb = "", ""
+ for pos in sample_positions:
+ codona, codonb = "---", "---"
+ # The sequence to be resampled in this position is randomly chosen ; no "-" resampled
+ while "-" in codona :
+ codona = dict_seq.values()[random.randrange(0, len(dict_seq.keys())-1)][pos:pos+3]
+ while "-" in codonb :
+ codonb = dict_seq.values()[random.randrange(0, len(dict_seq.keys())-1)][pos:pos+3]
+ seqa += codona
+ seqb += codonb
+
+ # dictionaries : frequences of codons, aa, aatypes (seq1)
+ codons_occ_tmp, codons_freq_tmp, aa_occ_tmp, aa_freq_tmp, aatypes_occ_tmp, aatypes_freq_tmp = computeAllCountingsAndFreqs(seqa, list_codons, codons_0, aa_0, classif_0, genetic_code, aa_classif)
+ # dictionaries frequences of transitions (seqa->seqb)
+ codons_transitions_tmp, codons_transitions_freq_tmp, aa_transition_tmp, aa_transitions_freq_tmp, aatypes_transitions_tmp, aatypes_transitions_freq_tmp = computeAllBiases(seqa, seqb, codons_transitions_0, aa_transitions_0, classif_transitions_0, reversecode, reverseclassif)
+
+ # Adding occurrences in final dicts
+ for key in codons_freq_tmp.keys():
+ codons_lst[key].append(codons_freq_tmp[key])
+ for key in aa_freq_tmp.keys():
+ aa_lst[key].append(aa_freq_tmp[key])
+ for key in aatypes_freq_tmp.keys():
+ classif_lst[key].append(aatypes_freq_tmp[key])
+
+ # Adding occurrences in final dicts (transitions)
+ for key in codons_transitions_freq_tmp.keys():
+ for key2 in codons_transitions_freq_tmp[key].keys():
+ codons_transitions_lst[key][key2].append(codons_transitions_freq_tmp[key][key2])
+ for key in aa_transitions_freq_tmp.keys():
+ for key2 in aa_transitions_freq_tmp[key].keys():
+ aa_transitions_lst[key][key2].append(aa_transitions_freq_tmp[key][key2])
+ for key in aatypes_transitions_freq_tmp.keys():
+ for key2 in aatypes_transitions_freq_tmp[key].keys():
+ classif_transitions_lst[key][key2].append(aatypes_transitions_freq_tmp[key][key2])
+
+ return codons_lst, aa_lst, classif_lst, codons_transitions_lst, aa_transitions_lst, classif_transitions_lst
+
+def testPvalues(dict_counts, dict_resampling, nb_iter, method):
+ """ Computes where the observed value is located in the expected counting distribution
+
+ Args :
+ dict_counts (dict) : observed frequencies obtained from the functions computeAllCountingsAndFreqs() or computeAllBiases()
+ dict_resampling (dict) : expected frequencies obtained from the functions computeAllCountingsAndFreqs() or computeAllBiases() within the sampling() function
+
+ Return :
+ pvalue (dict, dict of dicts) : the pvalues of all observed countings (dict) and transitions (dict of dicts)
+
+
+ pnorm computes the pvalue to have a value inferior to the observed value under a normal distribution
+ One sided to left tail :
+ p < 0.05 indicates significantly lower counts
+ p > 0.95 indicates significantly higher counts
+ """
+
+
+ def p_resampling(obs, values, nb_iter):
+ """ The pvalue is the proportion of bootsrapped values smaller than the observed value
+ If p = 0.025 : 2.5% of the bootstrapped values are smaller than the observed value
+ p < 0.025 : the obs value is most likely significantly lower.
+ If p = 0.975 : 97.5% of the bootstrapped values are smaller than the observed value
+ p > 0.975 the obs value is most likely significantly higher.
+
+ Args :
+ obs : int or float - the observed value
+ values : list - values of resampling (int or floats)
+ nb_iter : int - the number of resampled values (=len(values))
+
+ Return :
+ pvalue (float)
+ """
+
+ num = len([x for x in values if x < obs])
+ return float(num + 1) / (nb_iter+1)
+
+ def testPvalue(obs, exp, nb_iter):
+ """ Compute a pvalue
+
+ Args :
+ exp (list of floatsà : a list of length nb_iter, containing expected frequencies of a codon/aa/aatype at each iteration
+ obs (float) : the observed value
+ nb_iter (int) : the number of iterations for resampling
+
+ Returns :
+ pvalue (float)
+ """
+
+ max_val = nb_iter-1
+ min_val = 0
+ test_val = (max_val+min_val)/2
+
+ while max_val-min_val > 1:
+ if obs > exp[test_val]:
+ min_val = test_val
+ test_val = (max_val+min_val)/2
+ elif obs < exp[test_val]:
+ max_val = test_val
+ test_val = (max_val+min_val)/2
+ else:
+ break
+
+ pvalue = float(test_val+1)/(nb_iter+1)
+
+ return pvalue
+
+ # ------ The function ------ #
+
+ pvalues = {}
+
+ for key in dict_resampling.keys():
+ if type(dict_resampling.values()[1]) is not dict :
+ if method == 'origin':
+ pvalues[key] = testPvalue(dict_counts[key], dict_resampling[key], nb_iter)
+ elif method == 'pnorm':
+ pvalues[key] = scipy.stats.norm.cdf(dict_counts[key], np.mean(dict_resampling[key]), np.std(dict_resampling[key]))
+ elif method == 'p_resampling':
+ pvalues[key] = p_resampling(dict_counts[key], dict_resampling[key], nb_iter)
+ else :
+ pvalues[key] = {}
+ for key2 in dict_resampling[key].keys():
+ if method == 'origin':
+ pvalues[key][key2] = testPvalue(dict_counts[key][key2], dict_resampling[key][key2], nb_iter)
+ elif method == 'pnorm':
+ pvalues[key][key2] = scipy.stats.norm.cdf(dict_counts[key][key2], np.mean(dict_resampling[key][key2]), np.std(dict_resampling[key][key2]))
+ elif method == 'p_resampling':
+ pvalues[key][key2] = p_resampling(dict_counts[key][key2], dict_resampling[key][key2], nb_iter)
+
+ return pvalues
+
+def main():
+
+ # arguments
+ parser = argparse.ArgumentParser()
+ parser.add_argument("sequences_file", help="File containing sequences (the output of the tool 'ConcatPhyl'")
+ parser.add_argument("considered_species", help="The species name, separated by commas (must be the same than in the sequences_file). It is possible to consider only a subset of species.")
+ parser.add_argument("species_for_bootstrap", help="The species which will be used for bootstrapping, separated by commas. It is possible to consider only a subset of species.")
+ parser.add_argument("iteration", help="The number of iterations for bootstrapping (better if => 1000)", type=int)
+ parser.add_argument("sample_length", help="The lenght of a bootstrapped sequences (better if >= 1000", type=int)
+ args = parser.parse_args()
+
+ print "\n ------ Occurences and frequencies of codons, amino-acids, amino-acids types -------\n"
+
+ print "The script counts the number of codons, amino acids, and types of amino acids in sequences,"
+ print "as well as the mutation bias from one item to another between 2 sequences.\n"
+
+ print "Counting are then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences."
+ print "In the output files, the pvalues indicate the position of the observed data in a distribution of empirical countings obtained from"
+ print "a resample of the data. Values above 0.95 indicate a significantly higher counting, values under 0.05 a significantly lower counting."
+
+ print " Sequences file : {}".format(args.sequences_file)
+ print " Species retained for countings : {}\n".format(args.considered_species)
+
+ print "Processing : reading input file, opening output files, building dictionaries."
+
+ # make pairs
+ list_species = str.split(args.considered_species, ",")
+ list_species_boot = str.split(args.species_for_bootstrap, ",")
+ pairs_list=list(itertools.combinations(list_species,2))
+
+ # read sequences
+ sequences_for_counts = {}
+ sequences_for_resampling = {}
+ with open(args.sequences_file, "r") as file:
+ for line1,line2 in itertools.izip_longest(*[file]*2):
+ species = line1.strip(">\r\n")
+ sequence = line2.strip("\r\n")
+ if species in list_species:
+ sequences_for_counts[species] = sequence
+ if species in list_species_boot:
+ sequences_for_resampling[species] = sequence
+
+ print " Warning : countings might be biased and show high differences between species because of high variations of the indels proportions among sequences."
+ print " Frequences are more representative."
+
+ print "\n Indels percent :"
+
+ for k,v in sequences_for_counts.items():
+ print " {} : {} %".format(k, float(v.count("-"))/len(v)*100)
+
+ # useful dictionaries
+ dict_genetic_code={"F":["ttt","ttc"],
+ "L":["tta","ttg","ctt","ctc","cta","ctg"],
+ "I":["att","atc","ata"],
+ "M":["atg"],
+ "V":["gtt","gtc","gta","gtg"],
+ "S":["tct","tcc","tca","tcg","agt","agc"],
+ "P":["cct","cca","ccg","ccc"],
+ "T":["act","acc","aca","acg"],
+ "A":["gct","gcc","gca","gcg"],
+ "Y":["tat","tac"],
+ "H":["cat","cac"],
+ "Q":["caa","cag"],
+ "N":["aat","aac"],
+ "K":["aaa","aag"],
+ "D":["gat","gac"],
+ "E":["gaa","gag"],
+ "C":["tgt","tgc"],
+ "W":["tgg"],
+ "R":["cgt","cgc","cga","cgg","aga","agg"],
+ "G":["ggt","ggc","gga","ggg"]}
+
+ dict_aa_classif={"unpolar":["G","A","V","L","M","I"],
+ "polar":["S","T","C","P","N","Q"],
+ "charged":["K","R","H","D","E"],
+ "aromatics":["F","Y","W"]}
+
+ reversecode={v:k for k in dict_genetic_code for v in dict_genetic_code[k]}
+ reverseclassif={v:k for k in dict_aa_classif for v in dict_aa_classif[k]}
+
+ # codons list (without stop codons)
+ nucleotides = ['a', 'c', 'g', 't']
+ list_codons = [''.join(comb) for comb in itertools.product(nucleotides, repeat=3)]
+ list_codons.remove("taa")
+ list_codons.remove("tag")
+ list_codons.remove("tga")
+
+ # Store already computed species + row.names in output files
+ index = []
+ index_transi = []
+
+ # Final dictionaries writed to csv files
+ all_codons = {}
+ all_aa = {}
+ all_aatypes = {}
+ all_various = {}
+ all_codons_transitions = {} # Not used because too much : 61*61 columns
+ all_aa_transitions = {}
+ all_aatypes_transitions = {}
+
+ # RUN
+
+ print "\nProcessing : resampling ..."
+ print " Parameters : {niter} iterations, {lensample} codon per resampled sequence, species used : {species}\n".format(niter=args.iteration, lensample=args.sample_length, species=args.species_for_bootstrap)
+
+ codons_boot, aa_boot, aatypes_boot, codons_transi_boot, aa_transi_boot, aatypes_transi_boot = sampling(sequences_for_resampling, args.iteration, args.sample_length, list_codons, dict_genetic_code, dict_aa_classif, reversecode, reverseclassif)
+ print " Done.\n"
+
+ print "Processing : countings....\n"
+
+ # Initialize empty dictionaries for countings and transitions
+ init_dict_codons, init_dict_aa, init_dict_classif, dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions = buildDicts(list_codons, 0, dict_genetic_code, dict_aa_classif)
+
+ for pair in pairs_list:
+ p1, p2 = pair[0], pair[1]
+ if p1 not in index:
+ print "Countings on {}".format(p1)
+
+ p1_codons_counts, p1_codons_freqs, p1_aa_counts, p1_aa_freqs, p1_aatypes_counts, p1_aatypes_freqs = computeAllCountingsAndFreqs(sequences_for_counts[p1], list_codons, init_dict_codons, init_dict_aa, init_dict_classif, dict_genetic_code, dict_aa_classif)
+ p1_GC3, p1_GC12, p1_IVYWREL, p1_EKQH, p1_PAYRESDGM, p1_purineload, p1_CvP = computeVarious(sequences_for_counts[p1], p1_aa_counts, p1_aatypes_freqs)
+
+
+ p1_codons_pvalues = testPvalues(p1_codons_freqs, codons_boot, args.iteration, 'p_resampling')
+ p1_aa_pvalues = testPvalues(p1_aa_freqs, aa_boot, args.iteration, 'p_resampling')
+ p1_aatypes_pvalues = testPvalues(p1_aatypes_freqs, aatypes_boot, args.iteration, 'p_resampling')
+
+ all_codons[p1+"_obs_counts"] = p1_codons_counts
+ all_codons[p1+"_obs_freqs"] = p1_codons_freqs
+ all_codons[p1+"_pvalues"] = p1_codons_pvalues
+ all_aa[p1+"_obs_counts"] = p1_aa_counts
+ all_aa[p1+"_obs_freqs"] = p1_aa_freqs
+ all_aa[p1+"_pvalues"] = p1_aa_pvalues
+ all_aatypes[p1+"_obs_counts"] = p1_aatypes_counts
+ all_aatypes[p1+"_obs_freqs"] = p1_aatypes_freqs
+ all_aatypes[p1+"_pvalues"] = p1_aatypes_pvalues
+ all_various[p1] = [p1_GC3, p1_GC12, p1_IVYWREL, p1_EKQH, p1_PAYRESDGM, p1_purineload, p1_CvP]
+
+ index.append(p1)
+
+ if p2 not in index:
+ print "Countings on {}".format(p2)
+
+ p2_codons_counts, p2_codons_freqs, p2_aa_counts, p2_aa_freqs, p2_aatypes_counts, p2_aatypes_freqs = computeAllCountingsAndFreqs(sequences_for_counts[p2], list_codons, init_dict_codons, init_dict_aa, init_dict_classif, dict_genetic_code, dict_aa_classif)
+ p2_GC3, p2_GC12, p2_IVYWREL, p2_EKQH, p2_PAYRESDGM, p2_purineload, p2_CvP = computeVarious(sequences_for_counts[p2], p2_aa_counts, p2_aatypes_freqs)
+
+ p2_codons_pvalues = testPvalues(p2_codons_freqs, codons_boot, args.iteration, 'p_resampling')
+ p2_aa_pvalues = testPvalues(p2_aa_freqs, aa_boot, args.iteration, 'p_resampling')
+ p2_aatypes_pvalues = testPvalues(p2_aatypes_freqs, aatypes_boot, args.iteration, 'p_resampling')
+
+ all_codons[p2+"_obs_counts"] = p2_codons_counts
+ all_codons[p2+"_obs_freqs"] = p2_codons_freqs
+ all_codons[p2+"_pvalues"] = p2_codons_pvalues
+ all_aa[p2+"_obs_counts"] = p2_aa_counts
+ all_aa[p2+"_obs_freqs"] = p2_aa_freqs
+ all_aa[p2+"_pvalues"] = p2_aa_pvalues
+ all_aatypes[p2+"_obs_counts"] = p2_aatypes_counts
+ all_aatypes[p2+"_obs_freqs"] = p2_aatypes_freqs
+ all_aatypes[p2+"_pvalues"] = p2_aatypes_pvalues
+ all_various[p2] = p2_GC3, p2_GC12, p2_IVYWREL, p2_EKQH, p2_PAYRESDGM, p2_purineload, p2_CvP
+
+ index.append(p2)
+
+ if (p1, p2) not in index_transi and p1 in sequences_for_counts and p2 in sequences_for_counts:
+ print "Countings transitions between {} and {}".format(p1, p2)
+ codons_transitions, codons_transitions_freqs, aa_transitions, aa_transitions_freqs, aatypes_transitions, aatypes_transitions_freqs = computeAllBiases(sequences_for_counts[p1], sequences_for_counts[p2], dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions, reversecode, reverseclassif)
+
+ # Ajout
+ codons_sed, aa_sed, aatypes_sed = all_sed(p1_codons_counts, p1_aa_counts, p1_aatypes_counts, codons_transitions, aa_transitions, aatypes_transitions, dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions)
+
+ index_transi.append((p1,p2))
+
+ p1p2_codons_pvalues = testPvalues(codons_transitions_freqs, codons_transi_boot, args.iteration, 'p_resampling')
+ p1p2_aa_pvalues = testPvalues(aa_transitions_freqs, aa_transi_boot, args.iteration, 'p_resampling')
+ p1p2_aatypes_pvalues = testPvalues(aatypes_transitions_freqs, aatypes_transi_boot, args.iteration, 'p_resampling')
+
+ all_codons_transitions[p1+">"+p2+"_obs_counts"] = codons_transitions
+ all_codons_transitions[p1+">"+p2+"_obs_freqs"] = codons_transitions_freqs
+ all_codons_transitions[p1+">"+p2+"_pvalues"] = p1p2_codons_pvalues
+ all_aa_transitions[p1+">"+p2+"_obs_counts"] = aa_transitions
+ all_aa_transitions[p1+">"+p2+"_obs_freqs"] = aa_transitions_freqs
+ all_aa_transitions[p1+">"+p2+"_pvalues"] = p1p2_aa_pvalues
+ all_aatypes_transitions[p1+">"+p2+"_obs_counts"] = aatypes_transitions
+ all_aatypes_transitions[p1+">"+p2+"_obs_freqs"] = aatypes_transitions_freqs
+ all_aatypes_transitions[p1+">"+p2+"_pvalues"] = p1p2_aatypes_pvalues
+
+ all_codons_transitions[p1+">"+p2+"_sed"] = codons_sed
+ all_aa_transitions[p1+">"+p2+"_sed"] = aa_sed
+ all_aatypes_transitions[p1+">"+p2+"_sed"] = aatypes_sed
+
+ index_transi.append((p1, p2))
+
+ print "\n Done.\n"
+
+ print "Processing : creating dataframes ..."
+
+ frame_codons = pd.DataFrame(all_codons).T.astype('object')
+ frame_aa = pd.DataFrame(all_aa).T.astype('object')
+ frame_aatypes = pd.DataFrame(all_aatypes).T.astype('object')
+
+ frame_codons_transitions = pd.concat({k: pd.DataFrame(v) for k, v in all_codons_transitions.items()}).unstack()
+ frame_codons_transitions.columns = frame_codons_transitions.columns.map('>'.join)
+
+ frame_aa_transitions = pd.concat({k: pd.DataFrame(v) for k, v in all_aa_transitions.items()}).unstack()
+ frame_aa_transitions.columns = frame_aa_transitions.columns.map('>'.join)
+
+ frame_aatypes_transitions = pd.concat({k: pd.DataFrame(v) for k, v in all_aatypes_transitions.items()}).unstack()
+ frame_aatypes_transitions.columns = frame_aatypes_transitions.columns.map('>'.join)
+
+ frame_various = pd.DataFrame(all_various).T
+ frame_various.columns = ["GC3","GC12","IVYWREL","EKQH","PAYRESDGM","purineload", "CvP"]
+
+ frame_codons.index.name, frame_aa.index.name, frame_aatypes.index.name = "Species", "Species","Species"
+ frame_aa_transitions.index.name, frame_aatypes_transitions.index.name, frame_various.index.name = "Species","Species","Species"
+
+ print "Writing dataframes to output files ...\n"
+
+ frame_codons.round(8).to_csv("codons_freqs.csv", sep=",", encoding="utf-8")
+ frame_aa.round(8).to_csv("aa_freqs.csv", sep=",", encoding="utf-8")
+ frame_aatypes.astype('object').round(8).to_csv("aatypes_freqs.csv", sep=",", encoding="utf-8")
+ frame_codons_transitions.round(8).to_csv("codons_transitions_freqs.csv", sep=",", encoding="utf-8")
+ frame_aa_transitions.round(8).to_csv("aa_transitions_freqs.csv", sep=",", encoding="utf-8")
+ frame_aatypes_transitions.round(8).to_csv("aatypes_transitions_freqs.csv", sep=",", encoding="utf-8")
+ frame_various.round(8).to_csv("gc_and_others_freqs.csv", sep=",", encoding="utf-8")
+
+ print "Done."
+
+if __name__ == "__main__":
+ main()
\ No newline at end of file
diff -r 000000000000 -r acc3674e515b scripts/S01b_extract_variable_nuc.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/S01b_extract_variable_nuc.py Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,121 @@
+#!/usr/bin/env python
+#coding: utf-8
+
+import argparse, os
+from functions import dico, write_output, fill_with_NaN
+
+""" Functions for nucleic format """
+
+def all_nuc_counts(seq):
+ """ Counts the number of nucleotides in a sequence
+
+ Args :
+ - seq (String) : a nucleic sequence
+
+ Return:
+ - nuc_counts (dict) : counts on nucleotides (key/value : nucleotide/count)
+ """
+ nuc_counts = {}
+ seqU = seq.upper()
+ LN =['A','C','T','G']
+
+ for base in LN:
+ nuc_counts[base] = seqU.count(base)
+
+ return nuc_counts
+
+def ratios(nuc_counts):
+ """ Compute GC and purine ratios from the counts of nucleotides in a sequence
+
+ Args :
+ - nuc_counts (dict) : dictionary of nucleotides counts (output of all_nuc_counts())
+
+ Return :
+ - ratios (dict) : dictionary with ratios
+ """
+
+ # Search for compositional bias in genome as marker of thermal adaptation
+ ratios = {}
+ ratios['GC_percent'] = float(nuc_counts['C'] + nuc_counts['G'])/(sum(nuc_counts.values())*100)
+ ratios['purine_percent'] = float(nuc_counts['A'] + nuc_counts['G'])/(sum(nuc_counts.values())*100)
+
+ ratios['DIFF_GC'] = nuc_counts['G'] - nuc_counts['C']
+ ratios['DIFF_AT'] = nuc_counts['A'] - nuc_counts['T']
+
+ # Per bp
+ ratios['PLI_GC'] = float(ratios['DIFF_GC'])/sum(nuc_counts.values())
+ ratios['PLI_AT'] = float(ratios['DIFF_AT'])/sum(nuc_counts.values())
+
+ # Per 1000 bp
+ ratios['PLI_GC_1000'] = ratios['PLI_GC']*1000
+ ratios['PLI_AT_1000'] = ratios['PLI_AT']*1000
+
+ return ratios
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument("species_list", help="List of species separated by commas")
+ args = parser.parse_args()
+
+ LN =['A','C','T','G']
+ Lratios = ['GC_percent', 'purine_percent', 'DIFF_GC', 'DIFF_AT', 'PLI_GC', 'PLI_AT', 'PLI_GC_1000', 'PLI_AT_1000']
+
+ list_inputs = []
+
+ path_inputs = '01_input_files'
+ list_inputs = os.listdir(path_inputs)
+
+ lsp = args.species_list.split(',')
+ lsp = sorted(lsp)
+ flsp = ''
+ for el in lsp:
+ flsp += el+','
+
+ path_outputs_1 = '02_tables_per_nucleotide'
+ path_outputs_2 = '02_tables_per_nuc_variable'
+ os.mkdir(path_outputs_1)
+ os.mkdir(path_outputs_2)
+
+ dict_for_files_nuc = {}
+ dict_for_file_var = {}
+
+ # All counts
+ for file in list_inputs:
+ # iterate over input files
+ sequences = dico(file, path_inputs)
+
+ # TEMPORARY CORRECTION FOR SEQUENCES CONTAINING ONLY INDELS
+ # It appears than CDS_Search can bug sometimes and return an alignement where a species' sequence is made of indels only
+ # This causes a crash here (in the ratios function). The correction skip the whole file.
+ # When CDS_Search is corrected, lines with 'skip' can be removed
+ skip = False
+ for key in sequences.keys():
+ if all(x == '-' for x in sequences[key]):
+ skip = True
+
+ if not skip:
+
+ nuc_counts_per_seq = {}
+ nuc_var_per_seq = {}
+
+ for key in sequences.keys():
+ # iterate over sequences in the file
+ nuc_counts_per_seq[key] = all_nuc_counts(sequences[key])
+ nuc_var_per_seq[key] = ratios(nuc_counts_per_seq[key])
+
+ # Add NaN for missing species
+ for key in set(lsp).difference(set(sequences.keys())):
+ nuc_counts_per_seq[key] = fill_with_NaN(LN)
+ nuc_var_per_seq[key] = fill_with_NaN(Lratios)
+
+ # Add computations to final dicts
+ dict_for_files_nuc[file] = nuc_counts_per_seq
+ dict_for_file_var[file] = nuc_var_per_seq
+
+
+ # Try with pandas ?
+ write_output(LN, flsp, path_outputs_1, dict_for_files_nuc) # one file per nuc
+ write_output(Lratios, flsp, path_outputs_2, dict_for_file_var) # one file per nuc_variable
+
+if __name__ == '__main__':
+ main()
diff -r 000000000000 -r acc3674e515b scripts/S01b_extract_variable_prot.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/S01b_extract_variable_prot.py Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,321 @@
+#!/usr/bin/env python
+#coding: utf-8
+#Author : Eric Fontanillas (2010) - Victor Mataigne (2018)
+
+# TODO :
+ # - Deal with missing data : do not do the sign test if missing species in a group
+ # - Find a way to avoid the list_species argument
+
+import argparse, os
+from functions import dico, write_output, fill_with_NaN
+
+def aa_properties(amino_acids_properties_file):
+ """ Read the file 'amino_acids_properties' and stores its content
+
+ Args :
+ amino_acids_properties_file (String) : the file
+
+ Return :
+ aa_properties (dict) : key/amino-acid - value/list of properties
+ """
+
+ dict_aa_properties={}
+ with open(amino_acids_properties_file, 'r') as f:
+ f.readline() #jump headers
+ for line in f.readlines():
+ S1 = line.split(",")
+ aa_name = S1[1]
+ S2 = aa_name.split("/")
+ aa_code = S2[1][:-1]
+
+ frequencies = S1[2][:-1]
+ residue_weight = S1[5]
+ residue_volume = S1[6]
+ partial_specific_volume = S1[7]
+ hydration = S1[8]
+
+ dict_aa_properties[aa_code] = [frequencies, residue_weight, residue_volume, partial_specific_volume, hydration]
+
+ return(dict_aa_properties)
+
+""" Functions for proteic format """
+
+def all_aa_counts(seq):
+ """ Count the occurrences of all amino-acids in a sequence
+
+ Args:
+ seq (String) : a proteic sequence
+
+ Returns: a dictionary with amino-acids counts
+ """
+
+ aa_counts = {}
+ seqU = seq.upper()
+ LAA =['K','R','A','F','I','L','M','V','W','N','Q','S','T','H','Y','C','D','E','P','G']
+
+ for aa in LAA:
+ aa_counts[aa] = seqU.count(aa)
+
+ return aa_counts
+
+def all_aa_props(seq_counts):
+ """ Converts a dictionnary of counts into a dictionnary of proportions
+
+ Args:
+ seq_counts (dict) : dictionnary computed by the function all_aa_counts()
+
+ Returns: a dictionary with counts replaced by proportions
+ """
+
+ aa_props = {}
+ for key in seq_counts.keys():
+ aa_props[key] = float(seq_counts[key]) / sum(seq_counts.values())
+ return aa_props
+
+def aa_variables_counts_and_props(aa_counts):
+ """ Computes several thermostability indices (summed occurrences of some AAs, and then various ratios)
+
+ Args:
+ aa_counts (dict) : dictionnary computed by the function all_aa_counts()
+
+ Returns:
+ aa_variables_counts : a dictionary with indices values
+ aa_variables_props : a dictionary with indices proportions (ratios excluded)
+ """
+
+ # Hyperthermophile Prokaryotes criterias
+ # IVYWREL : positivelly correlated with otpimal growth
+ # ERK : (i.e. ) => positivelly correlated with optimal growth temperature
+ # ERK/DNQTSHA (or DNQTSH ??)
+ # EK/QH
+
+ # Mutationnal bias hypothesis => AT rich: favor FYMINK // GC rich: favor GARP
+ # The mutational bias model predict a linear relationship between GARP vs FYMINK
+ # ==> so if outliers to that, it means that the excess of GARP or FYMINK are not explained by the mutationnal bias model but by something else (selection ?)
+
+
+ # Hydophobicity hypothesis [should INCREASE with thermal adaptation]
+ # AL
+ # Only non-aromatic : AVLIM
+ # Only aromatic : FYW
+
+ # Charged hypothesis => positivelly correlated with optimal growth temperature
+ # All charged : RHKDE
+ # Only positive : RHK
+ # Only negative : DE
+
+ # Neutral polar hypothesis [should DECREASE with thermal adaptation]
+ # STNQ
+
+ # Fontanillas' criteria
+ # PAYRE
+ # MVGDS
+ # PAYRE/MVGDS
+
+ # Jollivet's criteria
+ # AC
+ # MVGDS
+ # AC/MVGDS
+
+ aa_variables_counts = {}
+ aa_variables_props = {}
+ len_seq = sum(aa_counts.values()) # length of the sequence
+
+ # counts of variables
+ aa_variables_counts['AC'] = aa_counts['A'] + aa_counts['C']
+ aa_variables_counts['APGC'] = aa_counts['A'] + aa_counts['P'] + aa_counts['G'] + aa_counts['C']
+ aa_variables_counts['AVLIM'] = aa_counts['A'] + aa_counts['V'] + aa_counts['L'] + aa_counts['I'] + aa_counts['M']
+ aa_variables_counts['AVLIMFYW'] = aa_variables_counts['AVLIM'] + aa_counts['F'] + aa_counts['Y'] + aa_counts['W']
+ aa_variables_counts['DE'] = aa_counts['D'] + aa_counts['E']
+ aa_variables_counts['DNQTSHA'] = aa_counts['D'] + aa_counts['N'] + aa_counts['Q'] + aa_counts['T'] + aa_counts['S'] + aa_counts['H'] + aa_counts['A']
+ aa_variables_counts['EK'] = aa_counts['E'] + aa_counts['K']
+ aa_variables_counts['ERK'] = aa_counts['E'] + aa_counts['K'] + aa_counts['K']
+ aa_variables_counts['FYMINK'] = aa_counts['F'] + aa_counts['Y'] + aa_counts['M'] + aa_counts['I'] + aa_counts['N'] + aa_counts['K']
+ aa_variables_counts['FYW'] = aa_counts['F'] + aa_counts['Y'] + aa_counts['W']
+ aa_variables_counts['GARP'] = aa_counts['G'] + aa_counts['A'] + aa_counts['R'] + aa_counts['P']
+ aa_variables_counts['IVYWREL'] = aa_counts['I'] + aa_counts['V'] + aa_counts['Y'] + aa_counts['W'] + aa_counts['R'] + aa_counts['E'] + aa_counts['L']
+ aa_variables_counts['QH'] = aa_counts['Q'] + aa_counts['H']
+ aa_variables_counts['RHK'] = aa_counts['R'] + aa_counts['H'] + aa_counts['K']
+ aa_variables_counts['RHKDE'] = aa_counts['R'] + aa_counts['H'] + aa_counts['K'] + aa_counts['D'] + aa_counts['E']
+ aa_variables_counts['STNQ'] = aa_counts['S'] + aa_counts['T'] + aa_counts['N'] + aa_counts['Q']
+ aa_variables_counts['VLIM'] = aa_counts['V'] + aa_counts['L'] + aa_counts['I'] + aa_counts['M']
+ aa_variables_counts['PAYRE'] = aa_counts['P'] + aa_counts['A'] + aa_counts['Y'] + aa_counts['R'] + aa_counts['E']
+ aa_variables_counts['MVGDS'] = aa_counts['M'] + aa_counts['V'] + aa_counts['G'] + aa_counts['D'] + aa_counts['S']
+
+ # compute proportions
+ for key in aa_variables_counts.keys():
+ aa_variables_props[key] = float(aa_variables_counts[key]) / float(len_seq)
+
+ if aa_variables_counts['DNQTSHA'] != 0:
+ ratio_ERK_DNQTSHA = float(aa_variables_counts['ERK'])/float(aa_variables_counts['DNQTSHA'])
+ else :
+ ratio_ERK_DNQTSHA = -1
+
+ if aa_variables_counts['QH'] != 0:
+ ratio_EK_QH = float(aa_variables_counts['EK'])/float(aa_variables_counts['QH'])
+ else :
+ ratio_EK_QH = -1
+
+ if aa_variables_counts['FYMINK'] != 0:
+ ratio_GARP_FYMINK = float(aa_variables_counts['EK'])/float(aa_variables_counts['FYMINK'])
+ else :
+ ratio_GARP_FYMINK = -1
+
+ if aa_variables_counts['VLIM'] != 0:
+ ratio_AC_VLIM = float(aa_variables_counts['AC'])/float(aa_variables_counts['VLIM'])
+ ratio_APGC_VLIM = float(aa_variables_counts['APGC'])/float(aa_variables_counts['VLIM'])
+ else :
+ ratio_AC_VLIM = -1
+ ratio_APGC_VLIM = -1
+
+ if aa_variables_counts['MVGDS'] != 0:
+ ratio_PAYRE_MVGDS = float(aa_variables_counts['PAYRE'])/float(aa_variables_counts['MVGDS'])
+ else :
+ ratio_PAYRE_MVGDS = -1
+
+ if aa_variables_counts['MVGDS'] != 0:
+ ratio_AC_MVGDS = float(aa_variables_counts['AC'])/float(aa_variables_counts['MVGDS'])
+ else :
+ ratio_AC_MVGDS = -1
+
+ aa_variables_counts['ratio_ERK_DNQTSHA'] = ratio_ERK_DNQTSHA
+ aa_variables_counts['ratio_EK_QH'] = ratio_EK_QH
+ aa_variables_counts['ratio_GARP_FYMINK'] = ratio_GARP_FYMINK
+ aa_variables_counts['ratio_AC_VLIM'] = ratio_AC_VLIM
+ aa_variables_counts['ratio_APGC_VLIM'] = ratio_APGC_VLIM
+ aa_variables_counts['ratio_PAYRE_MVGDS'] = ratio_PAYRE_MVGDS
+ aa_variables_counts['ratio_AC_MVGDS'] = ratio_AC_MVGDS
+
+ return aa_variables_counts, aa_variables_props
+
+def sequence_properties_from_aa_properties(aa_counts, aa_properties):
+ """ Computes a sequence properties (based on an external data file)
+
+ Args:
+ - aa_counts (dict) : counts of amino-acids in the sequence
+ - aa_properties (dict) : key/amino-acid - value/list of properties extract from the external data file
+
+ Returns:
+ - seq_props (dict) : values of the sequence properties
+ """
+
+ LS = ['total_residue_weight', 'total_residue_volume', 'total_partial_specific_volume', 'total_hydratation']
+ seq_props = {}
+
+ for i in range(1,5):
+ seq_props[LS[i-1]] = 0
+ for key in aa_counts.keys():
+ seq_props[LS[i-1]] += aa_counts[key] * float(aa_properties[key][i])
+
+ return seq_props
+
+""" Main """
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument("species_list", help="List of species separated by commas")
+ parser.add_argument("aa_properties", help="File with all amino-acids properties")
+ args = parser.parse_args()
+
+ LAA = ['K','R','A','F','I','L','M','V','W','N','Q','S','T','H','Y','C','D','E','P','G']
+ LV = ['IVYWREL','EK','ERK','DNQTSHA','QH','ratio_ERK_DNQTSHA','ratio_EK_QH','FYMINK','GARP',
+ 'ratio_GARP_FYMINK','AVLIM','FYW','AVLIMFYW','STNQ','RHK','DE','RHKDE','APGC','AC',
+ 'VLIM','ratio_AC_VLIM','ratio_APGC_VLIM']
+ LS = ['total_residue_weight', 'total_residue_volume', 'total_partial_specific_volume', 'total_hydratation']
+
+ list_inputs = []
+
+ path_inputs = '01_input_files'
+ list_inputs = os.listdir(path_inputs)
+
+ lsp = args.species_list.split(',')
+ lsp = sorted(lsp)
+ flsp = ''
+ for el in lsp:
+ flsp += el+','
+
+ path_outputs_1 = '02_tables_per_aa'
+ path_outputs_2 = '02_tables_per_aa_variable'
+ os.mkdir(path_outputs_1)
+ os.mkdir(path_outputs_2)
+
+ # Init empty dicts for results
+ dict_for_files_aa_counts = {} # counts
+ dict_for_files_aa_props = {} # proportions
+ dict_for_files_variables_counts = {}
+ dict_for_files_variables_props = {}
+ dict_for_files_seq_properties = {}
+
+ aa_properties_file = aa_properties(args.aa_properties) # read the aa_properties file
+
+ # All counts and props
+ for file in list_inputs:
+ # iterate over input files
+ sequences = dico(file, path_inputs)
+
+ # TEMPORARY CORRECTION FOR SEQUENCES CONTAINING ONLY INDELS
+ # It appears than CDS_Search can bug sometimes and return an alignement where a species' sequence is made of indels only
+ # This causes a crash here (in the ratios function). The correction skip the whole file.
+ # When CDS_Search is corrected, lines with 'skip' can be removed
+ skip = False
+ for key in sequences.keys():
+ if all(x == '-' for x in sequences[key]):
+ skip = True
+
+ if not skip:
+
+ aa_counts_per_seq = {}
+ aa_props_per_seq = {}
+ aa_variables_counts_per_seq = {}
+ aa_variables_props_per_seq = {}
+ seq_properties = {}
+
+ for key in sequences.keys():
+ # iterate over sequences in the file
+ aa_counts_per_seq[key] = all_aa_counts(sequences[key])
+ aa_props_per_seq[key] = all_aa_props(aa_counts_per_seq[key])
+ aa_variables_counts_per_seq[key], aa_variables_props_per_seq[key] = aa_variables_counts_and_props(aa_counts_per_seq[key])
+ seq_properties[key] = sequence_properties_from_aa_properties(aa_counts_per_seq[key], aa_properties_file)
+
+ # Add NaN for missing species
+ for key in set(lsp).difference(set(sequences.keys())):
+ aa_counts_per_seq[key] = fill_with_NaN(LAA)
+ aa_props_per_seq[key] = fill_with_NaN(LAA)
+ aa_variables_counts_per_seq[key] = fill_with_NaN(LV)
+ seq_properties[key] = fill_with_NaN(LS)
+
+ # Add computations to final dicts
+ dict_for_files_aa_counts[file] = aa_counts_per_seq
+ dict_for_files_aa_props[file] = aa_props_per_seq
+ dict_for_files_variables_counts[file] = aa_variables_counts_per_seq
+ dict_for_files_variables_props[file] = aa_variables_props_per_seq
+ dict_for_files_seq_properties[file] = seq_properties
+
+ # Try with pandas ?
+ write_output(LAA, flsp, path_outputs_1, dict_for_files_aa_counts) # one file per AA
+ write_output(LV, flsp, path_outputs_2, dict_for_files_variables_counts) # one file per aa_variable
+ write_output(LS, flsp, path_outputs_2, dict_for_files_seq_properties) #one file per seq properties
+
+ # { file_name1 : { seq1: {'A' : 0, 'C':0, 'E':0, ...},
+ # seq2: {'A' : 0, 'C':0, 'E':0, ...}, ...
+ # },
+ # { file_name2 : { seq1: {'A' : 0, 'C':0, 'E':0, ...},
+ # seq2: {'A' : 0, 'C':0, 'E':0, ...},
+ # },
+ # ... }
+
+ # { file_name1 : {seq1 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...},
+ # seq2 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, ...
+ # },
+ # file_name2 : {seq1 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...},
+ # seq2 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...},
+ # },
+ # ... }
+
+ # { file_name1 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...},
+ # file_name2 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...},
+ # ...
+ # }
+
+if __name__ == '__main__':
+ main()
diff -r 000000000000 -r acc3674e515b scripts/S02b_extreme_2states.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/S02b_extreme_2states.py Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,159 @@
+#!/usr/bin/env python
+#coding: utf-8
+#Author : Eric Fontanillas (2010) - Victor Mataigne (2018)
+
+import pandas as pd
+import argparse, os
+
+def loop_on_elems(list_of_elems, path_in, path_out, sps_group_1, sps_group_2, colnames):
+
+ # sub-routine
+
+ def tableu(fileu, sps_group_1, sps_group_2):
+ """ a
+
+ Args :
+ fileu : input file with counts of AAs / AAs types per orthogorup
+ sps_group_1 : species for condition 1 (ex : hot water species)
+ sps_group_2 : species for condition 2 (ex : cold water species)
+
+ Returns :
+ greater_dict :
+ lower_dict :
+
+ """
+ df = pd.read_csv(fileu, sep=',', index_col=0, header=0)
+ # species = list(df) #columns names = species names
+
+ # initialize counts
+ greater_dict = {}
+ lower_dict = {}
+
+ for specie in sps_group_1+sps_group_2:
+ greater_dict[specie] = 0
+ lower_dict[specie] = 0
+
+ #nb_trials = 0
+ for (index, row) in df.iterrows():
+ # min and max counts for each condition
+ if not df.loc[index, sps_group_1+sps_group_2].isnull().values.any() :
+ #nb_trials += 1
+
+ max_cat1 = max(df.loc[index, sps_group_1]) # species in category 1 (ex : hots)
+ min_cat1 = min(df.loc[index, sps_group_1])
+ max_cat2 = max(df.loc[index, sps_group_2]) # species in category 2 (ex : colds)
+ min_cat2 = min(df.loc[index, sps_group_2])
+
+ for specie in sps_group_1:
+ if df.loc[index, specie] > max_cat2 :
+ greater_dict[specie] += 1
+ elif df.loc[index, specie] < min_cat2 :
+ lower_dict[specie] += 1
+
+ for specie in sps_group_2:
+ if df.loc[index, specie] > max_cat1 :
+ greater_dict[specie] += 1
+ elif df.loc[index, specie] < min_cat1 :
+ lower_dict[specie] += 1
+
+ return greater_dict, lower_dict#, nb_trials
+
+ # Function ------------------------------------------------------
+
+ for variable in list_of_elems:
+ print 'Processing : {} ...'.format(variable)
+ file_in = "{}/{}.csv".format(path_in, variable)
+ file_out = open('{}/{}.csv'.format(path_out,variable), 'w')
+
+ # Compute succeses and fails on each variable
+ greater_dict, lower_dict = tableu(file_in, sps_group_1, sps_group_2)
+
+ # totals and diffs
+ diff_dict = {}
+ total_dict = {}
+ for key in greater_dict.keys():
+ diff_dict[key] = greater_dict[key] - lower_dict[key]
+ total_dict[key] = greater_dict[key] + lower_dict[key]
+ #total_dict[key] = number_trials
+
+ # results frame
+ df = pd.DataFrame([greater_dict, lower_dict, diff_dict, total_dict])
+ df = df.rename({0:'Greater',1:'Lower',2:'Difference',3:'Trial_Number'}) #, axis='index' if pandas 0.15
+ df = df.rename(index=str, columns=colnames)
+
+ df.to_csv("{}/{}.csv".format(path_out, variable), sep=",", encoding="utf-8")
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument("sps_group_1", help="List of species separated by commas")
+ parser.add_argument("sps_group_2", help="List of species separated by commas")
+ parser.add_argument("format", choices=['nucleic', 'proteic'], help="input files format")
+ args = parser.parse_args()
+
+ # used only if format = nucleic
+ LN =['A','C','T','G']
+ Lratios = ['GC_percent', 'purine_percent', 'DIFF_GC', 'DIFF_AT', 'PLI_GC', 'PLI_AT', 'PLI_GC_1000', 'PLI_AT_1000']
+
+ # used only if format = proteic
+ LAA =['K','R','A','F','I','L','M','V','W','N','Q','S','T','H','Y','C','D','E','P','G']
+ LV = ['IVYWREL','EK','ERK','DNQTSHA','QH','ratio_ERK_DNQTSHA','ratio_EK_QH','FYMINK','GARP',
+ 'ratio_GARP_FYMINK','AVLIM','FYW','AVLIMFYW','STNQ','RHK','DE','RHKDE','APGC','AC',
+ 'VLIM','ratio_AC_VLIM','ratio_APGC_VLIM']
+ LS = ['total_residue_weight', 'total_residue_volume', 'total_partial_specific_volume', 'total_hydratation']
+
+ # inputs and outputs paths
+ if args.format == 'nucleic':
+ input_path_elem = '02_tables_per_nucleotide'
+ input_path_var = '02_tables_per_nuc_variable'
+ out_path_elem = '03_tables_counts_signTest_nucleotides'
+ out_path_var = '03_tables_counts_signTest_nuc_variables'
+ elif args.format == 'proteic':
+ input_path_elem = '02_tables_per_aa'
+ input_path_var = '02_tables_per_aa_variable'
+ out_path_elem = '03_tables_counts_signTest_aa'
+ out_path_var = '03_tables_counts_signTest_aa_variables'
+
+ os.mkdir(out_path_elem)
+ os.mkdir(out_path_var)
+
+ sps_group_1 = args.sps_group_1.split(',')
+ sps_group_2 = args.sps_group_2.split(',')
+
+ # Prepare colnames for final frames
+ colnames = {}
+ # for specie in sps_group_1:
+ # colnames[specie] = '{}_vs_condition_1'.format(specie)
+ # for specie in sps_group_2:
+ # colnames[specie] = '{}_vs_condition_2'.format(specie)
+
+ for specie in sps_group_1:
+ colnames[specie] = '{}_vs_{}'.format(specie, args.sps_group_2.replace(',',''))
+ for specie in sps_group_2:
+ colnames[specie] = '{}_vs_{}'.format(specie, args.sps_group_1.replace(',',''))
+
+ # Building tables
+ if args.format == 'nucleic':
+ loop_on_elems(LN, input_path_elem, out_path_elem, sps_group_1, sps_group_2, colnames)
+ loop_on_elems(Lratios, input_path_var, out_path_var, sps_group_1, sps_group_2, colnames)
+ elif args.format == 'proteic':
+ loop_on_elems(LAA, input_path_elem, out_path_elem, sps_group_1, sps_group_2, colnames)
+ loop_on_elems(LV, input_path_var, out_path_var, sps_group_1, sps_group_2, colnames)
+ loop_on_elems(LS, input_path_var, out_path_var, sps_group_1, sps_group_2, colnames)
+
+ # Final R script launching sign test
+ print 'Processing : binomial sign tests ...'
+
+ if args.format == 'nucleic':
+ final_output_elem = '04_outputs_nucleotides'
+ final_output_var = '04_outputs_nuc_variables'
+ elif args.format == 'proteic':
+ final_output_elem = '04_outputs_aa'
+ final_output_var = '04_outputs_aa_variables'
+
+ os.mkdir(final_output_elem)
+ os.mkdir(final_output_var)
+ os.system('Rscript S03b_sign_test_binomial.R --indir %s --outdir %s' %(out_path_elem, final_output_elem))
+ os.system('Rscript S03b_sign_test_binomial.R --indir %s --outdir %s' %(out_path_var, final_output_var))
+
+if __name__ == '__main__':
+ main()
diff -r 000000000000 -r acc3674e515b scripts/S03b_sign_test_binomial.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/S03b_sign_test_binomial.R Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,56 @@
+#!/usr/bin/env Rscript
+#coding: utf-8
+#Author : Eric Fontanillas (2010) - Victor Mataigne (2018)
+
+# binom test - null hypothesis :
+# The test computes the number of times where the value of the variable A is higher to the value of the variable B.
+# Under the null hypothesis, there is no difference between variables : A > B in 50% of the trials
+
+options(warn = -1)
+
+library(optparse)
+
+option_list = list(
+ make_option(c('-i', '--indir'), type='character', default=NULL, help='input directory name', metavar='character'),
+ make_option(c('-o', '--outdir'), type='character', default=NULL, help='output directory name', metavar='character')
+);
+
+opt_parser = OptionParser(option_list=option_list);
+opt = parse_args(opt_parser);
+path_IN <- opt$indir
+path_OUT <- opt$outdir
+files_OUT <- paste(path_OUT,"/*",sep='')
+unlink(files_OUT) ### clean the path_OUT folder from previous files
+list_files <- list.files(path_IN)
+
+# iterate over file
+for(file in list_files){
+ name_OUT = paste(path_OUT,"/", file, sep='')
+ name_IN = paste(path_IN,"/", file, sep='')
+
+ b <- read.table(name_IN, sep=",", header=T, row.names=1)
+
+ supplemental_cells <- matrix(0, nrow=4, ncol=ncol(b))
+ colnames(supplemental_cells) <- colnames(b)
+ row.names(supplemental_cells) <- c('p-value', 'probability_of_success', 'confidence_interval_low', 'confidence_interval_high')
+
+ # iterate over species groups
+ for (i in 1:ncol(b)) {
+ if (b[4,i] != 0) {
+ binom_test <- binom.test(b[1,i], b[4,i])
+ supplemental_cells[1,i] <- binom_test$p.value
+ supplemental_cells[2,i] <- binom_test$estimate
+ supplemental_cells[3,i] <- binom_test$conf.int[1]
+ supplemental_cells[4,i] <- binom_test$conf.int[2]
+ } else {
+ supplemental_cells[1,i] <- NA
+ supplemental_cells[2,i] <- NA
+ supplemental_cells[3,i] <- NA
+ supplemental_cells[4,i] <- NA
+ }
+ }
+
+ final <- rbind(b, supplemental_cells)
+ write.csv(final, file=name_OUT)
+}
+
diff -r 000000000000 -r acc3674e515b scripts/amino_acid_properties.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/amino_acid_properties.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,21 @@
+Groups,Amino Acid (Codes),Frequency,Genetic Codons,Substitution Probabilities (each > sign = factor of 10> than random chance),Residue Weight(Mr) (UNIT:Daltons),Residue Volume(Vr) (UNIT:cubic Angstroms),Partial Specific Volume(vr) (UNIT:cc/g),Hydration(hr)(UNIT:moles/mole),R-Group pKa,Extinction Coefficient @ maximum wavelength
+Acidic R-groups,Aspartate (Asp/D),5.30%,GAU/GAC,E>N Q>G H,114.08,91,0.6,6,4.5,
+Acidic R-groups,Glutamate (Glu/E),6.20%,GAA/GAG,D>Q>HN,128.11,109,0.66,7.5,4.6,
+Basic R-groups,Lysine (Lys/K),5.70%,AAA/AAG,R >> N Q,129.19,135,0.82,4.5,10.4,
+Basic R-groups,Arginine (Arg /R),5.70%,CGU/CGC/CGA/CGG/AGA/AGG,K>WH>Q,157.2,148,0.7,3,~12,
+Basic R-groups,Histidine (His /H),2.30%,CAU/CAC,Q>NR>DE,138.16,118,0.67,4,6.2,5860 @ 211.3
+Polar Uncharged (No H-bonding),Glycine (Gly /G),7.20%,GGU/GGC/GGA/GGG,ADS,57.07,48,0.64,1,,
+Polar Uncharged (H-bonding),Serine (Ser /S),6.90%,UCU/UCC/UCA/UCG/AGU/AGC,AGNPT,87.09,73,0.74,2,,
+Polar Uncharged (H-bonding),Threonine (Thr /T),5.80%,ACU/ACC/ACA/ACG,AS,101.12,93,0.7,2,,
+Polar Uncharged (H-bonding),Cysteine (Cys /C),1.70%,UGU/UGC,none,103.15,86,0.61,1,9.1 to 9.5,
+Polar Uncharged (H-bonding),Tyrosine (Tyr /Y),3.20%,UAU/UAC,F >>>>>>,163.12,141,0.61,3,9.6,1420 @ 274.6
+Polar Uncharged (H-bonding),Asparagine (Asn /N),4.40%,AAU/AAC,D H >K,114.1,96,0.62,2,,
+Polar Uncharged (H-bonding),Glutamine (Gln /Q),4.00%,CAA/CAG,H >D,128.14,114,0.67,2,,
+Non-Polar,Alanine (Ala /A),8.30%,GCU/GCC/GCA/GCG,GSTP,71.09,67,0.74,1,,
+Non-Polar,Valine (Val /V),6.60%,GUU/GUC/GUA/GUG,I >>L M >>,99.15,105,0.86,1,,
+Non-Polar,Leucine (Leu /L),9.00%,UUA/UUG/CUU/CUG/CUA/CUG,M >>F I V >>,113.18,124,0.9,1,,
+Non-Polar,Isoleucine (Ile /I),5.20%,AUU/AUC/AUA,V >> M L > F,113.18,124,0.9,1,,
+Non-Polar,Proline (Pro/P),5.10%,CCU/CCC/CCA/CCG,AS,97.13,90,0.76,3,,
+Non-Polar,Phenylalanine (Phe /F),3.90%,UUU/UUC,Y>>>>>L> I,147.19,135,0.77,0,,197 @ 257.4
+Non-Polar,Tryptophane (Trp /W),1.30%,UGG,R>,186.23,163,0.74,2,,5600 @ 279.8
+Non-Polar,Methionine (Met /M),2.40%,AUG,L>> I V>>,131.21,124,0.75,1,,
diff -r 000000000000 -r acc3674e515b scripts/functions.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/functions.py Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+#coding: utf-8
+
+import itertools, os
+
+def dico(fasta_file, path_in):
+ """
+ Stores a fasta file in a dictionary : key/value -> header/sequence
+
+ Args:
+ - fasta_file (String) : the name of fasta file
+ - path_in (String) : path to the fasta file
+
+ Return:
+ - bash1 (dict) : the dictionary header/sequence
+ """
+ bash1 = {}
+
+ with open(path_in+'/'+fasta_file, 'r') as F1:
+ for h,s in itertools.izip_longest(*[F1]*2):
+ fasta_name = h[1:3]
+ sequence = s[:-1]
+ if fasta_name not in bash1.keys():
+ bash1[fasta_name] = sequence
+ else:
+ print fasta_name
+
+ return bash1 # same length for all (alignment)
+
+def write_output(names, sps_list, out_dir, results_dict):
+ """ Write results in csv files. There is one file per counted element (one file per amino-acid, one file per indice ...)
+
+ Args:
+ - names (list) : list with the names of elems
+ - sps_list (list) : species names, sorted alphabetically
+ - out_dir (String) : output directory
+ - results_dict (dict) : vcounts values of each element for each input file (keys names : elems from 'names argument')
+
+ """
+ for name in names:
+ out = open(name+".csv", 'w')
+ out.write('Group,' + sps_list[0:-1]+'\n')
+ for group in results_dict.keys():
+ count_of_elems = ''
+ for specs in sorted(results_dict[group].keys()):
+ count_of_elems += str(results_dict[group][specs][name]) + ','
+ out.write(group + ',' + count_of_elems[0:-1] + '\n')
+ out.close()
+ os.system('mv %s.csv %s/' %(name, out_dir))
+
+def fill_with_NaN(what):
+ """ Used to create a dict only with NaN values ; used when a species is not present in an orthogroup
+
+ Args:
+ - what (list of Strings) : the names of the elements studied (nucleotide, amino-acids, indices of thermostability ...)
+
+ Return:
+ - NaN_values (dict) : dictionary with keys=elems of what, values=NaN
+ """
+
+ NaN_values = {}
+ for elem in what:
+ NaN_values[elem] = 'NaN'
+
+ return NaN_values
diff -r 000000000000 -r acc3674e515b static/images/adaptsearch_picture_helps.png
Binary file static/images/adaptsearch_picture_helps.png has changed
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/A.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/A.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,1,2,2,2,2,2
+locus_6sp_60.fasta,2,2,2,2,2,2
+locus_6sp_40.fasta,8,7,7,6,8,7
+locus_6sp_58.fasta,1,1,0,0,1,0
+locus_6sp_38.fasta,4,4,5,4,2,3
+locus_4sp_4.fasta,3,NaN,2,2,2,NaN
+locus_4sp_6.fasta,0,1,0,0,NaN,NaN
+locus_6sp_27.fasta,1,1,1,0,1,0
+locus_6sp_41.fasta,5,5,5,5,6,5
+locus_6sp_39.fasta,3,3,4,3,3,4
+locus_6sp_10.fasta,5,5,5,5,4,5
+locus_6sp_25.fasta,19,18,20,17,19,18
+locus_6sp_32.fasta,8,8,10,8,8,10
+locus_6sp_53.fasta,7,6,6,6,6,7
+locus_3sp_2.fasta,NaN,3,NaN,3,4,NaN
+locus_6sp_47.fasta,1,1,1,1,1,1
+locus_6sp_16.fasta,4,3,3,3,4,3
+locus_6sp_11.fasta,14,14,12,13,13,13
+locus_6sp_35.fasta,3,3,4,3,3,3
+locus_6sp_46.fasta,7,7,7,6,5,8
+locus_3sp_7.fasta,3,3,3,NaN,NaN,NaN
+locus_6sp_30.fasta,1,1,1,1,1,1
+locus_6sp_57.fasta,9,9,8,7,8,9
+locus_6sp_50.fasta,35,34,35,37,36,36
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/C.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/C.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0,0,0,0,0,0
+locus_6sp_60.fasta,1,1,1,1,1,1
+locus_6sp_40.fasta,0,0,1,0,0,1
+locus_6sp_58.fasta,0,0,0,0,0,0
+locus_6sp_38.fasta,0,0,0,0,0,0
+locus_4sp_4.fasta,3,NaN,5,4,5,NaN
+locus_4sp_6.fasta,13,13,13,13,NaN,NaN
+locus_6sp_27.fasta,1,2,2,2,1,2
+locus_6sp_41.fasta,2,2,2,2,2,2
+locus_6sp_39.fasta,0,0,0,0,0,0
+locus_6sp_10.fasta,3,3,3,3,3,3
+locus_6sp_25.fasta,1,1,1,1,1,1
+locus_6sp_32.fasta,1,1,1,1,1,1
+locus_6sp_53.fasta,0,0,0,0,0,1
+locus_3sp_2.fasta,NaN,0,NaN,0,0,NaN
+locus_6sp_47.fasta,0,0,0,0,0,0
+locus_6sp_16.fasta,1,1,1,1,1,1
+locus_6sp_11.fasta,2,2,2,2,2,2
+locus_6sp_35.fasta,5,5,2,4,3,4
+locus_6sp_46.fasta,0,0,0,0,0,0
+locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN
+locus_6sp_30.fasta,0,0,0,0,0,0
+locus_6sp_57.fasta,1,1,1,1,1,1
+locus_6sp_50.fasta,3,3,3,3,3,3
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/D.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/D.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0,0,0,0,0,0
+locus_6sp_60.fasta,2,2,2,3,2,2
+locus_6sp_40.fasta,6,5,4,4,6,3
+locus_6sp_58.fasta,3,3,3,3,3,3
+locus_6sp_38.fasta,5,5,4,6,6,5
+locus_4sp_4.fasta,1,NaN,2,1,2,NaN
+locus_4sp_6.fasta,7,7,6,7,NaN,NaN
+locus_6sp_27.fasta,1,1,1,1,0,1
+locus_6sp_41.fasta,2,2,2,2,2,2
+locus_6sp_39.fasta,2,2,2,2,2,2
+locus_6sp_10.fasta,2,2,2,2,2,2
+locus_6sp_25.fasta,23,23,23,23,22,24
+locus_6sp_32.fasta,7,7,6,6,7,5
+locus_6sp_53.fasta,4,4,4,3,3,5
+locus_3sp_2.fasta,NaN,4,NaN,3,3,NaN
+locus_6sp_47.fasta,4,4,4,4,4,4
+locus_6sp_16.fasta,3,3,3,2,5,3
+locus_6sp_11.fasta,9,9,9,8,8,8
+locus_6sp_35.fasta,1,1,1,1,1,1
+locus_6sp_46.fasta,4,4,3,4,4,3
+locus_3sp_7.fasta,4,5,4,NaN,NaN,NaN
+locus_6sp_30.fasta,1,1,1,1,1,1
+locus_6sp_57.fasta,4,4,5,4,5,4
+locus_6sp_50.fasta,7,8,7,7,8,7
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/E.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/E.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,2,2,2,2,2,2
+locus_6sp_60.fasta,2,2,2,1,2,2
+locus_6sp_40.fasta,7,8,9,8,7,9
+locus_6sp_58.fasta,0,0,0,0,0,0
+locus_6sp_38.fasta,7,7,8,6,6,7
+locus_4sp_4.fasta,1,NaN,1,1,1,NaN
+locus_4sp_6.fasta,7,7,8,7,NaN,NaN
+locus_6sp_27.fasta,0,0,2,0,1,0
+locus_6sp_41.fasta,1,1,1,1,1,1
+locus_6sp_39.fasta,5,4,5,4,4,5
+locus_6sp_10.fasta,2,2,2,2,2,2
+locus_6sp_25.fasta,18,18,19,17,17,18
+locus_6sp_32.fasta,12,12,13,15,12,14
+locus_6sp_53.fasta,13,13,13,13,12,12
+locus_3sp_2.fasta,NaN,1,NaN,2,1,NaN
+locus_6sp_47.fasta,2,2,2,2,2,2
+locus_6sp_16.fasta,6,6,5,6,6,5
+locus_6sp_11.fasta,13,13,13,14,13,13
+locus_6sp_35.fasta,1,1,1,1,1,1
+locus_6sp_46.fasta,22,22,24,22,22,23
+locus_3sp_7.fasta,3,2,3,NaN,NaN,NaN
+locus_6sp_30.fasta,2,2,2,2,3,2
+locus_6sp_57.fasta,8,8,7,8,7,8
+locus_6sp_50.fasta,4,3,3,4,3,3
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/F.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/F.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0,0,0,0,0,0
+locus_6sp_60.fasta,3,3,3,3,3,3
+locus_6sp_40.fasta,2,2,2,2,2,2
+locus_6sp_58.fasta,0,0,0,0,0,0
+locus_6sp_38.fasta,1,1,1,1,2,1
+locus_4sp_4.fasta,5,NaN,6,7,7,NaN
+locus_4sp_6.fasta,2,2,2,1,NaN,NaN
+locus_6sp_27.fasta,3,3,1,1,2,2
+locus_6sp_41.fasta,4,4,4,5,5,5
+locus_6sp_39.fasta,5,6,6,6,4,6
+locus_6sp_10.fasta,6,6,6,6,7,6
+locus_6sp_25.fasta,15,15,15,16,15,16
+locus_6sp_32.fasta,8,8,9,9,9,9
+locus_6sp_53.fasta,11,11,11,10,11,9
+locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN
+locus_6sp_47.fasta,0,0,0,0,0,0
+locus_6sp_16.fasta,2,2,1,2,2,1
+locus_6sp_11.fasta,6,6,6,5,7,6
+locus_6sp_35.fasta,8,8,9,7,8,11
+locus_6sp_46.fasta,7,6,6,6,6,6
+locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN
+locus_6sp_30.fasta,1,1,1,1,1,1
+locus_6sp_57.fasta,1,1,2,2,1,2
+locus_6sp_50.fasta,9,9,10,9,9,9
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/G.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/G.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,3,3,3,3,3,3
+locus_6sp_60.fasta,3,3,3,4,3,3
+locus_6sp_40.fasta,9,9,10,10,9,10
+locus_6sp_58.fasta,4,4,4,4,4,4
+locus_6sp_38.fasta,3,3,3,3,3,3
+locus_4sp_4.fasta,1,NaN,1,1,1,NaN
+locus_4sp_6.fasta,6,6,6,6,NaN,NaN
+locus_6sp_27.fasta,1,1,0,0,1,1
+locus_6sp_41.fasta,3,3,3,3,3,3
+locus_6sp_39.fasta,2,2,2,2,3,2
+locus_6sp_10.fasta,4,4,4,4,4,4
+locus_6sp_25.fasta,24,24,25,25,23,25
+locus_6sp_32.fasta,6,6,6,6,7,6
+locus_6sp_53.fasta,9,9,9,9,10,9
+locus_3sp_2.fasta,NaN,4,NaN,4,4,NaN
+locus_6sp_47.fasta,7,7,7,7,8,7
+locus_6sp_16.fasta,5,5,5,5,5,5
+locus_6sp_11.fasta,15,15,15,14,15,15
+locus_6sp_35.fasta,5,5,5,6,5,6
+locus_6sp_46.fasta,4,4,4,3,3,3
+locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN
+locus_6sp_30.fasta,0,0,0,0,0,0
+locus_6sp_57.fasta,8,8,8,8,8,8
+locus_6sp_50.fasta,39,39,39,39,40,39
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/H.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/H.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,1,1,1,1,1,1
+locus_6sp_60.fasta,0,0,0,0,0,0
+locus_6sp_40.fasta,2,2,2,3,2,3
+locus_6sp_58.fasta,1,1,1,2,1,1
+locus_6sp_38.fasta,11,11,10,10,8,10
+locus_4sp_4.fasta,6,NaN,4,4,5,NaN
+locus_4sp_6.fasta,2,3,2,3,NaN,NaN
+locus_6sp_27.fasta,3,3,3,3,2,3
+locus_6sp_41.fasta,1,1,1,1,0,1
+locus_6sp_39.fasta,4,4,4,4,3,4
+locus_6sp_10.fasta,2,2,2,2,2,2
+locus_6sp_25.fasta,10,10,11,10,10,11
+locus_6sp_32.fasta,1,1,2,2,1,1
+locus_6sp_53.fasta,3,3,5,3,3,1
+locus_3sp_2.fasta,NaN,0,NaN,0,0,NaN
+locus_6sp_47.fasta,3,3,3,3,3,3
+locus_6sp_16.fasta,1,1,1,1,1,1
+locus_6sp_11.fasta,0,1,1,1,1,0
+locus_6sp_35.fasta,2,2,2,2,2,3
+locus_6sp_46.fasta,0,0,0,0,0,0
+locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN
+locus_6sp_30.fasta,0,0,0,0,0,0
+locus_6sp_57.fasta,2,2,2,2,2,2
+locus_6sp_50.fasta,2,2,2,3,3,2
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/I.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/I.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,2,2,2,2,2,2
+locus_6sp_60.fasta,1,1,1,1,1,1
+locus_6sp_40.fasta,5,4,5,3,5,4
+locus_6sp_58.fasta,1,1,0,0,0,0
+locus_6sp_38.fasta,0,0,0,0,1,0
+locus_4sp_4.fasta,7,NaN,9,9,9,NaN
+locus_4sp_6.fasta,6,7,6,6,NaN,NaN
+locus_6sp_27.fasta,0,0,1,1,3,2
+locus_6sp_41.fasta,5,5,5,6,5,6
+locus_6sp_39.fasta,4,3,4,3,4,4
+locus_6sp_10.fasta,5,5,5,5,5,5
+locus_6sp_25.fasta,17,16,15,15,15,15
+locus_6sp_32.fasta,5,4,2,3,1,2
+locus_6sp_53.fasta,8,8,6,8,6,8
+locus_3sp_2.fasta,NaN,0,NaN,1,0,NaN
+locus_6sp_47.fasta,3,3,3,3,3,3
+locus_6sp_16.fasta,3,3,3,4,4,3
+locus_6sp_11.fasta,10,11,12,10,10,11
+locus_6sp_35.fasta,4,5,4,7,7,4
+locus_6sp_46.fasta,10,10,11,9,10,10
+locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN
+locus_6sp_30.fasta,0,0,0,0,0,0
+locus_6sp_57.fasta,3,3,3,3,4,3
+locus_6sp_50.fasta,23,22,24,20,20,24
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/K.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/K.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0,0,0,0,0,0
+locus_6sp_60.fasta,1,1,0,1,1,0
+locus_6sp_40.fasta,9,8,10,10,9,10
+locus_6sp_58.fasta,1,1,1,1,1,1
+locus_6sp_38.fasta,15,15,15,15,15,15
+locus_4sp_4.fasta,1,NaN,1,1,0,NaN
+locus_4sp_6.fasta,5,5,8,6,NaN,NaN
+locus_6sp_27.fasta,1,1,0,1,0,1
+locus_6sp_41.fasta,1,2,1,1,1,1
+locus_6sp_39.fasta,4,3,3,3,4,3
+locus_6sp_10.fasta,2,2,2,2,2,2
+locus_6sp_25.fasta,18,17,20,20,21,19
+locus_6sp_32.fasta,19,20,19,19,19,19
+locus_6sp_53.fasta,11,11,10,10,11,10
+locus_3sp_2.fasta,NaN,4,NaN,4,4,NaN
+locus_6sp_47.fasta,10,10,10,10,10,10
+locus_6sp_16.fasta,2,2,2,2,2,2
+locus_6sp_11.fasta,16,16,15,15,15,15
+locus_6sp_35.fasta,2,2,2,2,2,2
+locus_6sp_46.fasta,23,24,25,22,26,24
+locus_3sp_7.fasta,4,4,4,NaN,NaN,NaN
+locus_6sp_30.fasta,4,4,4,4,3,3
+locus_6sp_57.fasta,5,5,5,5,5,5
+locus_6sp_50.fasta,7,5,6,6,6,6
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/L.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/L.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,3,3,4,3,2,3
+locus_6sp_60.fasta,2,2,1,1,2,1
+locus_6sp_40.fasta,8,7,9,10,9,9
+locus_6sp_58.fasta,0,0,0,0,0,0
+locus_6sp_38.fasta,1,1,0,0,0,0
+locus_4sp_4.fasta,11,NaN,10,8,10,NaN
+locus_4sp_6.fasta,4,4,5,4,NaN,NaN
+locus_6sp_27.fasta,9,9,8,9,10,8
+locus_6sp_41.fasta,7,7,7,6,8,8
+locus_6sp_39.fasta,3,3,3,3,5,3
+locus_6sp_10.fasta,2,2,3,2,3,3
+locus_6sp_25.fasta,25,24,24,25,24,26
+locus_6sp_32.fasta,13,14,14,13,14,14
+locus_6sp_53.fasta,6,6,7,7,7,9
+locus_3sp_2.fasta,NaN,2,NaN,2,2,NaN
+locus_6sp_47.fasta,6,6,6,6,6,6
+locus_6sp_16.fasta,3,3,3,3,3,3
+locus_6sp_11.fasta,11,11,11,11,11,11
+locus_6sp_35.fasta,8,8,8,6,6,7
+locus_6sp_46.fasta,14,13,13,14,14,13
+locus_3sp_7.fasta,8,8,8,NaN,NaN,NaN
+locus_6sp_30.fasta,0,0,0,0,0,0
+locus_6sp_57.fasta,8,8,8,8,8,8
+locus_6sp_50.fasta,27,27,26,27,26,26
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/M.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/M.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,3,3,2,3,3,3
+locus_6sp_60.fasta,0,0,0,0,0,0
+locus_6sp_40.fasta,9,9,9,9,9,9
+locus_6sp_58.fasta,0,0,0,0,0,0
+locus_6sp_38.fasta,0,0,0,0,0,0
+locus_4sp_4.fasta,2,NaN,2,2,5,NaN
+locus_4sp_6.fasta,2,2,2,2,NaN,NaN
+locus_6sp_27.fasta,0,0,0,1,0,0
+locus_6sp_41.fasta,2,2,2,1,2,1
+locus_6sp_39.fasta,0,0,0,1,0,0
+locus_6sp_10.fasta,5,5,4,5,4,4
+locus_6sp_25.fasta,3,3,3,4,6,4
+locus_6sp_32.fasta,7,7,7,7,9,7
+locus_6sp_53.fasta,1,1,1,1,1,2
+locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN
+locus_6sp_47.fasta,0,1,0,0,0,0
+locus_6sp_16.fasta,0,0,0,0,0,0
+locus_6sp_11.fasta,6,5,6,6,4,6
+locus_6sp_35.fasta,1,1,2,1,1,2
+locus_6sp_46.fasta,4,4,2,4,3,3
+locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN
+locus_6sp_30.fasta,2,2,2,2,2,2
+locus_6sp_57.fasta,4,4,4,4,4,4
+locus_6sp_50.fasta,18,18,19,20,20,20
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/N.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/N.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0,0,0,0,0,0
+locus_6sp_60.fasta,1,1,2,2,1,2
+locus_6sp_40.fasta,1,1,0,1,0,1
+locus_6sp_58.fasta,1,1,1,1,2,1
+locus_6sp_38.fasta,5,5,5,5,5,5
+locus_4sp_4.fasta,1,NaN,1,3,1,NaN
+locus_4sp_6.fasta,6,5,4,4,NaN,NaN
+locus_6sp_27.fasta,0,0,0,0,0,0
+locus_6sp_41.fasta,3,2,2,2,2,3
+locus_6sp_39.fasta,2,2,2,2,2,2
+locus_6sp_10.fasta,1,1,1,1,1,1
+locus_6sp_25.fasta,17,19,14,13,17,13
+locus_6sp_32.fasta,3,3,3,3,3,3
+locus_6sp_53.fasta,4,4,4,4,3,5
+locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN
+locus_6sp_47.fasta,1,1,1,1,1,1
+locus_6sp_16.fasta,0,0,1,1,0,0
+locus_6sp_11.fasta,6,6,7,7,8,7
+locus_6sp_35.fasta,3,3,1,2,3,2
+locus_6sp_46.fasta,3,3,3,3,4,3
+locus_3sp_7.fasta,3,3,3,NaN,NaN,NaN
+locus_6sp_30.fasta,2,2,2,2,2,2
+locus_6sp_57.fasta,2,2,3,3,2,3
+locus_6sp_50.fasta,6,6,7,7,8,7
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/P.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/P.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,1,1,1,1,1,1
+locus_6sp_60.fasta,0,0,0,0,0,0
+locus_6sp_40.fasta,4,4,3,4,4,4
+locus_6sp_58.fasta,0,0,0,1,0,0
+locus_6sp_38.fasta,8,7,7,7,7,7
+locus_4sp_4.fasta,3,NaN,3,3,4,NaN
+locus_4sp_6.fasta,4,4,4,4,NaN,NaN
+locus_6sp_27.fasta,1,1,2,0,0,2
+locus_6sp_41.fasta,1,1,1,1,1,1
+locus_6sp_39.fasta,2,2,2,2,2,2
+locus_6sp_10.fasta,2,2,2,2,2,2
+locus_6sp_25.fasta,16,15,14,15,14,14
+locus_6sp_32.fasta,4,4,4,4,5,4
+locus_6sp_53.fasta,6,6,6,6,6,5
+locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN
+locus_6sp_47.fasta,0,0,0,0,0,0
+locus_6sp_16.fasta,1,1,1,1,1,1
+locus_6sp_11.fasta,6,6,6,5,6,6
+locus_6sp_35.fasta,4,4,3,4,3,3
+locus_6sp_46.fasta,2,2,2,2,2,2
+locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN
+locus_6sp_30.fasta,1,1,1,1,1,1
+locus_6sp_57.fasta,2,2,2,2,2,2
+locus_6sp_50.fasta,13,13,13,13,13,13
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/Q.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/Q.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0,0,0,0,0,0
+locus_6sp_60.fasta,0,0,0,0,0,0
+locus_6sp_40.fasta,2,2,2,1,2,1
+locus_6sp_58.fasta,0,0,0,0,0,0
+locus_6sp_38.fasta,2,2,2,2,2,1
+locus_4sp_4.fasta,0,NaN,0,0,0,NaN
+locus_4sp_6.fasta,4,4,4,4,NaN,NaN
+locus_6sp_27.fasta,2,2,1,2,3,2
+locus_6sp_41.fasta,2,2,2,2,3,2
+locus_6sp_39.fasta,3,4,2,3,4,2
+locus_6sp_10.fasta,1,1,1,1,1,1
+locus_6sp_25.fasta,11,11,10,10,11,8
+locus_6sp_32.fasta,4,3,4,2,3,4
+locus_6sp_53.fasta,4,4,3,5,4,5
+locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN
+locus_6sp_47.fasta,3,3,3,3,3,3
+locus_6sp_16.fasta,1,1,2,1,1,2
+locus_6sp_11.fasta,9,8,8,7,7,9
+locus_6sp_35.fasta,0,0,0,0,0,0
+locus_6sp_46.fasta,6,5,6,8,8,7
+locus_3sp_7.fasta,5,5,5,NaN,NaN,NaN
+locus_6sp_30.fasta,0,0,0,0,0,0
+locus_6sp_57.fasta,3,3,3,3,3,3
+locus_6sp_50.fasta,5,5,5,4,5,5
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/R.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/R.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0,0,0,0,0,0
+locus_6sp_60.fasta,2,2,3,3,2,3
+locus_6sp_40.fasta,7,8,5,5,6,5
+locus_6sp_58.fasta,8,8,8,7,8,8
+locus_6sp_38.fasta,16,16,17,17,19,18
+locus_4sp_4.fasta,5,NaN,5,4,6,NaN
+locus_4sp_6.fasta,10,9,8,9,NaN,NaN
+locus_6sp_27.fasta,1,0,3,2,2,2
+locus_6sp_41.fasta,6,5,8,7,4,4
+locus_6sp_39.fasta,1,2,4,3,2,4
+locus_6sp_10.fasta,1,1,1,1,1,1
+locus_6sp_25.fasta,12,13,13,11,11,12
+locus_6sp_32.fasta,7,7,6,6,6,6
+locus_6sp_53.fasta,7,7,7,7,6,7
+locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN
+locus_6sp_47.fasta,10,10,10,10,10,10
+locus_6sp_16.fasta,0,0,0,0,0,0
+locus_6sp_11.fasta,6,6,7,8,7,7
+locus_6sp_35.fasta,2,2,4,3,3,2
+locus_6sp_46.fasta,14,15,14,16,12,15
+locus_3sp_7.fasta,1,1,1,NaN,NaN,NaN
+locus_6sp_30.fasta,1,1,1,1,1,2
+locus_6sp_57.fasta,4,4,5,5,4,5
+locus_6sp_50.fasta,11,12,11,11,10,11
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/S.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/S.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0,0,0,0,0,0
+locus_6sp_60.fasta,5,5,5,4,5,5
+locus_6sp_40.fasta,7,7,6,6,6,6
+locus_6sp_58.fasta,32,33,34,33,33,34
+locus_6sp_38.fasta,21,21,23,23,21,23
+locus_4sp_4.fasta,5,NaN,3,4,2,NaN
+locus_4sp_6.fasta,2,1,1,2,NaN,NaN
+locus_6sp_27.fasta,2,2,2,3,1,2
+locus_6sp_41.fasta,11,12,10,11,11,11
+locus_6sp_39.fasta,1,1,1,2,1,1
+locus_6sp_10.fasta,3,3,3,3,3,3
+locus_6sp_25.fasta,14,15,13,17,15,15
+locus_6sp_32.fasta,6,6,5,5,6,5
+locus_6sp_53.fasta,6,6,6,6,8,6
+locus_3sp_2.fasta,NaN,0,NaN,0,0,NaN
+locus_6sp_47.fasta,4,4,4,4,3,4
+locus_6sp_16.fasta,3,3,3,3,2,3
+locus_6sp_11.fasta,2,2,3,4,4,3
+locus_6sp_35.fasta,3,3,5,4,6,3
+locus_6sp_46.fasta,3,3,3,4,4,4
+locus_3sp_7.fasta,2,2,1,NaN,NaN,NaN
+locus_6sp_30.fasta,0,0,0,0,0,0
+locus_6sp_57.fasta,9,9,8,9,10,8
+locus_6sp_50.fasta,15,16,15,14,16,15
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/T.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/T.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,2,2,2,2,2,2
+locus_6sp_60.fasta,1,1,1,1,1,1
+locus_6sp_40.fasta,3,3,4,4,5,3
+locus_6sp_58.fasta,2,1,1,2,1,1
+locus_6sp_38.fasta,5,6,3,4,6,3
+locus_4sp_4.fasta,9,NaN,10,11,7,NaN
+locus_4sp_6.fasta,4,4,4,4,NaN,NaN
+locus_6sp_27.fasta,1,1,1,2,1,1
+locus_6sp_41.fasta,7,7,7,7,7,7
+locus_6sp_39.fasta,4,5,3,5,3,3
+locus_6sp_10.fasta,5,5,5,5,5,5
+locus_6sp_25.fasta,15,14,17,17,14,17
+locus_6sp_32.fasta,7,7,8,10,6,8
+locus_6sp_53.fasta,7,8,8,8,8,6
+locus_3sp_2.fasta,NaN,2,NaN,2,1,NaN
+locus_6sp_47.fasta,4,3,4,4,4,4
+locus_6sp_16.fasta,2,2,2,2,2,3
+locus_6sp_11.fasta,5,5,4,4,7,5
+locus_6sp_35.fasta,5,5,3,4,5,4
+locus_6sp_46.fasta,5,5,2,3,4,3
+locus_3sp_7.fasta,0,0,1,NaN,NaN,NaN
+locus_6sp_30.fasta,0,0,0,0,0,0
+locus_6sp_57.fasta,7,7,7,7,6,6
+locus_6sp_50.fasta,12,12,12,11,9,12
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/V.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/V.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,1,0,0,0,1,0
+locus_6sp_60.fasta,1,1,1,0,1,1
+locus_6sp_40.fasta,4,7,5,7,4,6
+locus_6sp_58.fasta,0,0,1,0,0,1
+locus_6sp_38.fasta,0,0,1,1,2,3
+locus_4sp_4.fasta,6,NaN,4,4,3,NaN
+locus_4sp_6.fasta,2,2,2,3,NaN,NaN
+locus_6sp_27.fasta,5,5,4,4,3,3
+locus_6sp_41.fasta,5,5,5,5,5,5
+locus_6sp_39.fasta,3,3,3,2,3,3
+locus_6sp_10.fasta,2,2,2,2,3,2
+locus_6sp_25.fasta,26,28,27,27,28,28
+locus_6sp_32.fasta,8,8,8,8,9,8
+locus_6sp_53.fasta,6,6,7,7,8,6
+locus_3sp_2.fasta,NaN,2,NaN,1,3,NaN
+locus_6sp_47.fasta,5,5,5,5,5,5
+locus_6sp_16.fasta,4,5,4,3,2,4
+locus_6sp_11.fasta,10,10,9,11,8,9
+locus_6sp_35.fasta,10,9,10,10,8,9
+locus_6sp_46.fasta,4,5,7,6,5,5
+locus_3sp_7.fasta,1,1,1,NaN,NaN,NaN
+locus_6sp_30.fasta,1,1,1,1,1,1
+locus_6sp_57.fasta,10,10,10,10,10,10
+locus_6sp_50.fasta,21,23,20,23,23,19
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/W.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/W.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0,0,0,0,0,0
+locus_6sp_60.fasta,0,0,0,0,0,0
+locus_6sp_40.fasta,1,1,1,1,1,1
+locus_6sp_58.fasta,0,0,0,0,0,0
+locus_6sp_38.fasta,0,0,0,0,0,0
+locus_4sp_4.fasta,0,NaN,0,1,0,NaN
+locus_4sp_6.fasta,5,5,5,5,NaN,NaN
+locus_6sp_27.fasta,1,1,1,1,1,1
+locus_6sp_41.fasta,1,1,1,1,1,1
+locus_6sp_39.fasta,1,1,0,0,1,0
+locus_6sp_10.fasta,4,4,4,4,4,4
+locus_6sp_25.fasta,2,2,2,2,2,2
+locus_6sp_32.fasta,1,1,1,1,1,1
+locus_6sp_53.fasta,2,2,2,2,2,2
+locus_3sp_2.fasta,NaN,2,NaN,2,2,NaN
+locus_6sp_47.fasta,1,1,1,1,1,1
+locus_6sp_16.fasta,0,0,0,0,0,0
+locus_6sp_11.fasta,2,2,2,2,2,2
+locus_6sp_35.fasta,3,3,3,2,3,3
+locus_6sp_46.fasta,3,3,3,3,3,3
+locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN
+locus_6sp_30.fasta,2,2,2,2,2,2
+locus_6sp_57.fasta,0,0,0,0,0,0
+locus_6sp_50.fasta,3,3,3,3,3,3
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa/Y.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa/Y.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,2,2,2,2,2,2
+locus_6sp_60.fasta,0,0,0,0,0,0
+locus_6sp_40.fasta,2,2,2,2,2,2
+locus_6sp_58.fasta,0,0,0,0,0,0
+locus_6sp_38.fasta,12,12,12,12,11,12
+locus_4sp_4.fasta,2,NaN,3,2,2,NaN
+locus_4sp_6.fasta,5,5,6,6,NaN,NaN
+locus_6sp_27.fasta,0,0,0,0,1,0
+locus_6sp_41.fasta,0,0,0,0,0,0
+locus_6sp_39.fasta,3,2,2,2,2,2
+locus_6sp_10.fasta,6,6,6,6,5,6
+locus_6sp_25.fasta,12,12,12,13,13,12
+locus_6sp_32.fasta,5,5,4,4,5,5
+locus_6sp_53.fasta,4,4,4,4,4,4
+locus_3sp_2.fasta,NaN,2,NaN,2,2,NaN
+locus_6sp_47.fasta,2,2,2,2,2,2
+locus_6sp_16.fasta,1,1,2,2,1,2
+locus_6sp_11.fasta,1,1,1,2,1,1
+locus_6sp_35.fasta,2,2,3,3,2,2
+locus_6sp_46.fasta,2,2,2,2,2,2
+locus_3sp_7.fasta,1,1,1,NaN,NaN,NaN
+locus_6sp_30.fasta,0,0,0,0,0,0
+locus_6sp_57.fasta,3,3,2,2,3,2
+locus_6sp_50.fasta,14,14,14,13,13,14
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/AC.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/AC.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,1,2,2,2,2,2
+locus_6sp_60.fasta,3,3,3,3,3,3
+locus_6sp_40.fasta,8,7,8,6,8,8
+locus_6sp_58.fasta,1,1,0,0,1,0
+locus_6sp_38.fasta,4,4,5,4,2,3
+locus_4sp_4.fasta,6,NaN,7,6,7,NaN
+locus_4sp_6.fasta,13,14,13,13,NaN,NaN
+locus_6sp_41.fasta,7,7,7,7,8,7
+locus_6sp_27.fasta,2,3,3,2,2,2
+locus_6sp_39.fasta,3,3,4,3,3,4
+locus_6sp_10.fasta,8,8,8,8,7,8
+locus_6sp_25.fasta,20,19,21,18,20,19
+locus_6sp_32.fasta,9,9,11,9,9,11
+locus_6sp_53.fasta,7,6,6,6,6,8
+locus_3sp_2.fasta,NaN,3,NaN,3,4,NaN
+locus_6sp_47.fasta,1,1,1,1,1,1
+locus_6sp_16.fasta,5,4,4,4,5,4
+locus_6sp_11.fasta,16,16,14,15,15,15
+locus_6sp_35.fasta,8,8,6,7,6,7
+locus_6sp_46.fasta,7,7,7,6,5,8
+locus_3sp_7.fasta,3,3,3,NaN,NaN,NaN
+locus_6sp_30.fasta,1,1,1,1,1,1
+locus_6sp_57.fasta,10,10,9,8,9,10
+locus_6sp_50.fasta,38,37,38,40,39,39
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/APGC.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/APGC.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,5,6,6,6,6,6
+locus_6sp_60.fasta,6,6,6,7,6,6
+locus_6sp_40.fasta,21,20,21,20,21,22
+locus_6sp_58.fasta,5,5,4,5,5,4
+locus_6sp_38.fasta,15,14,15,14,12,13
+locus_4sp_4.fasta,10,NaN,11,10,12,NaN
+locus_4sp_6.fasta,23,24,23,23,NaN,NaN
+locus_6sp_41.fasta,11,11,11,11,12,11
+locus_6sp_27.fasta,4,5,5,2,3,5
+locus_6sp_39.fasta,7,7,8,7,8,8
+locus_6sp_10.fasta,14,14,14,14,13,14
+locus_6sp_25.fasta,60,58,60,58,57,58
+locus_6sp_32.fasta,19,19,21,19,21,21
+locus_6sp_53.fasta,22,21,21,21,22,22
+locus_3sp_2.fasta,NaN,8,NaN,8,9,NaN
+locus_6sp_47.fasta,8,8,8,8,9,8
+locus_6sp_16.fasta,11,10,10,10,11,10
+locus_6sp_11.fasta,37,37,35,34,36,36
+locus_6sp_35.fasta,17,17,14,17,14,16
+locus_6sp_46.fasta,13,13,13,11,10,13
+locus_3sp_7.fasta,3,3,3,NaN,NaN,NaN
+locus_6sp_30.fasta,2,2,2,2,2,2
+locus_6sp_57.fasta,20,20,19,18,19,20
+locus_6sp_50.fasta,90,89,90,92,92,91
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/AVLIM.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/AVLIM.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,10,10,10,10,10,10
+locus_6sp_60.fasta,6,6,5,4,6,5
+locus_6sp_40.fasta,34,34,35,35,35,35
+locus_6sp_58.fasta,2,2,1,0,1,1
+locus_6sp_38.fasta,5,5,6,5,5,6
+locus_4sp_4.fasta,29,NaN,27,25,29,NaN
+locus_4sp_6.fasta,14,16,15,15,NaN,NaN
+locus_6sp_41.fasta,24,24,24,23,26,25
+locus_6sp_27.fasta,15,15,14,15,17,13
+locus_6sp_39.fasta,13,12,14,12,15,14
+locus_6sp_10.fasta,19,19,19,19,19,19
+locus_6sp_25.fasta,90,89,89,88,92,91
+locus_6sp_32.fasta,41,41,41,39,41,41
+locus_6sp_53.fasta,28,27,27,29,28,32
+locus_3sp_2.fasta,NaN,8,NaN,8,10,NaN
+locus_6sp_47.fasta,15,16,15,15,15,15
+locus_6sp_16.fasta,14,14,13,13,13,13
+locus_6sp_11.fasta,51,51,50,51,46,50
+locus_6sp_35.fasta,26,26,28,27,25,25
+locus_6sp_46.fasta,39,39,40,39,37,39
+locus_3sp_7.fasta,12,12,12,NaN,NaN,NaN
+locus_6sp_30.fasta,4,4,4,4,4,4
+locus_6sp_57.fasta,34,34,33,32,34,34
+locus_6sp_50.fasta,124,124,124,127,125,125
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/AVLIMFYW.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/AVLIMFYW.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,12,12,12,12,12,12
+locus_6sp_60.fasta,9,9,8,7,9,8
+locus_6sp_40.fasta,39,39,40,40,40,40
+locus_6sp_58.fasta,2,2,1,0,1,1
+locus_6sp_38.fasta,18,18,19,18,18,19
+locus_4sp_4.fasta,36,NaN,36,35,38,NaN
+locus_4sp_6.fasta,26,28,28,27,NaN,NaN
+locus_6sp_41.fasta,29,29,29,29,32,31
+locus_6sp_27.fasta,19,19,16,17,21,16
+locus_6sp_39.fasta,22,21,22,20,22,22
+locus_6sp_10.fasta,35,35,35,35,35,35
+locus_6sp_25.fasta,119,118,118,119,122,121
+locus_6sp_32.fasta,55,55,55,53,56,56
+locus_6sp_53.fasta,45,44,44,45,45,47
+locus_3sp_2.fasta,NaN,13,NaN,13,15,NaN
+locus_6sp_47.fasta,18,19,18,18,18,18
+locus_6sp_16.fasta,17,17,16,17,16,16
+locus_6sp_11.fasta,60,60,59,60,56,59
+locus_6sp_35.fasta,39,39,43,39,38,41
+locus_6sp_46.fasta,51,50,51,50,48,50
+locus_3sp_7.fasta,13,13,13,NaN,NaN,NaN
+locus_6sp_30.fasta,7,7,7,7,7,7
+locus_6sp_57.fasta,38,38,37,36,38,38
+locus_6sp_50.fasta,150,150,151,152,150,151
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/DE.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/DE.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,2,2,2,2,2,2
+locus_6sp_60.fasta,4,4,4,4,4,4
+locus_6sp_40.fasta,13,13,13,12,13,12
+locus_6sp_58.fasta,3,3,3,3,3,3
+locus_6sp_38.fasta,12,12,12,12,12,12
+locus_4sp_4.fasta,2,NaN,3,2,3,NaN
+locus_4sp_6.fasta,14,14,14,14,NaN,NaN
+locus_6sp_41.fasta,3,3,3,3,3,3
+locus_6sp_27.fasta,1,1,3,1,1,1
+locus_6sp_39.fasta,7,6,7,6,6,7
+locus_6sp_10.fasta,4,4,4,4,4,4
+locus_6sp_25.fasta,41,41,42,40,39,42
+locus_6sp_32.fasta,19,19,19,21,19,19
+locus_6sp_53.fasta,17,17,17,16,15,17
+locus_3sp_2.fasta,NaN,5,NaN,5,4,NaN
+locus_6sp_47.fasta,6,6,6,6,6,6
+locus_6sp_16.fasta,9,9,8,8,11,8
+locus_6sp_11.fasta,22,22,22,22,21,21
+locus_6sp_35.fasta,2,2,2,2,2,2
+locus_6sp_46.fasta,26,26,27,26,26,26
+locus_3sp_7.fasta,7,7,7,NaN,NaN,NaN
+locus_6sp_30.fasta,3,3,3,3,4,3
+locus_6sp_57.fasta,12,12,12,12,12,12
+locus_6sp_50.fasta,11,11,10,11,11,10
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/DNQTSHA.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/DNQTSHA.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,4,5,5,5,5,5
+locus_6sp_60.fasta,11,11,12,12,11,12
+locus_6sp_40.fasta,29,27,25,25,29,24
+locus_6sp_58.fasta,40,40,40,41,41,40
+locus_6sp_38.fasta,53,54,52,54,50,50
+locus_4sp_4.fasta,25,NaN,22,25,19,NaN
+locus_4sp_6.fasta,25,25,21,24,NaN,NaN
+locus_6sp_41.fasta,31,31,29,30,31,31
+locus_6sp_27.fasta,10,10,9,11,8,9
+locus_6sp_39.fasta,19,21,18,21,18,18
+locus_6sp_10.fasta,19,19,19,19,18,19
+locus_6sp_25.fasta,109,110,108,107,108,106
+locus_6sp_32.fasta,36,35,38,36,34,36
+locus_6sp_53.fasta,35,35,36,35,35,35
+locus_3sp_2.fasta,NaN,11,NaN,10,10,NaN
+locus_6sp_47.fasta,20,19,20,20,19,20
+locus_6sp_16.fasta,14,13,15,13,15,15
+locus_6sp_11.fasta,45,45,44,44,48,45
+locus_6sp_35.fasta,17,17,16,16,20,16
+locus_6sp_46.fasta,28,27,24,28,29,28
+locus_3sp_7.fasta,17,18,17,NaN,NaN,NaN
+locus_6sp_30.fasta,4,4,4,4,4,4
+locus_6sp_57.fasta,36,36,36,35,36,35
+locus_6sp_50.fasta,82,83,83,83,85,84
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/EK.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/EK.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,2,2,2,2,2,2
+locus_6sp_60.fasta,3,3,2,2,3,2
+locus_6sp_40.fasta,16,16,19,18,16,19
+locus_6sp_58.fasta,1,1,1,1,1,1
+locus_6sp_38.fasta,22,22,23,21,21,22
+locus_4sp_4.fasta,2,NaN,2,2,1,NaN
+locus_4sp_6.fasta,12,12,16,13,NaN,NaN
+locus_6sp_41.fasta,2,3,2,2,2,2
+locus_6sp_27.fasta,1,1,2,1,1,1
+locus_6sp_39.fasta,9,7,8,7,8,8
+locus_6sp_10.fasta,4,4,4,4,4,4
+locus_6sp_25.fasta,36,35,39,37,38,37
+locus_6sp_32.fasta,31,32,32,34,31,33
+locus_6sp_53.fasta,24,24,23,23,23,22
+locus_3sp_2.fasta,NaN,5,NaN,6,5,NaN
+locus_6sp_47.fasta,12,12,12,12,12,12
+locus_6sp_16.fasta,8,8,7,8,8,7
+locus_6sp_11.fasta,29,29,28,29,28,28
+locus_6sp_35.fasta,3,3,3,3,3,3
+locus_6sp_46.fasta,45,46,49,44,48,47
+locus_3sp_7.fasta,7,6,7,NaN,NaN,NaN
+locus_6sp_30.fasta,6,6,6,6,6,5
+locus_6sp_57.fasta,13,13,12,13,12,13
+locus_6sp_50.fasta,11,8,9,10,9,9
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/ERK.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/ERK.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,2,2,2,2,2,2
+locus_6sp_60.fasta,4,4,2,3,4,2
+locus_6sp_40.fasta,25,24,29,28,25,29
+locus_6sp_58.fasta,2,2,2,2,2,2
+locus_6sp_38.fasta,37,37,38,36,36,37
+locus_4sp_4.fasta,3,NaN,3,3,1,NaN
+locus_4sp_6.fasta,17,17,24,19,NaN,NaN
+locus_6sp_41.fasta,3,5,3,3,3,3
+locus_6sp_27.fasta,2,2,2,2,1,2
+locus_6sp_39.fasta,13,10,11,10,12,11
+locus_6sp_10.fasta,6,6,6,6,6,6
+locus_6sp_25.fasta,54,52,59,57,59,56
+locus_6sp_32.fasta,50,52,51,53,50,52
+locus_6sp_53.fasta,35,35,33,33,34,32
+locus_3sp_2.fasta,NaN,9,NaN,10,9,NaN
+locus_6sp_47.fasta,22,22,22,22,22,22
+locus_6sp_16.fasta,10,10,9,10,10,9
+locus_6sp_11.fasta,45,45,43,44,43,43
+locus_6sp_35.fasta,5,5,5,5,5,5
+locus_6sp_46.fasta,68,70,74,66,74,71
+locus_3sp_7.fasta,11,10,11,NaN,NaN,NaN
+locus_6sp_30.fasta,10,10,10,10,9,8
+locus_6sp_57.fasta,18,18,17,18,17,18
+locus_6sp_50.fasta,18,13,15,16,15,15
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/FYMINK.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/FYMINK.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,7,7,6,7,7,7
+locus_6sp_60.fasta,6,6,6,7,6,6
+locus_6sp_40.fasta,28,26,28,27,27,28
+locus_6sp_58.fasta,3,3,2,2,3,2
+locus_6sp_38.fasta,33,33,33,33,34,33
+locus_4sp_4.fasta,18,NaN,22,24,24,NaN
+locus_4sp_6.fasta,26,26,28,25,NaN,NaN
+locus_6sp_41.fasta,15,15,14,15,15,16
+locus_6sp_27.fasta,4,4,2,4,6,5
+locus_6sp_39.fasta,18,16,17,17,16,17
+locus_6sp_10.fasta,25,25,24,25,24,24
+locus_6sp_25.fasta,82,82,79,81,87,79
+locus_6sp_32.fasta,47,47,44,45,46,45
+locus_6sp_53.fasta,39,39,36,37,36,38
+locus_3sp_2.fasta,NaN,9,NaN,10,9,NaN
+locus_6sp_47.fasta,16,17,16,16,16,16
+locus_6sp_16.fasta,8,8,9,11,9,8
+locus_6sp_11.fasta,45,45,47,45,45,46
+locus_6sp_35.fasta,20,21,21,22,23,23
+locus_6sp_46.fasta,49,49,49,46,51,48
+locus_3sp_7.fasta,8,8,8,NaN,NaN,NaN
+locus_6sp_30.fasta,9,9,9,9,8,8
+locus_6sp_57.fasta,18,18,19,19,19,19
+locus_6sp_50.fasta,77,74,80,75,76,80
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/FYW.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/FYW.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,2,2,2,2,2,2
+locus_6sp_60.fasta,3,3,3,3,3,3
+locus_6sp_40.fasta,5,5,5,5,5,5
+locus_6sp_58.fasta,0,0,0,0,0,0
+locus_6sp_38.fasta,13,13,13,13,13,13
+locus_4sp_4.fasta,7,NaN,9,10,9,NaN
+locus_4sp_6.fasta,12,12,13,12,NaN,NaN
+locus_6sp_41.fasta,5,5,5,6,6,6
+locus_6sp_27.fasta,4,4,2,2,4,3
+locus_6sp_39.fasta,9,9,8,8,7,8
+locus_6sp_10.fasta,16,16,16,16,16,16
+locus_6sp_25.fasta,29,29,29,31,30,30
+locus_6sp_32.fasta,14,14,14,14,15,15
+locus_6sp_53.fasta,17,17,17,16,17,15
+locus_3sp_2.fasta,NaN,5,NaN,5,5,NaN
+locus_6sp_47.fasta,3,3,3,3,3,3
+locus_6sp_16.fasta,3,3,3,4,3,3
+locus_6sp_11.fasta,9,9,9,9,10,9
+locus_6sp_35.fasta,13,13,15,12,13,16
+locus_6sp_46.fasta,12,11,11,11,11,11
+locus_3sp_7.fasta,1,1,1,NaN,NaN,NaN
+locus_6sp_30.fasta,3,3,3,3,3,3
+locus_6sp_57.fasta,4,4,4,4,4,4
+locus_6sp_50.fasta,26,26,27,25,25,26
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/GARP.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/GARP.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,5,6,6,6,6,6
+locus_6sp_60.fasta,7,7,8,9,7,8
+locus_6sp_40.fasta,28,28,25,25,27,26
+locus_6sp_58.fasta,13,13,12,12,13,12
+locus_6sp_38.fasta,31,30,32,31,31,31
+locus_4sp_4.fasta,12,NaN,11,10,13,NaN
+locus_4sp_6.fasta,20,20,18,19,NaN,NaN
+locus_6sp_41.fasta,15,14,17,16,14,13
+locus_6sp_27.fasta,4,3,6,2,4,5
+locus_6sp_39.fasta,8,9,12,10,10,12
+locus_6sp_10.fasta,12,12,12,12,11,12
+locus_6sp_25.fasta,71,70,72,68,67,69
+locus_6sp_32.fasta,25,25,26,24,26,26
+locus_6sp_53.fasta,29,28,28,28,28,28
+locus_3sp_2.fasta,NaN,9,NaN,9,10,NaN
+locus_6sp_47.fasta,18,18,18,18,19,18
+locus_6sp_16.fasta,10,9,9,9,10,9
+locus_6sp_11.fasta,41,41,40,40,41,41
+locus_6sp_35.fasta,14,14,16,16,14,14
+locus_6sp_46.fasta,27,28,27,27,22,28
+locus_3sp_7.fasta,4,4,4,NaN,NaN,NaN
+locus_6sp_30.fasta,3,3,3,3,3,4
+locus_6sp_57.fasta,23,23,23,22,22,24
+locus_6sp_50.fasta,98,98,98,100,99,99
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/IVYWREL.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/IVYWREL.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,10,9,10,9,9,9
+locus_6sp_60.fasta,8,8,8,6,8,8
+locus_6sp_40.fasta,34,37,36,36,34,36
+locus_6sp_58.fasta,9,9,9,7,8,9
+locus_6sp_38.fasta,36,36,38,36,39,40
+locus_4sp_4.fasta,32,NaN,32,29,31,NaN
+locus_4sp_6.fasta,39,39,40,40,NaN,NaN
+locus_6sp_41.fasta,25,24,27,26,24,25
+locus_6sp_27.fasta,16,15,19,17,21,16
+locus_6sp_39.fasta,20,18,21,17,21,21
+locus_6sp_10.fasta,22,22,23,22,23,23
+locus_6sp_25.fasta,112,113,112,110,110,113
+locus_6sp_32.fasta,51,51,48,50,48,50
+locus_6sp_53.fasta,46,46,46,48,45,48
+locus_3sp_2.fasta,NaN,10,NaN,11,11,NaN
+locus_6sp_47.fasta,29,29,29,29,29,29
+locus_6sp_16.fasta,17,18,17,18,16,17
+locus_6sp_11.fasta,53,54,55,58,52,54
+locus_6sp_35.fasta,30,30,33,32,30,28
+locus_6sp_46.fasta,69,70,74,72,68,71
+locus_3sp_7.fasta,14,13,14,NaN,NaN,NaN
+locus_6sp_30.fasta,6,6,6,6,7,7
+locus_6sp_57.fasta,36,36,35,36,36,36
+locus_6sp_50.fasta,103,104,101,101,98,100
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/QH.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/QH.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,1,1,1,1,1,1
+locus_6sp_60.fasta,0,0,0,0,0,0
+locus_6sp_40.fasta,4,4,4,4,4,4
+locus_6sp_58.fasta,1,1,1,2,1,1
+locus_6sp_38.fasta,13,13,12,12,10,11
+locus_4sp_4.fasta,6,NaN,4,4,5,NaN
+locus_4sp_6.fasta,6,7,6,7,NaN,NaN
+locus_6sp_41.fasta,3,3,3,3,3,3
+locus_6sp_27.fasta,5,5,4,5,5,5
+locus_6sp_39.fasta,7,8,6,7,7,6
+locus_6sp_10.fasta,3,3,3,3,3,3
+locus_6sp_25.fasta,21,21,21,20,21,19
+locus_6sp_32.fasta,5,4,6,4,4,5
+locus_6sp_53.fasta,7,7,8,8,7,6
+locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN
+locus_6sp_47.fasta,6,6,6,6,6,6
+locus_6sp_16.fasta,2,2,3,2,2,3
+locus_6sp_11.fasta,9,9,9,8,8,9
+locus_6sp_35.fasta,2,2,2,2,2,3
+locus_6sp_46.fasta,6,5,6,8,8,7
+locus_3sp_7.fasta,5,5,5,NaN,NaN,NaN
+locus_6sp_30.fasta,0,0,0,0,0,0
+locus_6sp_57.fasta,5,5,5,5,5,5
+locus_6sp_50.fasta,7,7,7,7,8,7
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/RHK.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/RHK.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,1,1,1,1,1,1
+locus_6sp_60.fasta,3,3,3,4,3,3
+locus_6sp_40.fasta,18,18,17,18,17,18
+locus_6sp_58.fasta,10,10,10,10,10,10
+locus_6sp_38.fasta,42,42,42,42,42,43
+locus_4sp_4.fasta,12,NaN,10,9,11,NaN
+locus_4sp_6.fasta,17,17,18,18,NaN,NaN
+locus_6sp_41.fasta,8,8,10,9,5,6
+locus_6sp_27.fasta,5,4,6,6,4,6
+locus_6sp_39.fasta,9,9,11,10,9,11
+locus_6sp_10.fasta,5,5,5,5,5,5
+locus_6sp_25.fasta,40,40,44,41,42,42
+locus_6sp_32.fasta,27,28,27,27,26,26
+locus_6sp_53.fasta,21,21,22,20,20,18
+locus_3sp_2.fasta,NaN,5,NaN,5,5,NaN
+locus_6sp_47.fasta,23,23,23,23,23,23
+locus_6sp_16.fasta,3,3,3,3,3,3
+locus_6sp_11.fasta,22,23,23,24,23,22
+locus_6sp_35.fasta,6,6,8,7,7,7
+locus_6sp_46.fasta,37,39,39,38,38,39
+locus_3sp_7.fasta,5,5,5,NaN,NaN,NaN
+locus_6sp_30.fasta,5,5,5,5,4,5
+locus_6sp_57.fasta,11,11,12,12,11,12
+locus_6sp_50.fasta,20,19,19,20,19,19
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/RHKDE.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/RHKDE.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,3,3,3,3,3,3
+locus_6sp_60.fasta,7,7,7,8,7,7
+locus_6sp_40.fasta,31,31,30,30,30,30
+locus_6sp_58.fasta,13,13,13,13,13,13
+locus_6sp_38.fasta,54,54,54,54,54,55
+locus_4sp_4.fasta,14,NaN,13,11,14,NaN
+locus_4sp_6.fasta,31,31,32,32,NaN,NaN
+locus_6sp_41.fasta,11,11,13,12,8,9
+locus_6sp_27.fasta,6,5,9,7,5,7
+locus_6sp_39.fasta,16,15,18,16,15,18
+locus_6sp_10.fasta,9,9,9,9,9,9
+locus_6sp_25.fasta,81,81,86,81,81,84
+locus_6sp_32.fasta,46,47,46,48,45,45
+locus_6sp_53.fasta,38,38,39,36,35,35
+locus_3sp_2.fasta,NaN,10,NaN,10,9,NaN
+locus_6sp_47.fasta,29,29,29,29,29,29
+locus_6sp_16.fasta,12,12,11,11,14,11
+locus_6sp_11.fasta,44,45,45,46,44,43
+locus_6sp_35.fasta,8,8,10,9,9,9
+locus_6sp_46.fasta,63,65,66,64,64,65
+locus_3sp_7.fasta,12,12,12,NaN,NaN,NaN
+locus_6sp_30.fasta,8,8,8,8,8,8
+locus_6sp_57.fasta,23,23,24,24,23,24
+locus_6sp_50.fasta,31,30,29,31,30,29
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/STNQ.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/STNQ.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,2,2,2,2,2,2
+locus_6sp_60.fasta,7,7,8,7,7,8
+locus_6sp_40.fasta,13,13,12,12,13,11
+locus_6sp_58.fasta,35,35,36,36,36,36
+locus_6sp_38.fasta,33,34,33,34,34,32
+locus_4sp_4.fasta,15,NaN,14,18,10,NaN
+locus_4sp_6.fasta,16,14,13,14,NaN,NaN
+locus_6sp_41.fasta,23,23,21,22,23,23
+locus_6sp_27.fasta,5,5,4,7,5,5
+locus_6sp_39.fasta,10,12,8,12,10,8
+locus_6sp_10.fasta,10,10,10,10,10,10
+locus_6sp_25.fasta,57,59,54,57,57,53
+locus_6sp_32.fasta,20,19,20,20,18,20
+locus_6sp_53.fasta,21,22,21,23,23,22
+locus_3sp_2.fasta,NaN,4,NaN,4,3,NaN
+locus_6sp_47.fasta,12,11,12,12,11,12
+locus_6sp_16.fasta,6,6,8,7,5,8
+locus_6sp_11.fasta,22,21,22,22,26,24
+locus_6sp_35.fasta,11,11,9,10,14,9
+locus_6sp_46.fasta,17,16,14,18,20,17
+locus_3sp_7.fasta,10,10,10,NaN,NaN,NaN
+locus_6sp_30.fasta,2,2,2,2,2,2
+locus_6sp_57.fasta,21,21,21,22,21,20
+locus_6sp_50.fasta,38,39,39,36,38,39
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/VLIM.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/VLIM.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,9,8,8,8,8,8
+locus_6sp_60.fasta,4,4,3,2,4,3
+locus_6sp_40.fasta,26,27,28,29,27,28
+locus_6sp_58.fasta,1,1,1,0,0,1
+locus_6sp_38.fasta,1,1,1,1,3,3
+locus_4sp_4.fasta,26,NaN,25,23,27,NaN
+locus_4sp_6.fasta,14,15,15,15,NaN,NaN
+locus_6sp_41.fasta,19,19,19,18,20,20
+locus_6sp_27.fasta,14,14,13,15,16,13
+locus_6sp_39.fasta,10,9,10,9,12,10
+locus_6sp_10.fasta,14,14,14,14,15,14
+locus_6sp_25.fasta,71,71,69,71,73,73
+locus_6sp_32.fasta,33,33,31,31,33,31
+locus_6sp_53.fasta,21,21,21,23,22,25
+locus_3sp_2.fasta,NaN,5,NaN,5,6,NaN
+locus_6sp_47.fasta,14,15,14,14,14,14
+locus_6sp_16.fasta,10,11,10,10,9,10
+locus_6sp_11.fasta,37,37,38,38,33,37
+locus_6sp_35.fasta,23,23,24,24,22,22
+locus_6sp_46.fasta,32,32,33,33,32,31
+locus_3sp_7.fasta,9,9,9,NaN,NaN,NaN
+locus_6sp_30.fasta,3,3,3,3,3,3
+locus_6sp_57.fasta,25,25,25,25,26,25
+locus_6sp_50.fasta,89,90,89,90,89,89
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/ratio_AC_VLIM.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_AC_VLIM.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0.111111111111,0.25,0.25,0.25,0.25,0.25
+locus_6sp_60.fasta,0.75,0.75,1.0,1.5,0.75,1.0
+locus_6sp_40.fasta,0.307692307692,0.259259259259,0.285714285714,0.206896551724,0.296296296296,0.285714285714
+locus_6sp_58.fasta,1.0,1.0,0.0,-1,-1,0.0
+locus_6sp_38.fasta,4.0,4.0,5.0,4.0,0.666666666667,1.0
+locus_4sp_4.fasta,0.230769230769,NaN,0.28,0.260869565217,0.259259259259,NaN
+locus_4sp_6.fasta,0.928571428571,0.933333333333,0.866666666667,0.866666666667,NaN,NaN
+locus_6sp_41.fasta,0.368421052632,0.368421052632,0.368421052632,0.388888888889,0.4,0.35
+locus_6sp_27.fasta,0.142857142857,0.214285714286,0.230769230769,0.133333333333,0.125,0.153846153846
+locus_6sp_39.fasta,0.3,0.333333333333,0.4,0.333333333333,0.25,0.4
+locus_6sp_10.fasta,0.571428571429,0.571428571429,0.571428571429,0.571428571429,0.466666666667,0.571428571429
+locus_6sp_25.fasta,0.281690140845,0.267605633803,0.304347826087,0.253521126761,0.27397260274,0.260273972603
+locus_6sp_32.fasta,0.272727272727,0.272727272727,0.354838709677,0.290322580645,0.272727272727,0.354838709677
+locus_6sp_53.fasta,0.333333333333,0.285714285714,0.285714285714,0.260869565217,0.272727272727,0.32
+locus_3sp_2.fasta,NaN,0.6,NaN,0.6,0.666666666667,NaN
+locus_6sp_47.fasta,0.0714285714286,0.0666666666667,0.0714285714286,0.0714285714286,0.0714285714286,0.0714285714286
+locus_6sp_16.fasta,0.5,0.363636363636,0.4,0.4,0.555555555556,0.4
+locus_6sp_11.fasta,0.432432432432,0.432432432432,0.368421052632,0.394736842105,0.454545454545,0.405405405405
+locus_6sp_35.fasta,0.347826086957,0.347826086957,0.25,0.291666666667,0.272727272727,0.318181818182
+locus_6sp_46.fasta,0.21875,0.21875,0.212121212121,0.181818181818,0.15625,0.258064516129
+locus_3sp_7.fasta,0.333333333333,0.333333333333,0.333333333333,NaN,NaN,NaN
+locus_6sp_30.fasta,0.333333333333,0.333333333333,0.333333333333,0.333333333333,0.333333333333,0.333333333333
+locus_6sp_57.fasta,0.4,0.4,0.36,0.32,0.346153846154,0.4
+locus_6sp_50.fasta,0.426966292135,0.411111111111,0.426966292135,0.444444444444,0.438202247191,0.438202247191
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/ratio_APGC_VLIM.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_APGC_VLIM.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0.555555555556,0.75,0.75,0.75,0.75,0.75
+locus_6sp_60.fasta,1.5,1.5,2.0,3.5,1.5,2.0
+locus_6sp_40.fasta,0.807692307692,0.740740740741,0.75,0.689655172414,0.777777777778,0.785714285714
+locus_6sp_58.fasta,5.0,5.0,4.0,-1,-1,4.0
+locus_6sp_38.fasta,15.0,14.0,15.0,14.0,4.0,4.33333333333
+locus_4sp_4.fasta,0.384615384615,NaN,0.44,0.434782608696,0.444444444444,NaN
+locus_4sp_6.fasta,1.64285714286,1.6,1.53333333333,1.53333333333,NaN,NaN
+locus_6sp_41.fasta,0.578947368421,0.578947368421,0.578947368421,0.611111111111,0.6,0.55
+locus_6sp_27.fasta,0.285714285714,0.357142857143,0.384615384615,0.133333333333,0.1875,0.384615384615
+locus_6sp_39.fasta,0.7,0.777777777778,0.8,0.777777777778,0.666666666667,0.8
+locus_6sp_10.fasta,1.0,1.0,1.0,1.0,0.866666666667,1.0
+locus_6sp_25.fasta,0.845070422535,0.816901408451,0.869565217391,0.816901408451,0.780821917808,0.794520547945
+locus_6sp_32.fasta,0.575757575758,0.575757575758,0.677419354839,0.612903225806,0.636363636364,0.677419354839
+locus_6sp_53.fasta,1.04761904762,1.0,1.0,0.913043478261,1.0,0.88
+locus_3sp_2.fasta,NaN,1.6,NaN,1.6,1.5,NaN
+locus_6sp_47.fasta,0.571428571429,0.533333333333,0.571428571429,0.571428571429,0.642857142857,0.571428571429
+locus_6sp_16.fasta,1.1,0.909090909091,1.0,1.0,1.22222222222,1.0
+locus_6sp_11.fasta,1.0,1.0,0.921052631579,0.894736842105,1.09090909091,0.972972972973
+locus_6sp_35.fasta,0.739130434783,0.739130434783,0.583333333333,0.708333333333,0.636363636364,0.727272727273
+locus_6sp_46.fasta,0.40625,0.40625,0.393939393939,0.333333333333,0.3125,0.41935483871
+locus_3sp_7.fasta,0.333333333333,0.333333333333,0.333333333333,NaN,NaN,NaN
+locus_6sp_30.fasta,0.666666666667,0.666666666667,0.666666666667,0.666666666667,0.666666666667,0.666666666667
+locus_6sp_57.fasta,0.8,0.8,0.76,0.72,0.730769230769,0.8
+locus_6sp_50.fasta,1.01123595506,0.988888888889,1.01123595506,1.02222222222,1.03370786517,1.02247191011
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/ratio_EK_QH.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_EK_QH.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,2.0,2.0,2.0,2.0,2.0,2.0
+locus_6sp_60.fasta,-1,-1,-1,-1,-1,-1
+locus_6sp_40.fasta,4.0,4.0,4.75,4.5,4.0,4.75
+locus_6sp_58.fasta,1.0,1.0,1.0,0.5,1.0,1.0
+locus_6sp_38.fasta,1.69230769231,1.69230769231,1.91666666667,1.75,2.1,2.0
+locus_4sp_4.fasta,0.333333333333,NaN,0.5,0.5,0.2,NaN
+locus_4sp_6.fasta,2.0,1.71428571429,2.66666666667,1.85714285714,NaN,NaN
+locus_6sp_41.fasta,0.666666666667,1.0,0.666666666667,0.666666666667,0.666666666667,0.666666666667
+locus_6sp_27.fasta,0.2,0.2,0.5,0.2,0.2,0.2
+locus_6sp_39.fasta,1.28571428571,0.875,1.33333333333,1.0,1.14285714286,1.33333333333
+locus_6sp_10.fasta,1.33333333333,1.33333333333,1.33333333333,1.33333333333,1.33333333333,1.33333333333
+locus_6sp_25.fasta,1.71428571429,1.66666666667,1.85714285714,1.85,1.80952380952,1.94736842105
+locus_6sp_32.fasta,6.2,8.0,5.33333333333,8.5,7.75,6.6
+locus_6sp_53.fasta,3.42857142857,3.42857142857,2.875,2.875,3.28571428571,3.66666666667
+locus_3sp_2.fasta,NaN,5.0,NaN,6.0,5.0,NaN
+locus_6sp_47.fasta,2.0,2.0,2.0,2.0,2.0,2.0
+locus_6sp_16.fasta,4.0,4.0,2.33333333333,4.0,4.0,2.33333333333
+locus_6sp_11.fasta,3.22222222222,3.22222222222,3.11111111111,3.625,3.5,3.11111111111
+locus_6sp_35.fasta,1.5,1.5,1.5,1.5,1.5,1.0
+locus_6sp_46.fasta,7.5,9.2,8.16666666667,5.5,6.0,6.71428571429
+locus_3sp_7.fasta,1.4,1.2,1.4,NaN,NaN,NaN
+locus_6sp_30.fasta,-1,-1,-1,-1,-1,-1
+locus_6sp_57.fasta,2.6,2.6,2.4,2.6,2.4,2.6
+locus_6sp_50.fasta,1.57142857143,1.14285714286,1.28571428571,1.42857142857,1.125,1.28571428571
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/ratio_ERK_DNQTSHA.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_ERK_DNQTSHA.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0.5,0.4,0.4,0.4,0.4,0.4
+locus_6sp_60.fasta,0.363636363636,0.363636363636,0.166666666667,0.25,0.363636363636,0.166666666667
+locus_6sp_40.fasta,0.862068965517,0.888888888889,1.16,1.12,0.862068965517,1.20833333333
+locus_6sp_58.fasta,0.05,0.05,0.05,0.0487804878049,0.0487804878049,0.05
+locus_6sp_38.fasta,0.698113207547,0.685185185185,0.730769230769,0.666666666667,0.72,0.74
+locus_4sp_4.fasta,0.12,NaN,0.136363636364,0.12,0.0526315789474,NaN
+locus_4sp_6.fasta,0.68,0.68,1.14285714286,0.791666666667,NaN,NaN
+locus_6sp_41.fasta,0.0967741935484,0.161290322581,0.103448275862,0.1,0.0967741935484,0.0967741935484
+locus_6sp_27.fasta,0.2,0.2,0.222222222222,0.181818181818,0.125,0.222222222222
+locus_6sp_39.fasta,0.684210526316,0.47619047619,0.611111111111,0.47619047619,0.666666666667,0.611111111111
+locus_6sp_10.fasta,0.315789473684,0.315789473684,0.315789473684,0.315789473684,0.333333333333,0.315789473684
+locus_6sp_25.fasta,0.495412844037,0.472727272727,0.546296296296,0.532710280374,0.546296296296,0.528301886792
+locus_6sp_32.fasta,1.38888888889,1.48571428571,1.34210526316,1.47222222222,1.47058823529,1.44444444444
+locus_6sp_53.fasta,1.0,1.0,0.916666666667,0.942857142857,0.971428571429,0.914285714286
+locus_3sp_2.fasta,NaN,0.818181818182,NaN,1.0,0.9,NaN
+locus_6sp_47.fasta,1.1,1.15789473684,1.1,1.1,1.15789473684,1.1
+locus_6sp_16.fasta,0.714285714286,0.769230769231,0.6,0.769230769231,0.666666666667,0.6
+locus_6sp_11.fasta,1.0,1.0,0.977272727273,1.0,0.895833333333,0.955555555556
+locus_6sp_35.fasta,0.294117647059,0.294117647059,0.3125,0.3125,0.25,0.3125
+locus_6sp_46.fasta,2.42857142857,2.59259259259,3.08333333333,2.35714285714,2.55172413793,2.53571428571
+locus_3sp_7.fasta,0.647058823529,0.555555555556,0.647058823529,NaN,NaN,NaN
+locus_6sp_30.fasta,2.5,2.5,2.5,2.5,2.25,2.0
+locus_6sp_57.fasta,0.5,0.5,0.472222222222,0.514285714286,0.472222222222,0.514285714286
+locus_6sp_50.fasta,0.219512195122,0.156626506024,0.180722891566,0.192771084337,0.176470588235,0.178571428571
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/ratio_GARP_FYMINK.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_GARP_FYMINK.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,0.285714285714,0.285714285714,0.333333333333,0.285714285714,0.285714285714,0.285714285714
+locus_6sp_60.fasta,0.5,0.5,0.333333333333,0.285714285714,0.5,0.333333333333
+locus_6sp_40.fasta,0.571428571429,0.615384615385,0.678571428571,0.666666666667,0.592592592593,0.678571428571
+locus_6sp_58.fasta,0.333333333333,0.333333333333,0.5,0.5,0.333333333333,0.5
+locus_6sp_38.fasta,0.666666666667,0.666666666667,0.69696969697,0.636363636364,0.617647058824,0.666666666667
+locus_4sp_4.fasta,0.111111111111,NaN,0.0909090909091,0.0833333333333,0.0416666666667,NaN
+locus_4sp_6.fasta,0.461538461538,0.461538461538,0.571428571429,0.52,NaN,NaN
+locus_6sp_41.fasta,0.133333333333,0.2,0.142857142857,0.133333333333,0.133333333333,0.125
+locus_6sp_27.fasta,0.25,0.25,1.0,0.25,0.166666666667,0.2
+locus_6sp_39.fasta,0.5,0.4375,0.470588235294,0.411764705882,0.5,0.470588235294
+locus_6sp_10.fasta,0.16,0.16,0.166666666667,0.16,0.166666666667,0.166666666667
+locus_6sp_25.fasta,0.439024390244,0.426829268293,0.493670886076,0.456790123457,0.436781609195,0.46835443038
+locus_6sp_32.fasta,0.659574468085,0.68085106383,0.727272727273,0.755555555556,0.673913043478,0.733333333333
+locus_6sp_53.fasta,0.615384615385,0.615384615385,0.638888888889,0.621621621622,0.638888888889,0.578947368421
+locus_3sp_2.fasta,NaN,0.555555555556,NaN,0.6,0.555555555556,NaN
+locus_6sp_47.fasta,0.75,0.705882352941,0.75,0.75,0.75,0.75
+locus_6sp_16.fasta,1.0,1.0,0.777777777778,0.727272727273,0.888888888889,0.875
+locus_6sp_11.fasta,0.644444444444,0.644444444444,0.595744680851,0.644444444444,0.622222222222,0.608695652174
+locus_6sp_35.fasta,0.15,0.142857142857,0.142857142857,0.136363636364,0.130434782609,0.130434782609
+locus_6sp_46.fasta,0.918367346939,0.938775510204,1.0,0.95652173913,0.941176470588,0.979166666667
+locus_3sp_7.fasta,0.875,0.75,0.875,NaN,NaN,NaN
+locus_6sp_30.fasta,0.666666666667,0.666666666667,0.666666666667,0.666666666667,0.75,0.625
+locus_6sp_57.fasta,0.722222222222,0.722222222222,0.631578947368,0.684210526316,0.631578947368,0.684210526316
+locus_6sp_50.fasta,0.142857142857,0.108108108108,0.1125,0.133333333333,0.118421052632,0.1125
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/total_hydration.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/total_hydration.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,45.0,45.0,45.0,45.0,45.0,45.0
+locus_6sp_60.fasta,61.5,61.5,61.0,62.0,61.5,61.0
+locus_6sp_40.fasta,247.0,247.0,246.5,245.0,245.0,245.5
+locus_6sp_58.fasta,126.5,126.5,127.5,130.5,127.5,127.5
+locus_6sp_38.fasta,376.0,375.0,374.5,372.5,367.5,374.0
+locus_4sp_4.fasta,135.0,NaN,134.0,129.0,130.5,NaN
+locus_4sp_6.fasta,257.0,256.0,264.0,262.5,NaN,NaN
+locus_6sp_41.fasta,126.0,127.5,128.0,126.0,118.0,121.0
+locus_6sp_27.fasta,57.5,55.5,74.0,61.5,55.5,62.5
+locus_6sp_39.fasta,138.5,129.5,135.0,130.5,130.0,135.0
+locus_6sp_10.fasta,125.0,125.0,125.0,125.0,122.0,125.0
+locus_6sp_25.fasta,747.0,745.5,758.5,744.5,742.0,749.5
+locus_6sp_32.fasta,359.5,362.0,359.0,372.0,356.5,359.5
+locus_6sp_53.fasta,317.0,318.0,319.5,311.5,305.5,307.0
+locus_3sp_2.fasta,NaN,85.5,NaN,87.0,79.5,NaN
+locus_6sp_47.fasta,180.0,179.0,180.0,180.0,179.0,180.0
+locus_6sp_16.fasta,114.0,114.0,112.5,112.0,123.0,112.5
+locus_6sp_11.fasta,378.5,380.5,380.0,384.5,378.0,374.0
+locus_6sp_35.fasta,118.5,118.5,119.5,121.5,121.5,114.5
+locus_6sp_46.fasta,429.5,435.0,442.5,432.0,440.0,437.5
+locus_3sp_7.fasta,102.5,101.0,102.5,NaN,NaN,NaN
+locus_6sp_30.fasta,57.0,57.0,57.0,57.0,60.0,55.5
+locus_6sp_57.fasta,226.5,226.5,224.0,226.5,225.0,224.5
+locus_6sp_50.fasta,473.5,468.0,463.5,469.0,467.5,464.5
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/total_partial_specific_volume.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/total_partial_specific_volume.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Ac,Ap,Pf,Pg,Pp,Ps
+locus_6sp_18.fasta,15.64,15.52,15.67,15.52,15.48,15.52
+locus_6sp_60.fasta,19.64,19.64,19.24,19.04,19.64,19.24
+locus_6sp_40.fasta,71.19,71.17,71.58,71.77,71.43,71.62
+locus_6sp_58.fasta,38.79,38.83,38.79,38.62,38.55,38.79
+locus_6sp_38.fasta,81.92,81.86,82.03,81.87,82.29,82.24
+locus_4sp_4.fasta,55.12,NaN,54.64,54.51,54.66,NaN
+locus_4sp_6.fasta,67.26,67.51,67.91,67.51,NaN,NaN
+locus_6sp_41.fasta,51.81,52.05,51.85,51.91,52.2,52.23
+locus_6sp_27.fasta,25.85,25.76,25.41,25.71,26.01,25.59
+locus_6sp_39.fasta,38.27,38.12,38.34,38.04,38.67,38.34
+locus_6sp_10.fasta,45.83,45.83,45.98,45.83,46.26,45.98
+locus_6sp_25.fasta,219.26,218.84,219.08,219.6,219.52,219.72
+locus_6sp_32.fasta,98.84,98.99,98.67,98.57,98.6,98.67
+locus_6sp_53.fasta,87.81,87.77,87.58,88.01,88.13,87.94
+locus_3sp_2.fasta,NaN,23.01,NaN,23.11,23.31,NaN
+locus_6sp_47.fasta,48.9,48.95,48.9,48.9,48.8,48.9
+locus_6sp_16.fasta,30.88,31.0,30.61,30.81,30.52,30.69
+locus_6sp_11.fasta,110.48,110.63,110.48,110.41,110.02,110.42
+locus_6sp_35.fasta,54.48,54.52,55.0,54.63,54.6,54.4
+locus_6sp_46.fasta,103.31,103.35,103.88,103.24,103.59,103.44
+locus_3sp_7.fasta,25.94,25.88,25.9,NaN,NaN,NaN
+locus_6sp_30.fasta,13.25,13.25,13.25,13.25,13.09,13.13
+locus_6sp_57.fasta,68.74,68.74,68.68,68.74,68.88,68.78
+locus_6sp_50.fasta,205.01,204.83,204.81,204.76,204.37,204.67
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/total_residue_volume.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/total_residue_volume.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/02_tables_per_aa_variable/total_residue_weight.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/02_tables_per_aa_variable/total_residue_weight.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/A.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/A.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/C.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/C.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/D.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/D.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/E.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/E.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/F.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/F.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/G.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/G.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/H.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/H.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/I.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/I.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/K.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/K.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"confidence_interval_low",0.118117248757025,0.0125791170934251,0.194120449683243,0
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/L.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/L.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"confidence_interval_low",0.0527449505263169,0.0527449505263169,0.146632799634673,0.146632799634673
+"confidence_interval_high",0.853367200365327,0.853367200365327,0.947255049473683,0.947255049473683
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/M.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/M.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"confidence_interval_low",0.00840375865961264,0.158113883008419,0.0942993240502461,0.158113883008419
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/N.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/N.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"confidence_interval_low",0.00840375865961264,0.025,0.222778095503512,0.158113883008419
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/P.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/P.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/Q.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/Q.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"confidence_interval_low",0.0125791170934251,0.00630946320970987,0.194120449683243,0.0989882784425079
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/R.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/R.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"Trial_Number",8,6,6,4
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+"probability_of_success",0.5,0.666666666666667,0.333333333333333,0.75
+"confidence_interval_low",0.157012770487058,0.222778095503512,0.0432718682927417,0.194120449683243
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/S.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/S.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"Trial_Number",5,7,7,4
+"p-value",1,0.453125,1,0.625
+"probability_of_success",0.4,0.714285714285714,0.571428571428571,0.25
+"confidence_interval_low",0.0527449505263169,0.290420863737343,0.184051567640083,0.00630946320970987
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/T.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/T.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"Trial_Number",4,6,4,5
+"p-value",1,0.6875,1,1
+"probability_of_success",0.5,0.666666666666667,0.5,0.4
+"confidence_interval_low",0.067585986488543,0.222778095503512,0.067585986488543,0.0527449505263169
+"confidence_interval_high",0.932414013511457,0.956728131707258,0.932414013511457,0.853367200365327
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/V.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/V.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"p-value",1,1,1,1
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+"confidence_interval_low",0.067585986488543,0.157012770487058,0.157012770487058,0.146632799634673
+"confidence_interval_high",0.932414013511457,0.842987229512942,0.842987229512942,0.947255049473683
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/W.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/W.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa/Y.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa/Y.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg"
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/AC.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/AC.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/APGC.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/APGC.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/AVLIM.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/AVLIM.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/AVLIMFYW.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/AVLIMFYW.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/DE.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/DE.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/DNQTSHA.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/DNQTSHA.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/EK.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/EK.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/ERK.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/ERK.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/FYMINK.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/FYMINK.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/FYW.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/FYW.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/GARP.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/GARP.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/IVYWREL.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/IVYWREL.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/QH.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/QH.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/RHK.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/RHK.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"confidence_interval_low",0.146632799634673,0.283582063881911,0,0.146632799634673
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/RHKDE.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/RHKDE.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/STNQ.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/STNQ.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"confidence_interval_low",0.0432718682927417,0.222778095503512,0.184051567640083,0.0602177341729066
+"confidence_interval_high",0.777221904496488,0.956728131707258,0.901011721557492,0.609742559572421
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/VLIM.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/VLIM.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"confidence_interval_low",0.146632799634673,0.244863216366552,0.184051567640083,0.067585986488543
+"confidence_interval_high",0.947255049473683,0.914766585862746,0.901011721557492,0.932414013511457
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/ratio_AC_VLIM.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_AC_VLIM.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"Trial_Number",10,12,14,9
+"p-value",0.75390625,0.14599609375,0.4239501953125,0.0390625
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+"confidence_interval_low",0.262378076606945,0.0548606445279928,0.127598429859159,0.517503485082663
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/ratio_APGC_VLIM.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_APGC_VLIM.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"p-value",1,0.1796875,0.4239501953125,0.109375
+"probability_of_success",0.5,0.222222222222222,0.357142857142857,0.8
+"confidence_interval_low",0.187086028447399,0.0281449734778982,0.127598429859159,0.443904537692359
+"confidence_interval_high",0.812913971552601,0.600093573716312,0.648619889384008,0.974789273673167
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/ratio_EK_QH.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_EK_QH.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"Trial_Number",7,6,6,9
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+"confidence_interval_low",0.0989882784425079,0.118117248757025,0.0432718682927417,0.212008506778868
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diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/ratio_ERK_DNQTSHA.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_ERK_DNQTSHA.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"Trial_Number",8,6,9,10
+"p-value",0.2890625,0.6875,0.5078125,0.75390625
+"probability_of_success",0.75,0.333333333333333,0.333333333333333,0.4
+"confidence_interval_low",0.349144205587176,0.0432718682927417,0.0748546314196918,0.121552258119827
+"confidence_interval_high",0.968145973750056,0.777221904496488,0.70070494379146,0.737621923393055
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/ratio_GARP_FYMINK.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_GARP_FYMINK.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"Trial_Number",10,7,9,9
+"p-value",1,1,1,1
+"probability_of_success",0.5,0.428571428571429,0.444444444444444,0.444444444444444
+"confidence_interval_low",0.187086028447399,0.0989882784425079,0.136995662265167,0.136995662265167
+"confidence_interval_high",0.812913971552601,0.815948432359917,0.787991493221132,0.787991493221132
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/total_hydratation.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/total_hydratation.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
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+"Greater",5,6,4,5
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+"Trial_Number",8,11,11,11
+"p-value",0.7265625,1,0.548828125,1
+"probability_of_success",0.625,0.545454545454545,0.363636363636364,0.454545454545455
+"confidence_interval_low",0.244863216366552,0.233793597659345,0.109263443819098,0.167488094063707
+"confidence_interval_high",0.914766585862746,0.832511905936293,0.692095284988323,0.766206402340655
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/total_partial_specific_volume.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/total_partial_specific_volume.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg"
+"Greater",6,3,8,5
+"Lower",5,7,8,3
+"Difference",1,-4,0,2
+"Trial_Number",11,10,16,8
+"p-value",1,0.34375,1,0.7265625
+"probability_of_success",0.545454545454545,0.3,0.5,0.625
+"confidence_interval_low",0.233793597659345,0.0667395111777345,0.246510111490575,0.244863216366552
+"confidence_interval_high",0.832511905936293,0.652452850059997,0.753489888509425,0.914766585862746
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/total_residue_volume.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/total_residue_volume.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg"
+"Greater",7,6,5,5
+"Lower",4,6,11,3
+"Difference",3,0,-6,2
+"Trial_Number",11,12,16,8
+"p-value",0.548828125,1,0.210113525390625,0.7265625
+"probability_of_success",0.636363636363636,0.5,0.3125,0.625
+"confidence_interval_low",0.307904715011677,0.210944638239297,0.110169954717117,0.244863216366552
+"confidence_interval_high",0.890736556180902,0.789055361760703,0.586620636451359,0.914766585862746
diff -r 000000000000 -r acc3674e515b test-data/OUT_aa/04_outputs_aa_variables/total_residue_weight.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_aa/04_outputs_aa_variables/total_residue_weight.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg"
+"Greater",6,6,5,6
+"Lower",5,6,8,5
+"Difference",1,0,-3,1
+"Trial_Number",11,12,13,11
+"p-value",1,1,0.5810546875,1
+"probability_of_success",0.545454545454545,0.5,0.384615384615385,0.545454545454545
+"confidence_interval_low",0.233793597659345,0.210944638239297,0.138579338890161,0.233793597659345
+"confidence_interval_high",0.832511905936293,0.789055361760703,0.684222397085937,0.832511905936293
diff -r 000000000000 -r acc3674e515b test-data/OUT_concat/MutCount_concat_log.output
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_concat/MutCount_concat_log.output Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,96 @@
+
+ ------ Occurences and frequencies of codons, amino-acids, amino-acids types -------
+
+The script counts the number of codons, amino acids, and types of amino acids in sequences,
+as well as the mutation bias from one item to another between 2 sequences.
+
+Counting are then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences.
+In the output files, the pvalues indicate the position of the observed data in a distribution of empirical countings obtained from
+a resample of the data. Values above 0.95 indicate a significantly higher counting, values under 0.05 a significantly lower counting.
+ Sequences file : concatenation.fasta
+ Species retained for countings : Ps,Pp,Pu,Ac,Ap,Pf,Pg,Ph,Pi
+
+Processing : reading input file, opening output files, building dictionaries.
+ Warning : countings might be biased and show high differences between species because of high variations of the indels proportions among sequences.
+ Frequences are more representative.
+
+ Indels percent :
+ Ps : 0.174520069808 %
+ Pp : 1.78883071553 %
+ Pu : 21.8586387435 %
+ Ac : 9.90401396161 %
+ Ap : 8.98778359511 %
+ Pf : 15.7504363002 %
+ Pg : 4.31937172775 %
+ Ph : 5.55555555556 %
+ Pi : 8.11518324607 %
+
+Processing : resampling ...
+ Parameters : 200 iterations, 200 codon per resampled sequence, species used : Ps,Pp,Pu,Pf
+
+ 10%
+ 20%
+ 30%
+ 40%
+ 50%
+ 60%
+ 70%
+ 80%
+ 90%
+ 100%
+ Done.
+
+Processing : countings....
+
+Countings on Ps
+Countings on Pp
+Countings transitions between Ps and Pp
+Countings on Pu
+Countings transitions between Ps and Pu
+Countings on Ac
+Countings transitions between Ps and Ac
+Countings on Ap
+Countings transitions between Ps and Ap
+Countings on Pf
+Countings transitions between Ps and Pf
+Countings on Pg
+Countings transitions between Ps and Pg
+Countings on Ph
+Countings transitions between Ps and Ph
+Countings on Pi
+Countings transitions between Ps and Pi
+Countings transitions between Pp and Pu
+Countings transitions between Pp and Ac
+Countings transitions between Pp and Ap
+Countings transitions between Pp and Pf
+Countings transitions between Pp and Pg
+Countings transitions between Pp and Ph
+Countings transitions between Pp and Pi
+Countings transitions between Pu and Ac
+Countings transitions between Pu and Ap
+Countings transitions between Pu and Pf
+Countings transitions between Pu and Pg
+Countings transitions between Pu and Ph
+Countings transitions between Pu and Pi
+Countings transitions between Ac and Ap
+Countings transitions between Ac and Pf
+Countings transitions between Ac and Pg
+Countings transitions between Ac and Ph
+Countings transitions between Ac and Pi
+Countings transitions between Ap and Pf
+Countings transitions between Ap and Pg
+Countings transitions between Ap and Ph
+Countings transitions between Ap and Pi
+Countings transitions between Pf and Pg
+Countings transitions between Pf and Ph
+Countings transitions between Pf and Pi
+Countings transitions between Pg and Ph
+Countings transitions between Pg and Pi
+Countings transitions between Ph and Pi
+
+ Done.
+
+Processing : creating dataframes ...
+Writing dataframes to output files ...
+
+Done.
diff -r 000000000000 -r acc3674e515b test-data/OUT_concat/aa_freqs.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_concat/aa_freqs.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,28 @@
+Species,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y
+Ac_obs_counts,176.0,48.0,122.0,115.0,96.0,128.0,43.0,107.0,122.0,193.0,42.0,92.0,84.0,62.0,119.0,118.0,129.0,147.0,39.0,83.0
+Ac_obs_freqs,0.0852300242131,0.0232445520581,0.0590799031477,0.0556900726392,0.0464891041162,0.061985472155,0.0208232445521,0.0518159806295,0.0590799031477,0.0934624697337,0.0203389830508,0.0445520581114,0.0406779661017,0.0300242130751,0.0576271186441,0.0571428571429,0.0624697336562,0.071186440678,0.0188861985472,0.0401937046005
+Ac_pvalues,1.0,1.0,0.00497512437811,1.0,1.0,0.626865671642,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.601990049751,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811
+Ap_obs_counts,166.0,47.0,130.0,112.0,101.0,136.0,46.0,106.0,113.0,194.0,44.0,93.0,90.0,58.0,120.0,127.0,125.0,154.0,38.0,86.0
+Ap_obs_freqs,0.0795781399808,0.0225311601151,0.0623202301055,0.0536912751678,0.0484180249281,0.065196548418,0.0220517737296,0.0508149568552,0.0541706615532,0.0930009587728,0.0210930009588,0.0445829338447,0.0431447746884,0.0278044103547,0.0575263662512,0.0608820709492,0.0599232981783,0.0738255033557,0.0182166826462,0.0412272291467
+Ap_pvalues,0.855721393035,1.0,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.870646766169,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811
+Pf_obs_counts,143.0,42.0,117.0,112.0,94.0,127.0,46.0,102.0,99.0,189.0,41.0,84.0,88.0,46.0,103.0,129.0,123.0,123.0,40.0,83.0
+Pf_obs_freqs,0.0740548938374,0.0217503883998,0.0605903676851,0.0580010357328,0.0486794407043,0.0657690315898,0.0238218539617,0.0528223718281,0.0512687726567,0.0978767477991,0.0212325220093,0.0435007767996,0.0455722423615,0.0238218539617,0.0533402382185,0.0668047643708,0.063697566028,0.063697566028,0.0207146556189,0.0429829104091
+Pf_pvalues,0.457711442786,1.0,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.965174129353,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811
+Pg_obs_counts,154.0,55.0,139.0,123.0,105.0,142.0,50.0,122.0,118.0,204.0,51.0,94.0,91.0,59.0,131.0,130.0,135.0,157.0,42.0,91.0
+Pg_obs_freqs,0.0702234382125,0.0250797993616,0.0633834929321,0.0560875512996,0.0478796169631,0.0647514819881,0.0227998176015,0.0556315549476,0.0538075695394,0.093023255814,0.0232558139535,0.0428636570907,0.0414956680347,0.0269037847697,0.0597355221158,0.0592795257638,0.0615595075239,0.0715914272686,0.0191518467852,0.0414956680347
+Pg_pvalues,0.457711442786,1.0,0.00497512437811,1.0,1.0,0.626865671642,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.601990049751,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811
+Ph_obs_counts,173.0,53.0,123.0,122.0,110.0,137.0,50.0,119.0,107.0,190.0,51.0,102.0,92.0,61.0,123.0,140.0,127.0,150.0,44.0,90.0
+Ph_obs_freqs,0.0799445471349,0.0244916820702,0.0568391866913,0.0563770794824,0.050831792976,0.0633086876155,0.0231053604436,0.0549907578558,0.0494454713494,0.0878003696858,0.0235674676525,0.047134935305,0.0425138632163,0.0281885397412,0.0568391866913,0.0646950092421,0.0586876155268,0.0693160813309,0.0203327171904,0.0415896487985
+Ph_pvalues,0.855721393035,1.0,0.00497512437811,1.0,1.0,0.626865671642,0.00497512437811,1.0,0.63184079602,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.870646766169,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811
+Pi_obs_counts,159.0,52.0,125.0,116.0,93.0,140.0,41.0,114.0,126.0,175.0,51.0,98.0,97.0,58.0,120.0,113.0,130.0,159.0,42.0,97.0
+Pi_obs_freqs,0.0754985754986,0.0246913580247,0.0593542260209,0.0550807217474,0.0441595441595,0.0664767331434,0.0194681861349,0.0541310541311,0.0598290598291,0.0830959164292,0.0242165242165,0.0465337132004,0.0460588793922,0.0275403608737,0.0569800569801,0.0536562203229,0.0617283950617,0.0754985754986,0.019943019943,0.0460588793922
+Pi_pvalues,0.855721393035,1.0,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.303482587065,0.00497512437811,0.00497512437811,0.00497512437811,0.323383084577
+Pp_obs_counts,163.0,53.0,139.0,124.0,110.0,146.0,50.0,128.0,125.0,207.0,52.0,98.0,96.0,64.0,132.0,128.0,136.0,161.0,45.0,94.0
+Pp_obs_freqs,0.0724122612172,0.0235450910706,0.0617503331853,0.0550866281653,0.0488671701466,0.0648600621946,0.0222123500666,0.0568636161706,0.0555308751666,0.0919591292759,0.0231008440693,0.0435362061306,0.0426477121279,0.0284318080853,0.0586406041759,0.0568636161706,0.0604175921813,0.0715237672146,0.01999111506,0.0417592181253
+Pp_pvalues,0.457711442786,1.0,0.00497512437811,1.0,1.0,0.626865671642,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.601990049751,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811
+Ps_obs_counts,179.0,50.0,141.0,128.0,106.0,148.0,54.0,129.0,127.0,212.0,49.0,95.0,97.0,62.0,129.0,136.0,136.0,166.0,46.0,98.0
+Ps_obs_freqs,0.0782342657343,0.0218531468531,0.0616258741259,0.0559440559441,0.0463286713287,0.0646853146853,0.0236013986014,0.0563811188811,0.055506993007,0.0926573426573,0.0214160839161,0.041520979021,0.0423951048951,0.0270979020979,0.0563811188811,0.0594405594406,0.0594405594406,0.0725524475524,0.0201048951049,0.0428321678322
+Ps_pvalues,0.855721393035,1.0,0.00497512437811,1.0,1.0,0.626865671642,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.601990049751,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811
+Pu_obs_counts,139.0,46.0,107.0,116.0,91.0,107.0,39.0,98.0,105.0,178.0,39.0,87.0,75.0,52.0,97.0,105.0,94.0,114.0,37.0,65.0
+Pu_obs_freqs,0.0776102735902,0.0256839754327,0.0597431602457,0.0647682858738,0.0508096035734,0.0597431602457,0.0217755443886,0.0547180346175,0.0586264656616,0.0993858179788,0.0217755443886,0.0485762144054,0.0418760469012,0.0290340591848,0.0541596873255,0.0586264656616,0.0524846454495,0.0636515912898,0.0206588498046,0.036292573981
+Pu_pvalues,0.855721393035,1.0,0.00497512437811,1.0,1.0,0.00497512437811,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.601990049751,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811
diff -r 000000000000 -r acc3674e515b test-data/OUT_concat/aa_transitions_freqs.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_concat/aa_transitions_freqs.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,145 @@
+Species,A>A,A>C,A>D,A>E,A>F,A>G,A>H,A>I,A>K,A>L,A>M,A>N,A>P,A>Q,A>R,A>S,A>T,A>V,A>W,A>Y,C>A,C>C,C>D,C>E,C>F,C>G,C>H,C>I,C>K,C>L,C>M,C>N,C>P,C>Q,C>R,C>S,C>T,C>V,C>W,C>Y,D>A,D>C,D>D,D>E,D>F,D>G,D>H,D>I,D>K,D>L,D>M,D>N,D>P,D>Q,D>R,D>S,D>T,D>V,D>W,D>Y,E>A,E>C,E>D,E>E,E>F,E>G,E>H,E>I,E>K,E>L,E>M,E>N,E>P,E>Q,E>R,E>S,E>T,E>V,E>W,E>Y,F>A,F>C,F>D,F>E,F>F,F>G,F>H,F>I,F>K,F>L,F>M,F>N,F>P,F>Q,F>R,F>S,F>T,F>V,F>W,F>Y,G>A,G>C,G>D,G>E,G>F,G>G,G>H,G>I,G>K,G>L,G>M,G>N,G>P,G>Q,G>R,G>S,G>T,G>V,G>W,G>Y,H>A,H>C,H>D,H>E,H>F,H>G,H>H,H>I,H>K,H>L,H>M,H>N,H>P,H>Q,H>R,H>S,H>T,H>V,H>W,H>Y,I>A,I>C,I>D,I>E,I>F,I>G,I>H,I>I,I>K,I>L,I>M,I>N,I>P,I>Q,I>R,I>S,I>T,I>V,I>W,I>Y,K>A,K>C,K>D,K>E,K>F,K>G,K>H,K>I,K>K,K>L,K>M,K>N,K>P,K>Q,K>R,K>S,K>T,K>V,K>W,K>Y,L>A,L>C,L>D,L>E,L>F,L>G,L>H,L>I,L>K,L>L,L>M,L>N,L>P,L>Q,L>R,L>S,L>T,L>V,L>W,L>Y,M>A,M>C,M>D,M>E,M>F,M>G,M>H,M>I,M>K,M>L,M>M,M>N,M>P,M>Q,M>R,M>S,M>T,M>V,M>W,M>Y,N>A,N>C,N>D,N>E,N>F,N>G,N>H,N>I,N>K,N>L,N>M,N>N,N>P,N>Q,N>R,N>S,N>T,N>V,N>W,N>Y,P>A,P>C,P>D,P>E,P>F,P>G,P>H,P>I,P>K,P>L,P>M,P>N,P>P,P>Q,P>R,P>S,P>T,P>V,P>W,P>Y,Q>A,Q>C,Q>D,Q>E,Q>F,Q>G,Q>H,Q>I,Q>K,Q>L,Q>M,Q>N,Q>P,Q>Q,Q>R,Q>S,Q>T,Q>V,Q>W,Q>Y,R>A,R>C,R>D,R>E,R>F,R>G,R>H,R>I,R>K,R>L,R>M,R>N,R>P,R>Q,R>R,R>S,R>T,R>V,R>W,R>Y,S>A,S>C,S>D,S>E,S>F,S>G,S>H,S>I,S>K,S>L,S>M,S>N,S>P,S>Q,S>R,S>S,S>T,S>V,S>W,S>Y,T>A,T>C,T>D,T>E,T>F,T>G,T>H,T>I,T>K,T>L,T>M,T>N,T>P,T>Q,T>R,T>S,T>T,T>V,T>W,T>Y,V>A,V>C,V>D,V>E,V>F,V>G,V>H,V>I,V>K,V>L,V>M,V>N,V>P,V>Q,V>R,V>S,V>T,V>V,V>W,V>Y,W>A,W>C,W>D,W>E,W>F,W>G,W>H,W>I,W>K,W>L,W>M,W>N,W>P,W>Q,W>R,W>S,W>T,W>V,W>W,W>Y,Y>A,Y>C,Y>D,Y>E,Y>F,Y>G,Y>H,Y>I,Y>K,Y>L,Y>M,Y>N,Y>P,Y>Q,Y>R,Y>S,Y>T,Y>V,Y>W,Y>Y
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diff -r 000000000000 -r acc3674e515b test-data/OUT_concat/aatypes_freqs.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_concat/aatypes_freqs.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,28 @@
+Species,aromatics,charged,polar,unpolar
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+Ap_obs_freqs,0.107861936721,0.249760306807,0.25886864813,0.383509108341
+Ap_pvalues,0.00497512437811,0.706467661692,0.00497512437811,1.0
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+Pf_obs_freqs,0.112377006732,0.247022268255,0.265147591921,0.375453133092
+Pf_pvalues,0.00497512437811,0.706467661692,0.00497512437811,1.0
+Pg_obs_counts,238.0,561.0,564.0,830.0
+Pg_obs_freqs,0.108527131783,0.255813953488,0.257181942544,0.378476972184
+Pg_pvalues,0.00497512437811,1.0,0.00497512437811,1.0
+Ph_obs_counts,244.0,525.0,575.0,820.0
+Ph_obs_freqs,0.112754158965,0.242606284658,0.265711645102,0.378927911275
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+Pi_obs_freqs,0.110161443495,0.250712250712,0.260208926876,0.378917378917
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+Pp_obs_freqs,0.110617503332,0.25322079076,0.255442025766,0.380719680142
+Pp_pvalues,0.00497512437811,0.950248756219,0.00497512437811,1.0
+Ps_obs_counts,250.0,579.0,576.0,883.0
+Ps_obs_freqs,0.109265734266,0.253059440559,0.251748251748,0.385926573427
+Ps_pvalues,0.00497512437811,0.950248756219,0.00497512437811,1.0
+Pu_obs_counts,193.0,464.0,459.0,675.0
+Pu_obs_freqs,0.107761027359,0.259073143495,0.256281407035,0.376884422111
+Pu_pvalues,0.00497512437811,1.0,0.00497512437811,1.0
diff -r 000000000000 -r acc3674e515b test-data/OUT_concat/aatypes_transitions_freqs.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_concat/aatypes_transitions_freqs.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,145 @@
+Species,aromatics>aromatics,aromatics>charged,aromatics>polar,aromatics>unpolar,charged>aromatics,charged>charged,charged>polar,charged>unpolar,polar>aromatics,polar>charged,polar>polar,polar>unpolar,unpolar>aromatics,unpolar>charged,unpolar>polar,unpolar>unpolar
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diff -r 000000000000 -r acc3674e515b test-data/OUT_concat/codons_freqs.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_concat/codons_freqs.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,28 @@
+Species,aaa,aac,aag,aat,aca,acc,acg,act,aga,agc,agg,agt,ata,atc,atg,att,caa,cac,cag,cat,cca,ccc,ccg,cct,cga,cgc,cgg,cgt,cta,ctc,ctg,ctt,gaa,gac,gag,gat,gca,gcc,gcg,gct,gga,ggc,ggg,ggt,gta,gtc,gtg,gtt,tac,tat,tca,tcc,tcg,tct,tgc,tgg,tgt,tta,ttc,ttg,ttt
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diff -r 000000000000 -r acc3674e515b test-data/OUT_concat/codons_transitions_freqs.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_concat/codons_transitions_freqs.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,145 @@
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diff -r 000000000000 -r acc3674e515b test-data/OUT_concat/gc_and_others_freqs.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_concat/gc_and_others_freqs.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,10 @@
+Species,GC3,GC12,IVYWREL,EKQH,PAYRESDGM,purineload,CvP
+Ac,0.43499127,0.41710297,0.35034904,2.25714286,1.40731707,42.61198371,-0.00581114
+Ap,0.46858639,0.42539267,0.35340314,2.16346154,1.31350114,31.12274578,-0.00910834
+Pf,0.42801047,0.3872164,0.32809773,2.29347826,1.27777778,26.61431065,-0.01812532
+Pg,0.45244328,0.43695462,0.37958115,2.21100917,1.27705628,41.44851658,-0.00136799
+Ph,0.46073298,0.43455497,0.36561955,2.06306306,1.33037694,28.21407795,-0.02310536
+Pi,0.44851658,0.42146597,0.35907504,2.44444444,1.37296037,44.5026178,-0.00949668
+Pp,0.45898778,0.44698953,0.38874346,2.18421053,1.30967742,46.39325189,-0.00222124
+Ps,0.45724258,0.45811518,0.39616056,2.19827586,1.33122363,38.39441536,0.00131119
+Pu,0.42233857,0.35536649,0.30759162,2.42857143,1.37430168,31.26817917,0.00279174
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/02_tables_per_nuc_variable/DIFF_AT.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/DIFF_AT.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Bj,Bs,Ha,Lf
+orthogroup_253_with_2_species.fasta,-3,NaN,-2,NaN
+orthogroup_544_with_4_species.fasta,33,37,32,30
+orthogroup_546_with_4_species.fasta,-1,6,3,3
+orthogroup_761_with_4_species.fasta,16,13,21,31
+orthogroup_299_with_2_species.fasta,-2,-7,NaN,NaN
+orthogroup_404_with_4_species.fasta,-16,-14,-15,-16
+orthogroup_316_with_4_species.fasta,90,92,91,87
+orthogroup_487_with_4_species.fasta,-2,-4,-2,3
+orthogroup_109_with_3_species.fasta,-3,7,NaN,-5
+orthogroup_696_with_4_species.fasta,12,9,20,7
+orthogroup_442_with_4_species.fasta,20,15,17,8
+orthogroup_508_with_4_species.fasta,-18,-13,-21,-14
+orthogroup_588_with_4_species.fasta,9,20,-15,6
+orthogroup_727_with_4_species.fasta,10,9,9,12
+orthogroup_335_with_4_species.fasta,-21,-10,-5,-4
+orthogroup_660_with_4_species.fasta,4,1,1,1
+orthogroup_623_with_4_species.fasta,1,6,-3,2
+orthogroup_283_with_2_species.fasta,NaN,-2,-7,NaN
+orthogroup_651_with_4_species.fasta,0,4,4,2
+orthogroup_368_with_4_species.fasta,3,13,8,11
+orthogroup_343_with_4_species.fasta,0,3,1,-6
+orthogroup_301_with_4_species.fasta,14,13,9,6
+orthogroup_707_with_4_species.fasta,-7,1,-4,-2
+orthogroup_113_with_4_species.fasta,10,21,22,29
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/02_tables_per_nuc_variable/DIFF_GC.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/DIFF_GC.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Bj,Bs,Ha,Lf
+orthogroup_253_with_2_species.fasta,10,NaN,9,NaN
+orthogroup_544_with_4_species.fasta,13,7,22,26
+orthogroup_546_with_4_species.fasta,-5,-4,-19,-11
+orthogroup_761_with_4_species.fasta,-3,-22,-8,-20
+orthogroup_299_with_2_species.fasta,-4,15,NaN,NaN
+orthogroup_404_with_4_species.fasta,-2,-2,-7,0
+orthogroup_316_with_4_species.fasta,26,26,9,35
+orthogroup_487_with_4_species.fasta,3,5,7,2
+orthogroup_109_with_3_species.fasta,15,17,NaN,15
+orthogroup_696_with_4_species.fasta,-7,-8,-25,-18
+orthogroup_442_with_4_species.fasta,-8,-1,-13,-2
+orthogroup_508_with_4_species.fasta,-16,-15,-7,-10
+orthogroup_588_with_4_species.fasta,-50,-99,-102,-45
+orthogroup_727_with_4_species.fasta,-2,7,13,12
+orthogroup_335_with_4_species.fasta,4,-3,2,-13
+orthogroup_660_with_4_species.fasta,9,14,14,20
+orthogroup_623_with_4_species.fasta,10,17,16,17
+orthogroup_283_with_2_species.fasta,NaN,0,5,NaN
+orthogroup_651_with_4_species.fasta,10,6,8,4
+orthogroup_368_with_4_species.fasta,16,8,-1,12
+orthogroup_343_with_4_species.fasta,-3,-8,0,-1
+orthogroup_301_with_4_species.fasta,12,9,9,16
+orthogroup_707_with_4_species.fasta,5,1,6,8
+orthogroup_113_with_4_species.fasta,16,1,8,7
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/02_tables_per_nuc_variable/GC_percent.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/GC_percent.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Bj,Bs,Ha,Lf
+orthogroup_253_with_2_species.fasta,0.00679245283019,NaN,0.00672955974843,NaN
+orthogroup_544_with_4_species.fasta,0.00516949152542,0.00539548022599,0.00514124293785,0.0054802259887
+orthogroup_546_with_4_species.fasta,0.00625,0.00611111111111,0.00541666666667,0.00625
+orthogroup_761_with_4_species.fasta,0.00518763796909,0.00591611479029,0.00534216335541,0.00582781456954
+orthogroup_299_with_2_species.fasta,0.00484848484848,0.00598484848485,NaN,NaN
+orthogroup_404_with_4_species.fasta,0.005,0.00566666666667,0.0055,0.00533333333333
+orthogroup_316_with_4_species.fasta,0.00553571428571,0.00583333333333,0.00575892857143,0.00566964285714
+orthogroup_487_with_4_species.fasta,0.00578947368421,0.00578947368421,0.00649122807018,0.00561403508772
+orthogroup_109_with_3_species.fasta,0.00537037037037,0.00524691358025,NaN,0.00598765432099
+orthogroup_696_with_4_species.fasta,0.00502222222222,0.00515555555556,0.0052,0.0056
+orthogroup_442_with_4_species.fasta,0.00455555555556,0.0045,0.00461111111111,0.00422222222222
+orthogroup_508_with_4_species.fasta,0.00545454545455,0.00537878787879,0.00492424242424,0.00560606060606
+orthogroup_588_with_4_species.fasta,0.00548854604956,0.00569892473118,0.00565684899486,0.00541841982235
+orthogroup_727_with_4_species.fasta,0.00575757575758,0.00583333333333,0.00477272727273,0.00515151515152
+orthogroup_335_with_4_species.fasta,0.00590717299578,0.00611814345992,0.00599156118143,0.00662447257384
+orthogroup_660_with_4_species.fasta,0.00525925925926,0.00503703703704,0.00503703703704,0.00474074074074
+orthogroup_623_with_4_species.fasta,0.00598290598291,0.00606837606838,0.00615384615385,0.00589743589744
+orthogroup_283_with_2_species.fasta,NaN,0.00352941176471,0.00401960784314,NaN
+orthogroup_651_with_4_species.fasta,0.00588235294118,0.0056862745098,0.00509803921569,0.00549019607843
+orthogroup_368_with_4_species.fasta,0.00533333333333,0.00551111111111,0.00493333333333,0.00542222222222
+orthogroup_343_with_4_species.fasta,0.00560975609756,0.00585365853659,0.00552845528455,0.00626016260163
+orthogroup_301_with_4_species.fasta,0.00515151515152,0.0055303030303,0.0055303030303,0.00515151515152
+orthogroup_707_with_4_species.fasta,0.00583333333333,0.00561111111111,0.00533333333333,0.00611111111111
+orthogroup_113_with_4_species.fasta,0.00505952380952,0.00532738095238,0.00541666666667,0.00556547619048
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_AT.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_AT.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Bj,Bs,Ha,Lf
+orthogroup_253_with_2_species.fasta,-0.0188679245283,NaN,-0.0125786163522,NaN
+orthogroup_544_with_4_species.fasta,0.0932203389831,0.104519774011,0.090395480226,0.0847457627119
+orthogroup_546_with_4_species.fasta,-0.0138888888889,0.0833333333333,0.0416666666667,0.0416666666667
+orthogroup_761_with_4_species.fasta,0.0353200883002,0.0286975717439,0.046357615894,0.0684326710817
+orthogroup_299_with_2_species.fasta,-0.0151515151515,-0.0530303030303,NaN,NaN
+orthogroup_404_with_4_species.fasta,-0.266666666667,-0.233333333333,-0.25,-0.266666666667
+orthogroup_316_with_4_species.fasta,0.133928571429,0.136904761905,0.135416666667,0.129464285714
+orthogroup_487_with_4_species.fasta,-0.0350877192982,-0.0701754385965,-0.0350877192982,0.0526315789474
+orthogroup_109_with_3_species.fasta,-0.0185185185185,0.0432098765432,NaN,-0.0308641975309
+orthogroup_696_with_4_species.fasta,0.0533333333333,0.04,0.0888888888889,0.0311111111111
+orthogroup_442_with_4_species.fasta,0.111111111111,0.0833333333333,0.0944444444444,0.0444444444444
+orthogroup_508_with_4_species.fasta,-0.136363636364,-0.0984848484848,-0.159090909091,-0.106060606061
+orthogroup_588_with_4_species.fasta,0.00420757363254,0.00935016362786,-0.0070126227209,0.00280504908836
+orthogroup_727_with_4_species.fasta,0.0757575757576,0.0681818181818,0.0681818181818,0.0909090909091
+orthogroup_335_with_4_species.fasta,-0.0886075949367,-0.042194092827,-0.0210970464135,-0.0168776371308
+orthogroup_660_with_4_species.fasta,0.0296296296296,0.00740740740741,0.00740740740741,0.00740740740741
+orthogroup_623_with_4_species.fasta,0.00854700854701,0.0512820512821,-0.025641025641,0.017094017094
+orthogroup_283_with_2_species.fasta,NaN,-0.0196078431373,-0.0686274509804,NaN
+orthogroup_651_with_4_species.fasta,0.0,0.0392156862745,0.0392156862745,0.0196078431373
+orthogroup_368_with_4_species.fasta,0.0133333333333,0.0577777777778,0.0355555555556,0.0488888888889
+orthogroup_343_with_4_species.fasta,0.0,0.0243902439024,0.00813008130081,-0.0487804878049
+orthogroup_301_with_4_species.fasta,0.106060606061,0.0984848484848,0.0681818181818,0.0454545454545
+orthogroup_707_with_4_species.fasta,-0.0388888888889,0.00555555555556,-0.0222222222222,-0.0111111111111
+orthogroup_113_with_4_species.fasta,0.0297619047619,0.0625,0.0654761904762,0.0863095238095
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_AT_1000.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_AT_1000.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Bj,Bs,Ha,Lf
+orthogroup_253_with_2_species.fasta,-18.8679245283,NaN,-12.5786163522,NaN
+orthogroup_544_with_4_species.fasta,93.2203389831,104.519774011,90.395480226,84.7457627119
+orthogroup_546_with_4_species.fasta,-13.8888888889,83.3333333333,41.6666666667,41.6666666667
+orthogroup_761_with_4_species.fasta,35.3200883002,28.6975717439,46.357615894,68.4326710817
+orthogroup_299_with_2_species.fasta,-15.1515151515,-53.0303030303,NaN,NaN
+orthogroup_404_with_4_species.fasta,-266.666666667,-233.333333333,-250.0,-266.666666667
+orthogroup_316_with_4_species.fasta,133.928571429,136.904761905,135.416666667,129.464285714
+orthogroup_487_with_4_species.fasta,-35.0877192982,-70.1754385965,-35.0877192982,52.6315789474
+orthogroup_109_with_3_species.fasta,-18.5185185185,43.2098765432,NaN,-30.8641975309
+orthogroup_696_with_4_species.fasta,53.3333333333,40.0,88.8888888889,31.1111111111
+orthogroup_442_with_4_species.fasta,111.111111111,83.3333333333,94.4444444444,44.4444444444
+orthogroup_508_with_4_species.fasta,-136.363636364,-98.4848484848,-159.090909091,-106.060606061
+orthogroup_588_with_4_species.fasta,4.20757363254,9.35016362786,-7.0126227209,2.80504908836
+orthogroup_727_with_4_species.fasta,75.7575757576,68.1818181818,68.1818181818,90.9090909091
+orthogroup_335_with_4_species.fasta,-88.6075949367,-42.194092827,-21.0970464135,-16.8776371308
+orthogroup_660_with_4_species.fasta,29.6296296296,7.40740740741,7.40740740741,7.40740740741
+orthogroup_623_with_4_species.fasta,8.54700854701,51.2820512821,-25.641025641,17.094017094
+orthogroup_283_with_2_species.fasta,NaN,-19.6078431373,-68.6274509804,NaN
+orthogroup_651_with_4_species.fasta,0.0,39.2156862745,39.2156862745,19.6078431373
+orthogroup_368_with_4_species.fasta,13.3333333333,57.7777777778,35.5555555556,48.8888888889
+orthogroup_343_with_4_species.fasta,0.0,24.3902439024,8.13008130081,-48.7804878049
+orthogroup_301_with_4_species.fasta,106.060606061,98.4848484848,68.1818181818,45.4545454545
+orthogroup_707_with_4_species.fasta,-38.8888888889,5.55555555556,-22.2222222222,-11.1111111111
+orthogroup_113_with_4_species.fasta,29.7619047619,62.5,65.4761904762,86.3095238095
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_GC.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_GC.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Bj,Bs,Ha,Lf
+orthogroup_253_with_2_species.fasta,0.062893081761,NaN,0.0566037735849,NaN
+orthogroup_544_with_4_species.fasta,0.0367231638418,0.0197740112994,0.0621468926554,0.0734463276836
+orthogroup_546_with_4_species.fasta,-0.0694444444444,-0.0555555555556,-0.263888888889,-0.152777777778
+orthogroup_761_with_4_species.fasta,-0.00662251655629,-0.0485651214128,-0.0176600441501,-0.0441501103753
+orthogroup_299_with_2_species.fasta,-0.030303030303,0.113636363636,NaN,NaN
+orthogroup_404_with_4_species.fasta,-0.0333333333333,-0.0333333333333,-0.116666666667,0.0
+orthogroup_316_with_4_species.fasta,0.0386904761905,0.0386904761905,0.0133928571429,0.0520833333333
+orthogroup_487_with_4_species.fasta,0.0526315789474,0.0877192982456,0.122807017544,0.0350877192982
+orthogroup_109_with_3_species.fasta,0.0925925925926,0.104938271605,NaN,0.0925925925926
+orthogroup_696_with_4_species.fasta,-0.0311111111111,-0.0355555555556,-0.111111111111,-0.08
+orthogroup_442_with_4_species.fasta,-0.0444444444444,-0.00555555555556,-0.0722222222222,-0.0111111111111
+orthogroup_508_with_4_species.fasta,-0.121212121212,-0.113636363636,-0.0530303030303,-0.0757575757576
+orthogroup_588_with_4_species.fasta,-0.0233754090697,-0.0462833099579,-0.0476858345021,-0.0210378681627
+orthogroup_727_with_4_species.fasta,-0.0151515151515,0.0530303030303,0.0984848484848,0.0909090909091
+orthogroup_335_with_4_species.fasta,0.0168776371308,-0.0126582278481,0.0084388185654,-0.0548523206751
+orthogroup_660_with_4_species.fasta,0.0666666666667,0.103703703704,0.103703703704,0.148148148148
+orthogroup_623_with_4_species.fasta,0.0854700854701,0.145299145299,0.136752136752,0.145299145299
+orthogroup_283_with_2_species.fasta,NaN,0.0,0.0490196078431,NaN
+orthogroup_651_with_4_species.fasta,0.0980392156863,0.0588235294118,0.078431372549,0.0392156862745
+orthogroup_368_with_4_species.fasta,0.0711111111111,0.0355555555556,-0.00444444444444,0.0533333333333
+orthogroup_343_with_4_species.fasta,-0.0243902439024,-0.0650406504065,0.0,-0.00813008130081
+orthogroup_301_with_4_species.fasta,0.0909090909091,0.0681818181818,0.0681818181818,0.121212121212
+orthogroup_707_with_4_species.fasta,0.0277777777778,0.00555555555556,0.0333333333333,0.0444444444444
+orthogroup_113_with_4_species.fasta,0.047619047619,0.00297619047619,0.0238095238095,0.0208333333333
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_GC_1000.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_GC_1000.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Bj,Bs,Ha,Lf
+orthogroup_253_with_2_species.fasta,62.893081761,NaN,56.6037735849,NaN
+orthogroup_544_with_4_species.fasta,36.7231638418,19.7740112994,62.1468926554,73.4463276836
+orthogroup_546_with_4_species.fasta,-69.4444444444,-55.5555555556,-263.888888889,-152.777777778
+orthogroup_761_with_4_species.fasta,-6.62251655629,-48.5651214128,-17.6600441501,-44.1501103753
+orthogroup_299_with_2_species.fasta,-30.303030303,113.636363636,NaN,NaN
+orthogroup_404_with_4_species.fasta,-33.3333333333,-33.3333333333,-116.666666667,0.0
+orthogroup_316_with_4_species.fasta,38.6904761905,38.6904761905,13.3928571429,52.0833333333
+orthogroup_487_with_4_species.fasta,52.6315789474,87.7192982456,122.807017544,35.0877192982
+orthogroup_109_with_3_species.fasta,92.5925925926,104.938271605,NaN,92.5925925926
+orthogroup_696_with_4_species.fasta,-31.1111111111,-35.5555555556,-111.111111111,-80.0
+orthogroup_442_with_4_species.fasta,-44.4444444444,-5.55555555556,-72.2222222222,-11.1111111111
+orthogroup_508_with_4_species.fasta,-121.212121212,-113.636363636,-53.0303030303,-75.7575757576
+orthogroup_588_with_4_species.fasta,-23.3754090697,-46.2833099579,-47.6858345021,-21.0378681627
+orthogroup_727_with_4_species.fasta,-15.1515151515,53.0303030303,98.4848484848,90.9090909091
+orthogroup_335_with_4_species.fasta,16.8776371308,-12.6582278481,8.4388185654,-54.8523206751
+orthogroup_660_with_4_species.fasta,66.6666666667,103.703703704,103.703703704,148.148148148
+orthogroup_623_with_4_species.fasta,85.4700854701,145.299145299,136.752136752,145.299145299
+orthogroup_283_with_2_species.fasta,NaN,0.0,49.0196078431,NaN
+orthogroup_651_with_4_species.fasta,98.0392156863,58.8235294118,78.431372549,39.2156862745
+orthogroup_368_with_4_species.fasta,71.1111111111,35.5555555556,-4.44444444444,53.3333333333
+orthogroup_343_with_4_species.fasta,-24.3902439024,-65.0406504065,0.0,-8.13008130081
+orthogroup_301_with_4_species.fasta,90.9090909091,68.1818181818,68.1818181818,121.212121212
+orthogroup_707_with_4_species.fasta,27.7777777778,5.55555555556,33.3333333333,44.4444444444
+orthogroup_113_with_4_species.fasta,47.619047619,2.97619047619,23.8095238095,20.8333333333
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/02_tables_per_nuc_variable/purine_percent.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/purine_percent.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Bj,Bs,Ha,Lf
+orthogroup_253_with_2_species.fasta,0.00522012578616,NaN,0.00522012578616,NaN
+orthogroup_544_with_4_species.fasta,0.00564971751412,0.00562146892655,0.00576271186441,0.00579096045198
+orthogroup_546_with_4_species.fasta,0.00458333333333,0.00513888888889,0.00388888888889,0.00444444444444
+orthogroup_761_with_4_species.fasta,0.00514348785872,0.00490066225166,0.00514348785872,0.00512141280353
+orthogroup_299_with_2_species.fasta,0.00477272727273,0.00530303030303,NaN,NaN
+orthogroup_404_with_4_species.fasta,0.0035,0.00366666666667,0.00316666666667,0.00366666666667
+orthogroup_316_with_4_species.fasta,0.0058630952381,0.00587797619048,0.00574404761905,0.00590773809524
+orthogroup_487_with_4_species.fasta,0.00508771929825,0.00508771929825,0.00543859649123,0.00543859649123
+orthogroup_109_with_3_species.fasta,0.00537037037037,0.00574074074074,NaN,0.00530864197531
+orthogroup_696_with_4_species.fasta,0.00511111111111,0.00502222222222,0.00488888888889,0.00475555555556
+orthogroup_442_with_4_species.fasta,0.00533333333333,0.00538888888889,0.00511111111111,0.00516666666667
+orthogroup_508_with_4_species.fasta,0.00371212121212,0.00393939393939,0.00393939393939,0.00409090909091
+orthogroup_588_with_4_species.fasta,0.00490416082281,0.00481533426835,0.00472650771388,0.00490883590463
+orthogroup_727_with_4_species.fasta,0.00530303030303,0.00560606060606,0.00583333333333,0.00590909090909
+orthogroup_335_with_4_species.fasta,0.00464135021097,0.00472573839662,0.00493670886076,0.00464135021097
+orthogroup_660_with_4_species.fasta,0.00548148148148,0.00555555555556,0.00555555555556,0.00577777777778
+orthogroup_623_with_4_species.fasta,0.00547008547009,0.00598290598291,0.00555555555556,0.00581196581197
+orthogroup_283_with_2_species.fasta,NaN,0.00490196078431,0.00490196078431,NaN
+orthogroup_651_with_4_species.fasta,0.00549019607843,0.00549019607843,0.00558823529412,0.00529411764706
+orthogroup_368_with_4_species.fasta,0.00542222222222,0.00546666666667,0.00515555555556,0.00551111111111
+orthogroup_343_with_4_species.fasta,0.00487804878049,0.00479674796748,0.0050406504065,0.00471544715447
+orthogroup_301_with_4_species.fasta,0.00598484848485,0.00583333333333,0.00568181818182,0.00583333333333
+orthogroup_707_with_4_species.fasta,0.00494444444444,0.00505555555556,0.00505555555556,0.00516666666667
+orthogroup_113_with_4_species.fasta,0.0053869047619,0.00532738095238,0.00544642857143,0.00553571428571
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/02_tables_per_nucleotide/A.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/02_tables_per_nucleotide/A.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Bj,Bs,Ha,Lf
+orthogroup_253_with_2_species.fasta,24,NaN,25,NaN
+orthogroup_544_with_4_species.fasta,102,100,102,95
+orthogroup_546_with_4_species.fasta,13,17,18,15
+orthogroup_761_with_4_species.fasta,117,99,116,110
+orthogroup_299_with_2_species.fasta,33,23,NaN,NaN
+orthogroup_404_with_4_species.fasta,7,6,6,6
+orthogroup_316_with_4_species.fasta,195,186,188,189
+orthogroup_487_with_4_species.fasta,11,10,9,14
+orthogroup_109_with_3_species.fasta,36,42,NaN,30
+orthogroup_696_with_4_species.fasta,62,59,64,53
+orthogroup_442_with_4_species.fasta,59,57,57,56
+orthogroup_508_with_4_species.fasta,21,24,23,22
+orthogroup_588_with_4_species.fasta,487,470,457,493
+orthogroup_727_with_4_species.fasta,33,32,39,38
+orthogroup_335_with_4_species.fasta,38,41,45,38
+orthogroup_660_with_4_species.fasta,34,34,34,36
+orthogroup_623_with_4_species.fasta,24,26,21,25
+orthogroup_283_with_2_species.fasta,NaN,32,27,NaN
+orthogroup_651_with_4_species.fasta,21,24,27,24
+orthogroup_368_with_4_species.fasta,54,57,61,57
+orthogroup_343_with_4_species.fasta,27,27,28,20
+orthogroup_301_with_4_species.fasta,39,36,34,35
+orthogroup_707_with_4_species.fasta,34,40,40,34
+orthogroup_113_with_4_species.fasta,88,89,88,89
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/02_tables_per_nucleotide/C.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/02_tables_per_nucleotide/C.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Bj,Bs,Ha,Lf
+orthogroup_253_with_2_species.fasta,49,NaN,49,NaN
+orthogroup_544_with_4_species.fasta,85,92,80,84
+orthogroup_546_with_4_species.fasta,25,24,29,28
+orthogroup_761_with_4_species.fasta,119,145,125,142
+orthogroup_299_with_2_species.fasta,34,32,NaN,NaN
+orthogroup_404_with_4_species.fasta,16,18,20,16
+orthogroup_316_with_4_species.fasta,173,183,189,173
+orthogroup_487_with_4_species.fasta,15,14,15,15
+orthogroup_109_with_3_species.fasta,36,34,NaN,41
+orthogroup_696_with_4_species.fasta,60,62,71,72
+orthogroup_442_with_4_species.fasta,45,41,48,39
+orthogroup_508_with_4_species.fasta,44,43,36,42
+orthogroup_588_with_4_species.fasta,612,659,656,602
+orthogroup_727_with_4_species.fasta,39,35,25,28
+orthogroup_335_with_4_species.fasta,68,74,70,85
+orthogroup_660_with_4_species.fasta,31,27,27,22
+orthogroup_623_with_4_species.fasta,30,27,28,26
+orthogroup_283_with_2_species.fasta,NaN,18,18,NaN
+orthogroup_651_with_4_species.fasta,25,26,22,26
+orthogroup_368_with_4_species.fasta,52,58,56,55
+orthogroup_343_with_4_species.fasta,36,40,34,39
+orthogroup_301_with_4_species.fasta,28,32,32,26
+orthogroup_707_with_4_species.fasta,50,50,45,51
+orthogroup_113_with_4_species.fasta,77,89,87,90
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/02_tables_per_nucleotide/G.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/02_tables_per_nucleotide/G.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Bj,Bs,Ha,Lf
+orthogroup_253_with_2_species.fasta,59,NaN,58,NaN
+orthogroup_544_with_4_species.fasta,98,99,102,110
+orthogroup_546_with_4_species.fasta,20,20,10,17
+orthogroup_761_with_4_species.fasta,116,123,117,122
+orthogroup_299_with_2_species.fasta,30,47,NaN,NaN
+orthogroup_404_with_4_species.fasta,14,16,13,16
+orthogroup_316_with_4_species.fasta,199,209,198,208
+orthogroup_487_with_4_species.fasta,18,19,22,17
+orthogroup_109_with_3_species.fasta,51,51,NaN,56
+orthogroup_696_with_4_species.fasta,53,54,46,54
+orthogroup_442_with_4_species.fasta,37,40,35,37
+orthogroup_508_with_4_species.fasta,28,28,29,32
+orthogroup_588_with_4_species.fasta,562,560,554,557
+orthogroup_727_with_4_species.fasta,37,42,38,40
+orthogroup_335_with_4_species.fasta,72,71,72,72
+orthogroup_660_with_4_species.fasta,40,41,41,42
+orthogroup_623_with_4_species.fasta,40,44,44,43
+orthogroup_283_with_2_species.fasta,NaN,18,23,NaN
+orthogroup_651_with_4_species.fasta,35,32,30,30
+orthogroup_368_with_4_species.fasta,68,66,55,67
+orthogroup_343_with_4_species.fasta,33,32,34,38
+orthogroup_301_with_4_species.fasta,40,41,41,42
+orthogroup_707_with_4_species.fasta,55,51,51,59
+orthogroup_113_with_4_species.fasta,93,90,95,97
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/02_tables_per_nucleotide/T.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/02_tables_per_nucleotide/T.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,25 @@
+Group,Bj,Bs,Ha,Lf
+orthogroup_253_with_2_species.fasta,27,NaN,27,NaN
+orthogroup_544_with_4_species.fasta,69,63,70,65
+orthogroup_546_with_4_species.fasta,14,11,15,12
+orthogroup_761_with_4_species.fasta,101,86,95,79
+orthogroup_299_with_2_species.fasta,35,30,NaN,NaN
+orthogroup_404_with_4_species.fasta,23,20,21,22
+orthogroup_316_with_4_species.fasta,105,94,97,102
+orthogroup_487_with_4_species.fasta,13,14,11,11
+orthogroup_109_with_3_species.fasta,39,35,NaN,35
+orthogroup_696_with_4_species.fasta,50,50,44,46
+orthogroup_442_with_4_species.fasta,39,42,40,48
+orthogroup_508_with_4_species.fasta,39,37,44,36
+orthogroup_588_with_4_species.fasta,478,450,472,487
+orthogroup_727_with_4_species.fasta,23,23,30,26
+orthogroup_335_with_4_species.fasta,59,51,50,42
+orthogroup_660_with_4_species.fasta,30,33,33,35
+orthogroup_623_with_4_species.fasta,23,20,24,23
+orthogroup_283_with_2_species.fasta,NaN,34,34,NaN
+orthogroup_651_with_4_species.fasta,21,20,23,22
+orthogroup_368_with_4_species.fasta,51,44,53,46
+orthogroup_343_with_4_species.fasta,27,24,27,26
+orthogroup_301_with_4_species.fasta,25,23,25,29
+orthogroup_707_with_4_species.fasta,41,39,44,36
+orthogroup_113_with_4_species.fasta,78,68,66,60
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/04_outputs_nuc_variables/DIFF_AT.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/04_outputs_nuc_variables/DIFF_AT.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj"
+"Greater",5,11,4,5
+"Lower",7,4,5,7
+"Difference",-2,7,-1,-2
+"Trial_Number",12,15,9,12
+"p-value",0.7744140625,0.11846923828125,1,0.7744140625
+"probability_of_success",0.416666666666667,0.733333333333333,0.444444444444444,0.416666666666667
+"confidence_interval_low",0.15165222980843,0.448996758963029,0.136995662265167,0.15165222980843
+"confidence_interval_high",0.723330314317894,0.922128453708956,0.787991493221132,0.723330314317894
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/04_outputs_nuc_variables/DIFF_GC.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/04_outputs_nuc_variables/DIFF_GC.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj"
+"Greater",7,3,6,10
+"Lower",7,7,7,5
+"Difference",0,-4,-1,5
+"Trial_Number",14,10,13,15
+"p-value",1,0.34375,1,0.3017578125
+"probability_of_success",0.5,0.3,0.461538461538462,0.666666666666667
+"confidence_interval_low",0.230360541448062,0.0667395111777345,0.192232441801288,0.383803732541154
+"confidence_interval_high",0.769639458551938,0.652452850059997,0.748654517729696,0.881758896633119
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/04_outputs_nuc_variables/GC_percent.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/04_outputs_nuc_variables/GC_percent.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj"
+"Greater",3,7,5,7
+"Lower",6,2,8,7
+"Difference",-3,5,-3,0
+"Trial_Number",9,9,13,14
+"p-value",0.5078125,0.1796875,0.5810546875,1
+"probability_of_success",0.333333333333333,0.777777777777778,0.384615384615385,0.5
+"confidence_interval_low",0.0748546314196918,0.399906426283688,0.138579338890161,0.230360541448062
+"confidence_interval_high",0.70070494379146,0.971855026522102,0.684222397085937,0.769639458551938
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/04_outputs_nuc_variables/PLI_AT.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/04_outputs_nuc_variables/PLI_AT.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj"
+"Greater",5,11,4,5
+"Lower",7,4,5,7
+"Difference",-2,7,-1,-2
+"Trial_Number",12,15,9,12
+"p-value",0.7744140625,0.11846923828125,1,0.7744140625
+"probability_of_success",0.416666666666667,0.733333333333333,0.444444444444444,0.416666666666667
+"confidence_interval_low",0.15165222980843,0.448996758963029,0.136995662265167,0.15165222980843
+"confidence_interval_high",0.723330314317894,0.922128453708956,0.787991493221132,0.723330314317894
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/04_outputs_nuc_variables/PLI_AT_1000.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/04_outputs_nuc_variables/PLI_AT_1000.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj"
+"Greater",5,11,4,5
+"Lower",7,4,5,7
+"Difference",-2,7,-1,-2
+"Trial_Number",12,15,9,12
+"p-value",0.7744140625,0.11846923828125,1,0.7744140625
+"probability_of_success",0.416666666666667,0.733333333333333,0.444444444444444,0.416666666666667
+"confidence_interval_low",0.15165222980843,0.448996758963029,0.136995662265167,0.15165222980843
+"confidence_interval_high",0.723330314317894,0.922128453708956,0.787991493221132,0.723330314317894
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/04_outputs_nuc_variables/PLI_GC.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/04_outputs_nuc_variables/PLI_GC.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj"
+"Greater",7,3,6,10
+"Lower",7,7,7,5
+"Difference",0,-4,-1,5
+"Trial_Number",14,10,13,15
+"p-value",1,0.34375,1,0.3017578125
+"probability_of_success",0.5,0.3,0.461538461538462,0.666666666666667
+"confidence_interval_low",0.230360541448062,0.0667395111777345,0.192232441801288,0.383803732541154
+"confidence_interval_high",0.769639458551938,0.652452850059997,0.748654517729696,0.881758896633119
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/04_outputs_nuc_variables/PLI_GC_1000.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/04_outputs_nuc_variables/PLI_GC_1000.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj"
+"Greater",7,3,6,10
+"Lower",7,7,7,5
+"Difference",0,-4,-1,5
+"Trial_Number",14,10,13,15
+"p-value",1,0.34375,1,0.3017578125
+"probability_of_success",0.5,0.3,0.461538461538462,0.666666666666667
+"confidence_interval_low",0.230360541448062,0.0667395111777345,0.192232441801288,0.383803732541154
+"confidence_interval_high",0.769639458551938,0.652452850059997,0.748654517729696,0.881758896633119
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/04_outputs_nuc_variables/purine_percent.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/04_outputs_nuc_variables/purine_percent.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj"
+"Greater",4,4,7,10
+"Lower",8,5,8,5
+"Difference",-4,-1,-1,5
+"Trial_Number",12,9,15,15
+"p-value",0.3876953125,1,1,0.3017578125
+"probability_of_success",0.333333333333333,0.444444444444444,0.466666666666667,0.666666666666667
+"confidence_interval_low",0.0992460911495833,0.136995662265167,0.212666729519308,0.383803732541154
+"confidence_interval_high",0.651124493581186,0.787991493221132,0.734138652722603,0.881758896633119
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/04_outputs_nucleotides/A.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/04_outputs_nucleotides/A.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj"
+"Greater",5,3,7,4
+"Lower",5,3,4,5
+"Difference",0,0,3,-1
+"Trial_Number",10,6,11,9
+"p-value",1,1,0.548828125,1
+"probability_of_success",0.5,0.5,0.636363636363636,0.444444444444444
+"confidence_interval_low",0.187086028447399,0.118117248757025,0.307904715011677,0.136995662265167
+"confidence_interval_high",0.812913971552601,0.881882751242975,0.890736556180902,0.787991493221132
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/04_outputs_nucleotides/C.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/04_outputs_nucleotides/C.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj"
+"Greater",5,7,5,5
+"Lower",6,3,6,8
+"Difference",-1,4,-1,-3
+"Trial_Number",11,10,11,13
+"p-value",1,0.34375,1,0.5810546875
+"probability_of_success",0.454545454545455,0.7,0.454545454545455,0.384615384615385
+"confidence_interval_low",0.167488094063707,0.347547149940003,0.167488094063707,0.138579338890161
+"confidence_interval_high",0.766206402340655,0.933260488822266,0.766206402340655,0.684222397085937
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/04_outputs_nucleotides/G.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/04_outputs_nucleotides/G.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj"
+"Greater",4,7,5,7
+"Lower",9,5,8,4
+"Difference",-5,2,-3,3
+"Trial_Number",13,12,13,11
+"p-value",0.266845703125,0.7744140625,0.5810546875,0.548828125
+"probability_of_success",0.307692307692308,0.583333333333333,0.384615384615385,0.636363636363636
+"confidence_interval_low",0.0909203945720966,0.276669685682106,0.138579338890161,0.307904715011677
+"confidence_interval_high",0.614261661750705,0.84834777019157,0.684222397085937,0.890736556180902
diff -r 000000000000 -r acc3674e515b test-data/OUT_nuc/04_outputs_nucleotides/T.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/OUT_nuc/04_outputs_nucleotides/T.csv Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,9 @@
+"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj"
+"Greater",7,4,8,6
+"Lower",4,11,4,7
+"Difference",3,-7,4,-1
+"Trial_Number",11,15,12,13
+"p-value",0.548828125,0.11846923828125,0.3876953125,1
+"probability_of_success",0.636363636363636,0.266666666666667,0.666666666666667,0.461538461538462
+"confidence_interval_low",0.307904715011677,0.0778715462910436,0.348875506418814,0.192232441801288
+"confidence_interval_high",0.890736556180902,0.551003241036971,0.900753908850417,0.748654517729696
diff -r 000000000000 -r acc3674e515b test-data/concatenation.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/concatenation.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,18 @@
+>Ps
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+>Pp
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+>Pu
+cacattggtttgaagccatttcctgatagcagcatgcacttcttgagcctgctcaggacttgcagtcttacctgtgcctatggcccatactggttcatatgcaatcacaacacgactccagtcagttactgcatcagctatagccttcatttgtcggaaaacaacttcctctgtcttatttgcctctctttcttcaaagaaactattcttgacctttccaaataccttgataaagccatcagagttaaattcagtggtgggcgagaagttactggtgtgctgaagggatttgatccactgctgaaccttgtattagatggaaccactgaatatctcagagatccagatgatccatttaaattgactgaagataccagacaggggctttgtatgtcgaggaacatctgttgtactgatttgtccttc---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cttgggtttgctgagaacttcgccttgagtggcgctgcagctgttatatcaaagactgctgctgcccccattgaacgagtaaagttgatggtacagaaccaagatgagatgatgaaagctggtcgtttagacaagccgtacaagggtgtcgttgactgtacagttaggacattcaaggctgaaggtatccttccattttggcgtggtaatctggccaactgcattcgttacttcccaacacaggctctgaactttgccttcaaagacaaggtgaaggccttgttcgatgaacaagaaaagacaggacaggctgaggaattggctggactgctgaaattcacacgaccttttctgcctctggttagcaaggccaaggctgccaaactggtacgccatctagtggacaaattcctggacatgaaagctggtactggccaggagatagagttgtgtaaagaatgtattgattgggccactgatgagaaacgcatatatctgcgacaagctcttgaggcgaccctcgttgctctgtactttgataatggccgatatacagatgccctagcactaggagaaaaattgttgaaggaactaaaaaagttagatgacaaggctctgctggttgaagtgcagctgttggagagcaaaacataccatgca---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------acacttggagtcgaagttcatccacttgtgttccacacaaacagaggcccaataagattcaatgtttgggatactgctggccaggagaaattcggtggtcttcgtgatggatattacattcaaggccagtgtgctatcatcatgtttgatgtcacagctcgcatcacatataaaaatgtaccaaactggcatcgtgatttagttagagtctgtgaaaatatccctattgtgctgtgtggtaacaaggttgacatcaaagacagaaaggacctggagatgaacagtgacctaaaggcacagcttagagaattgtatattactgcggcaaaggagattgatgttcagggaaagaaggccatcatcatctttgtacctgtgcctcagttgaaagccttccagaagatccagactcgtttagtccgagagctagagaagaaattcagtgggaagcatgttgttgttatagctcaggagtctaccaaaacctac---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------acgcacgccggcttcgtcggcggcctgaccgaccacttcgacgagagccacaagcgcatcatggagctgcgcccggagagcctgccgagggccgtcgagatggtcgagcagtgcttcccgctctacagcatgctgctcgccatcaaccggacgcacatcgactacttctcgctggacgtcgagggctccgagctcgacatcctcaagacgctgccgttcgacaagctcgccatcgacatcatcaccgtcgagtacggcgtgcgcggcatcaagacgcgcgacgagagctccatcgagcgcctgaaggccatccgcaggttcttcaagaacgtcaagggcaagtacgaggagatcggcgtcataccgagcaagttcatacacgcacaacgatattttcctgaagggcgtttatatcaggtagagtatgccatggaggccattggtcatgcaggtacctgtcttggcatcctagcaaaagatggtgtcattctggctgctgaaaagcgcaacacaaacaaactgttggatgaggtgtcgtactctgaaaagatctataaactatacaatgacatggcatgcagtgtggcaggaatcacgtctgatgcaaatgtgttgaccaatgagctggctcgtggctatcctggaaccttggtctatgacaagaatgacttcaacacgttggcagatattgagggggaattggacaacctcgccagtcagtgtgccagtgtggggttgacgtgcaccacttactacctaccaggaccacccttacacgaaggacaccagatcaaaatattggagatgatcaaccctaacagcgctcacaggaattcaattctctgggagtccatgctacacgcccgtgaatggttggccggagctacgttgatgaatgtcctagacaagatggtcaaggaatacggcaccgatccagacgtgacgctgcttctggacacttacgatttctatttcatcccggtcatgaatcccgacggctatcaattttcatgggacgaagatcgatactggagaaagaacaggagaaacaacgagggatctctttgctatggagtggatctgaatagaaactgggacaacaactggggtggacccggcgccagcgacaatccatgcgaagacacgtaccacggaccaaacatggtggataacatggctgctatggccccagatgtcatctgcttattgtgttcatgttcgtacatcttcagacgtgcttccactatctttgtcagtgttaagacatcaccatggaaaccagcacagcccaagactgttgtgtctgtcagtttgaagttcctagcctgtggtactcaccttggctccaataatgtcgatttccagatggagcagtatgtgtacaaacgtaaaccagatggtgttttcatcttgaatttgagaaagacttgggagaagctgctgctagctgcccgtgccatcgcagccattgagagcccagctgatgtgtgcgttatttctgcgcgaccttatggacagcgcgctgtactgaaatttgcttcctacgttggcgctacacctgttgctggaaggttcacgcctggagcattcaccaaccagttccaggctgccttccgtgagccacgtctgcttgtggtgactgacccacgtattgaccatcagccagtcactgaggcatcctatgtcaacattcctgtgattgccatgtgtaacaccgactcgcctctgaagtttgtggacattgccatcccatgcaacaacaagagtcagcattctattggtttgatgtggtggatgctggcacgtgaagtactgcgccttcgtggtacaatctcgcgtgaggtgccctgggaagtgatggttgatctgttcttctacagggatccagaagaggctgaaaaggaagagcaagcagcgctggaagcacagctcgccgtcccagattgggccagtgagggtgccattgcctggaggggttgctcctggaattggtcgtgcagctggccgtggtatggctggtggatatcaccaggccggtccatcggctggtcttcaaggccccgtgcatggcgtgggtgggccaggtcaacaacacatgcagcccggtggtcggggtgcccagttctctgcccctccgcaaatgagacaaggcccaccacgtgccatgatgcagggcccaccgccaggcatgagaccaccaatgggtcgtggtggacagcagccaggaatgagaccaccgaatggatgaattttcaaaagggttactgcagtgaatatgagctggattttgctcgatgtgctagtcgagttggggcagtgaatgccatacgggattgccgaaaatttatggaggatatgcaagaatgtgcatttcacaagaagtcgcttgaaagatacaagatcatgcaggcagaaagaaagaaacaaattctgaattttcttctgcaattctatttgcttctcctttcgttcatatatttccataatcttaactctttgctgctgcaccaggcgacccttttcaatgttgaactcttcctcagccttcgcatcaatttcttcagccttttcattagcttcctgatcaatgaaagccatcatttgcttgatctggacagcaaaaatgaagcattgaatgcagaggaggtgtacagtaaattaacaacacctgtgtttggtaaaggtgtagcatatgatgtaccaaacccaatcttcttggagcagaagaagatgcttaagacaggtttgaatattgccagatttagacagcacattcccataattgaagaagaaaccattgaatacttcaagagatggggagaacaggggcagagagatttgtttgaaggtctttctgagttgattattttgacagcaagtcgatgtcttcatggtagaggatatgctgatatggccgctaacgtgaaacaagttgatgttccttcattcagtggtagttttggtatccttcctaatcatgtacctacactagcagttcttaagccaggtgttattacagtcattgaagaagatggtacacagaagaaatatttcgtgagcagtggtactatcagtataaatgaggattcctctgtccaaatcctagctgaggagtcagtgaaagtagaggatttagatgctgaggccatcagagatggtgcgaacaaagcagcccaatttaatatcagcttcttcagatcaggctggcaggtgtcacttgaagatgctatcaccccaagtcacttctgtggtgccgtagtcctgaaccaagattacaacgtttggggaattagtaacgtcgcctgcagcgccgaatacgacggcatcacctcggccatgatctgcgcagattcgtccggaaacgacagagatgcctgccaaggtgattccggtggcccgctggtgtacaagagaaatggacggtttggcgtgccatacttagaaatggacgattttaagttatctcagagcaacacaatagcgagatttctcgccagaaggtttggtttggccggaaagaacgaccttgaggaggccaaggcagacatggtagtcgactgcgtcgaggaaatgcttaagcctctcttccatctgatgttctacgcttccaaagacgaaaagtcagatctt------------------------------------------------atggataacatgttcaacacctacggcacggatccagacgtcactcgccttctggatacctacaactggcacttcgtgcacgttgtcaatcccgatggctacgagttcacgtggacagacgagaggctcttccggaagaacagaaattccaattactgcacatgggag
+>Ac
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aaagagacaatacttgatctttctaagtacctggataaagctataagagtcaaattcagtggtggaagggaagttactggtgtgctgaagggatttgatccactgcttaacttggtattagatggaactactgaatatctcagagatccagatgacccattcaagcttacagaagacacaagacaggggacttgtctgtcgaggcacttctgttgtattaatatgtccttcacagctgtatttgccagagacttggaactacatccaccatcttacccatggagctacaagggcatctttgattcatatgaccatgccagtgtccgtcgaggctatcaggtatataaacaggtttgtgcagcttgtcactccatggacttcctgtattatagaaaccttgttggcactatcatgacagaggacgaagccaaggcagaagctgcagagatccaggttgttgatggaccagatgatgagggtaacatgttcaagcgcccaggcaaattgtctgaccgcttcccacagccatatgccaatgaggaggctgccaaggctgccaacagtggagcataccctccagatttgacatttatcgtcaatgcaagagaaggtggagctgattacatattctcattgttgactggatactgtgacccgcctgctggatgcgaggaacgagaaggtctacactacaatccatacttccttggaggatacattgctatggctaaagcactctataatgaaattattgagtatgatgatggtacaccagccacaagcagtcagttggctaaagatgtgaccacattcttggcttggagcatgacgaatacaaagggttaccgccgtggtactagggatctgttttcccgacccttccgcaggaagggagtgatcccactgtctacctatatgaaagtgtacaaagtgggtgacatagtggatattaagggaaatggagctgtccaaaaaggtatgcctcacaaatactaccatggcaagactggtcgtgtgtacaatgttacacagcatgctgttggcgtgatacttggatttgccgagaacttcgctctcagcggagctgcagcagttatatccaagaccgctgctgcacccattgagcgagtcaagctcatggtacagaatcaggatgagatgatcaaagctggtcggcttgacaagccatacaagggtgttatagattgcacagttaggacattcaagtcagaaggtattttgccattctggcgtggtaatctggccaactgtattaggtacttccccacacaggctttgaactttgccttcaaggacaaagtgaaggctgcattcgatgaacaagacaagacaggtcaagctgaggaactagctggtttactgaagtttgctcgacctttcctgccattagtcagcaaggctaaggcagctaagttggttagacatcttgtggacaaatttctggacatgaaagctggcactggaaaggagatagaactatgcaaagaatgtattgattgggccactgatgagaagcgtatatatttgaggcaagctcttgaggcaacactgattgctttgtactttgataatggccgatacacagatgccttggcactaggagacaaactgctgaaggagttgaaaaagttggatgacaaagctctcttagttgaagtccagcttttagaaagtaaaacataccatgcatcaacaatgaaaaccaaggtgttgttgtcttcgatctttttcattgcagactcagtggtcaaaggatacttgacaatcttgtatttgtcaagcctaggtctccttggtgtgctttttcgaggatacttcggctgcctcggcaagcgcagtgtccttggtcggtttgtggagattggccgtgtggcctacgtcgccatcggtccggatgcaggcaaactggttgccattgttgatgttgttgatcagaatcgggtgctagttgatggaccatgcactggagtgggccgtaagattctcaacctgaagcagcttaacctaacaaactttgtcctcaagttctcacacactgccaggacaaaggtcgtgcggaaagaatgggagactcttggagttgaagttcatcctcttgtgttccacaccaacagaggtccaataaggtttaatgtttgggatactgctggtcaggagaaatttggaggactacgtgatggatattatattcaaggtcaatgtgctatcatcatgtttgatgtcactgctcgtatcacatacaaaaatgtaccaaattggcatcgtgatttagtaagagtatgtgagaatatccccattgttctctgtggtaacaaggttgacatcaaagacagaaaagacctggagatgaacagtgacctaaaggcacagcttagagaattgtatatcactgcggctaaagagatagatgtccagggaaaaaaggccatcattttatttgtgcctgtgccacagctgaaagccttccagaagatccagactcgtttagtccgagagctggaaaagaagttcagcgggaagcatgttgttgtaattgcacagaagtctgccgaagcctaccgttcgccagcccgtactggctacagcaatgggagctttcgttcaacaccttcaacaacatgggtctgtgggaggcttgctttcacaattacatgcaccaccgagacgatttacaggaaatatacaacggctgcttctgggtgtacgatcccgcgatacaacaagctcagagactggctcgtaccaccttggttcatttcctgccaggtcatgtcgaccatcgttctcttagttctcattgctgttgttatcatg---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atacaaggaccactatattttcccgaagggcggctatatcaggtggagtatgctatggaagctattggtcatgctggcacctgccttggcatattagcaaaagatggcgtcatccttgctgcagagaaacgcaacaccaacaaactgctagatgaggtgtcctactctgaaaagatttataaactctatgatgatatggcatgcagtgttgcaggaattacatctgatgcaaatgtgttgacaaatgagttagctcgcggctatccacacacaatggcttatgacatcaacgacttcaatacactaactgatattgaagctgagatggataacttggccagtcagtgtgctgctgtcggtctggagtgttctacaagttacctacctggcccacctttacacgaaggtcaccagattaaagtgtttcagatgatcaatccaaatggagcccgaaagaactccgttctttgggagtcgacgatacacgctcgtgaatggttggctggagctacgttaatgaacatcttggataagatggtaaaggaatacggcacggatgctgacgtcacaagacttctggataattacgactttcattttatacccgtcgttaatccagacgggtatcagttctcctgggacgaggatcgttactggagaaagaacaggaga---------------------------------------------------------------------------------------------------------------aacatcgtagacaacatggcagctatcgctccagatgtcatccgcttgttgtgttcgtgctcatacatcttcagccgtgcttcaactatctttgtaagtgttaacacatcaccatggaagccagcacaacctagaactgtttggtcagtcagcttgaaattcttagcttgtggcactcacctcggctccaacaatgtcgacttccagatggagcagtatgtctacaaacgtaaaccagatggtgtctacattctaaacttgaggaagacctgggagaagcttcttctggcagctcgtgctattgcagccattgagaaccccgctgatgtctgtgtcatatcagctcgtccttacggacagcgtgctgtgctgaagtttgcttcctatgttggtgccacacctgttgccggaagattcacacctggggcatttaccaatcagttccaggctgccttccgtgagcctcgcctgcttgttgtcacagatcctcgtattgaccatcaaccagtaacagaagcatcctatgtcaacatccctgtcattgctatgtgcaacactgactcgcctctgaagtttgttgatattgccatcccgtgtaacaacaagagtcagcactctgttggcctgatgtggtggatgctggcccgtgaggtacttcgtctgcgtggcacaatttcacgtgaggtgccatgggatgtcatggtcgatctgttcttctacagggatccagaagaggccgagaaggaggaacaagcagctctggaggcccagctggctgccccagattgggccaccgagagtaccactgccaggtggtgttggacccggcatggggcgtgctgcaggtcgcggtatgtctggtggttaccaccaagccggcccctcagctggactgcagggaccagtacacggtgttggaggcccaggacaacaacacatgcagccaggaggaagaggagctcagttctctgctcctccgcagatgagacaaggtcctcctcgtgccatgatgcagggaccacctcctggcatgagaccaccaatggggcgtggtggtcagcagcctggaatgagaccaccgaatggatgaattatcaaaagggtcactgtagtgcctatgagctagattttgcacgttgtgcaagtcatgtgggtgctgtccgggcaataaaagactgcaggaagttcatggaagacatgcaggagtgtgcacgccacacaaaatcgctggagaggtacaagatcatgcaagctgaaaggaagaagcaggttctgaatctttttttggagttcaatttgcttttcttttcgttcataaatttccatgatcttaactctctgctgctgaaccaagcgacctttttcaatgttaaactcttcttcagccttagcatcaatctcctcagccttctcattggcttcttgatcaatgaaagccatcatctgtttgatctggatagcaagaatgaagctctgaatgctgaggaagtatacagtaaactcactacaccggtgtttggcaaaggtgtggcttatgatgttcctaacccagtgttcttggaacagaagaagatgctgaaaactggtctgaacattgccaggttcaggcagcacattcctataattgaagaggagacaattgattatttcaagagatggggagagcaggggacaaaagatttgtttgaaggcttgtcagagttaatcatattgacagccagtcgatgtcttcatggcagaagttatgctgacatgtccgctaatgtgaagcaggttgatgtcccttcattcagtggcagctttggtatacttcctaaccatgtacctacattagcagttctaaagcctggtgttataacagtgattgaggaagatggcacacaaaagaagtactttgttagcagtggcacgatcagtataaatgatgactcatctgtccagatactagcagaagaaatagccagattagaagaattagatgccgaggcaatcagggatggtgcaaacaaggcagcccagtttagcatcagccacaacagaacaagctggcaggtgtcgctggaggatgtcataaccccgagccacttctgtggcggcgtcgttctgaatcaggactacaacgtttggggaattagtaacgcccagtgtagtacagaatatgatggcatcacccaggccatgctgtgtgccgattcgtctggtaataacagggatgcttgccagggtgattctggtggccctttggtatacaataggaatggacgttttggtgtgccttgcttagaagtggacgacttcaagttggcacaaagtaacaccatcgctcgtttcctcgccagaaggttcggactggcgggtaagaacgacttggaagaggctaaggcagacatggttgttgactgcgttgaagaaatgctgaaacctcttttccatctgatgttttacgccactgaagaccagaagtcagaacttttgacacacgccagggaatggctgacaacagcaacaaccttgtatctgatggacaacatgtttaacacgtatggaacggatccggacgtgacacgactgctggatagctataactggcactttgtccacgtggtcaatccggacggatacgaattcacgtggaccgatgagagaatgtatcgaaagaatagaaatcccagttactgtacatgggcg
+>Ap
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+>Pf
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+>Pg
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+>Ph
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ggtggtgttgggcctggtatgggtcgtgctgcaggccgtggaatgtctggtggttttcatcagggcggtccttctgcaggactacagggacctgtacatggtgtaggtggacctggacaacagcacatgcagcctggaggtcgaggtgctcaattctctgctccaccccagatgagacaagggccaccccgtgctatgatgcaagggccacctccaggtatgaggccaccaatgggtcgtggcggtcagcaaccaggaatgcgaccaccgaatggatgaatttccagaagggttactgtcaagcctatgaactggattttgctcgttgtgctgctagggttggcgcagtaaatgcagtaacacaatgcagaaagtacatggatgatatgcaagagtgtgcatttcacagaaaatcgcttgaaagatacagaattatgcaggcagaaagaaagaaacaaattctgaattttcttctgcaattctatttgcttctcctttcgttcatatatttccataatcttaactctttgctgctgcaccaggcgacccttttcaatgttgaactcttcctcagccttcgcatcaatttcttcagccttttcattagcttcctgatcaatgaaagccatcatttgcttgatctggacagcaaaaatgaagcattgaatgcagaggaggtgtacagtaaattaacaacacctgtgtttggtaaaggtgtagcatatgatgtaccaaacccaatcttcttggagcagaagaagatgcttaagacaggtttgaatattgccagatttagacagcacattcccataattgaagaagaaaccattgaatacttcaagagatggggagaacaggggcagagagatttgtttgaaggtctttctgagttgattattttgacagcaagtcgatgtcttcatggcagaggatatgctgatatggccgctaacgtgaaacaagttgatgttccttcattcagtggtagttttggtatccttcctaatcatgtacctacactagcagttcttaagccaggtgttattacagtcattgaagaagatggtacacagaagaaatatttcgtgagcagtggtactatcagtataaatgaggattcctctgtccaaatcctagctgaggagtcagtgaaagtagaggatttagatgctgaggccatcagagacggtgcgaacaaagcagcccaatttaatatcagcttcttcagatcaggctggcaggtgtcgctcgaggacgttatcaccccgagccatttctgcggggcggtggtcctgaatcaggattacaacgtttggggaattagtaacgcccaatgtagttcggaatacgacggcataacattggccatgttgtgcgctgattcctcaggaaacgacagagatgcttgccagggtgactccggcggtccacttgtttacaagaggaatgg-cgttttggcgtgccatacttagaaatggacgattttaagttatctcagagcaacacaatagcgagatttctcgccagaaggtttggtttggccggaaagaacgaccttgaggaggccaaggcagacatggtagtcgactgcgtcgaggaaatgcttaagcctctcttccatctgatgttctacgcttccaaggacgaaaagtcagatcttttgacgcacgcaagagaatggctgacaacagcaacaactctgtatctcatggataatatgtttaacacgtacggcacagatcctgatgtcactcgtcttctggatacatataactggcattttgttcatgttgttaatcctgacggctatgaatacagctggacagatgagagactctacaggaagaacagaaatcctgcttattgtacaggggcg
+>Pi
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-----tgttggtcctggaatgggtcgggcggctggtcgtggtatgtccggtggttatcatcaaggtgggccatctgctggcctacaaggtccagtccatggagtaggcggaccaggtccacaacatatgcagcctggaggtcgtggagcacaattctctgccccacctcagatgagacaagggccacctcgtgctatgatgcaagggccacccccaggaatgagaccacccatgggccgtggtggccagcagccaggaatgcggccaccgaatggatgaacttccagaagggctactgtagtgcatatgagctggattttgcacgttgtgcaagtcgagttggagctgttaatgcaataaaagattgcaggaagtacatggaagatatgcaagagtgtgcatatcatagaaaatcgcttcaaaggtacaagattatgcaggcagaaaggaagaaacaa------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gacagcaagaacgatgctctgaatgccgaagaggtctatggcaaattaacaaccccagtgtttggcaaaggtgtggcgtatgatgtaccaaatcctgttttcttggagcagaagaagatgctgaagacaggtttgaacatagccaggtttagacagcacattcccatgatagaggaggagacgatagaatacttcaaacgatggggggaatccggacaacatgacttatttgatgcgctgtcacagttgattattctgacagccagtcgctgtctccatggt------------------------aatgtgaagcaggtggatgtaccatcattcagcggcagctttggtatccttcctaaccacgtacctacactcgcagttctcaagccaggtgtaatcacagtgattgaggaagatggaacacccaaaaaatattttgttagcagtggtactattagtataaatgaa------------------------------------------------------------------------------------------------------------------------tggcaggtgtcgctggaggacgtaatcacgccgagtcacttctgtggcgccgtcgttctgaacgagaactacaacgtttggggaattagtaacgaccagtgttccacagagtacagcgggatcactcagggcatgctgtgcgccgacgcatccggaaacgacagagatgcttgtcagggagattctggtggtcccctggtttacaataggaatggaaag---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ctgactcacgctagagaatggctcaccactgctaccaccctgtatcttatggacaatatgtttaacacatacggttcggatgaagaactgactcgtcttctagatacgtataactggcacttcgtccacgttgtcaatccagatggttatgattatacttggaccgatgaaaggctctacagaaagaacaggaatcctacttactgtatccaggag
diff -r 000000000000 -r acc3674e515b test-data/phylogeny_concat.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phylogeny_concat.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,20 @@
+>Ac
+gtacatgggcaagtttttcttcgaatgataaggtgcatatggatcattggcataatacttgggtatcttaaagtatctgttgaccattctgtccagcatccagcactggcgctgtgtgcagaagacatggtgctgcaggtgtgccactctggcacccttcttcttccacagcttctcgtgtcggccgtgcatttcagagcttcctcagcgtactccagaagagtaacaaagctctctttggagccctcgggcagaattccattggggatctccacaatgagcttccgaccaagaagcagcgtttcccagctgacctccaagcaatctgtcagagtgatacggaagcacaaactcgaggcagtctgtgccttcgccaatgtgtttacattttccggcaggccattggcgctgacagggggctcttttaacacccccacaccgttgccctctgtcttttcagacacgttgacggcgtggggctcatcaggagcaccaccgaggcccaggacccaatcgtatacaataccgcgagggcaaaccaaagccataaccgtgcattgttcctgctgctcggttttcaatgacaactccaaacaaaccacgattcacacgcgagtcttccttttctttgccacttgttgtgaacccatattcaaatacttggtttatttgattatgaggaatgccaccaccacggtcagatattcttataatgaaatcaattttgttgttggcaatagtaacagacacaggtggcatattctccagggaattcagatgattttctactgtagctctcattgcattcttcagcatctcatgtataatgtactcaagtggtggtgcaatgtatggaaaggttgcatttacatgaccattgatacgaacatctggccagatcttgttgtatacatgtccttgtcttcaggatttgacatgccatggtcttctttgggtttcactgtctctgtgcttcctggtttgtctacaagtttgactacatccttatcagatgatggagctttgttctctgactgctttgaagaacttggatcagtcttggaaatattttcacctggaagtcttgctggtctccagaactccttggcttgttccttcgtcagaatccaggcttgtttagatatatccagagcctggtctgggatgggtgacgataataagaacaatgaacatattaacctcaaggttacaggacaggatggcagtgttgtacactttaaaatcaagaagaacactcccctgaggaagctgatgaatgcatactgtgacagaacaggtgtcaagagtggagcaatgcgattccgatttgatgggcaaccaatcaatgaaacagacactccaacacagctggacatggaagatggtgatgtgattgatgtattccaacagcagactggaggcgtcgagttgacccacgtaatgcttcacgtctggacacaagggatcccagacaggctgaaccacgacgtgctgcatcgcaaccagcagcacctaccccagcacaaagattacaggctccaccatcatctggaggaagcaatgggccaatttcatctcaggatcaggaaaagactgctctcatcatgcaggtgttacaacgtgctggtgctggtgccgaactatcaggtgatgaatgtggtgatcacgtcgttcgtgttcgtctgcgccgcccacgagatccactcgctgaccgtcaagctgacggactacgccgtgccaaacgactggagaatactgctgaggaacatggtctgctttactgccgttctgatacctgtggccataacacacggtgcatttggcgtatgtctgggaattgagtattctgtggcaatgacctacagaatggtgtcatgtcaaaagcatccacttctgcatcctttaaatgaggatctttatttattgcaggatttggtggataagggtgtgagatgccacttggtaccgaggtgtccttgctcgtggcaccaactgctgtatatgaaggtggtacagtcaaaagaaatgcaacgaataaaccggagctaccagaaaaaccaaaagtttcaagaatggagcaagtttatgaaaacataccgatgtccgaacaaaaacaaggtctgcagagagacgaaagtaatggaaaacgtcaccttccattccagcttcgtggagttgatggcacaacttacgctgacctcgagatcattctggtggcttgggctggcactgatagcagatggtgctcttggtggcggtgctatgcgtgtgcctcctgggggaggtggcagtattcccgtgccatgtccacggctacgctgcttgctggcattgcttgggctaccatgctccctgtttttctttgtagctatatttatcctaatggtttggccctctttgaagccaagatccagcttaggtccagagctaagtaggtctttgttgtccttctgttcttcaagtcttcagtacaacctggtgatcatgttatcccattgtacatccctcagtgtggtgaatgcaaattctgcaaaagtccgaagaccaacctctgctcgaaaatcagagctactcaaggtgcaggtaagatgcctgatggcacaagcaggttctcttgtaatggcaaggagctgtatcacttcatgggctgcagcacattcagtgaatataccgtggttgctgaaatatctgtgtgtaaggttaatccagaagctccactgggcaaggtttgcttacttggctgtggaatatcaactggttatggagctgccttccggaactgtagctgttttcggcttcctgtcgtcgtctggtgcggaagaacgcgcgcctgtccacctggctgtgtgtgcatgttgctgtttatgcatgttcatgtcagtgcttgtgatcggtgagttagaacgagcgagtgagcgggtgcgtgagacatccgacaacatcctgtctggtcgttcactgtgtactgcttttgaatcatttcctaaaggtgaaggtcgtctcgtggctgcttgccctcgttgtgtggagtgcgtgattgaccctgtaatgttgggagccaaacataatgtactgtggcgccacctggtggagaagaatgttgagcgccaagatgatgtacatgaggtgaaaggaagccatcagcaaggcttgaggcctcatcttatgtggccggatcttgaacaactgaatccaaagaaaccgaatgccaattgcttccattccaccaatggcacagctgagcaggaacaagattccactgtgatgtgtaccttctgtccctgtatgtcaatggattttaccaggtcgccatctgtcagtgtctgtttacgttctctggaatatttgggcatgagagtatctttgagagttctatgttcagttccttgttgtctgtcatcaatggcagcaattgtccatggcaatcctaagccaaggaagacattgacagagttggacccagttacatttccaattgagttgtcagcatatttctcctgtgtggcagcctgcttgctggcaaacagatctggcaaacttgttcccagagctacaaatgtgatggcagtgacgctgtccttcaggccaaccaaacaaccgaagatagatgccaagtccccaacaacggcagtaagtagaccaatcatgataagggcaatgaagaaggctaaccagccaccccagatggaaggaggaggcacaagtgcaaaaatgatcttccagccaaaggttaagaagtgcatgatgtctgtcttcactcgactgagatccgtccccaacgctgacgtcacaaatgtccggcccccgcgctgcgggaagaccttcaccattcacttcatgcgaatcctcgaccgccgctcgttcccctccataggcctccactgcctgctgaatgaccgactggacgaaatctctgacctgcacgtggaagcccatttccaactcagacgacatatacatggacagatatctcgctacttcctggatgacgtcatcaacgttagtcttgacttccctgatccacaaggttctatgagataccttgaagccaatacaacagccctgactccacctaacagagggccgttttggtactccacagatgttgatacgaggacacaggcaccctttggtaggtcagtcctccagtgtcgcagttcacaaatatctctagttggatgtggggccatgttgttgagcacatacttcatggtggatcttgttatatatgagcgtcttgtcataatcggcagtgtagttctttactgtgccataaactgcatctatactgaggatgttgaccacttctatacgatcaaagtaaataatgacacctccactggtaccacatggtacattcttgacctcatctgtttgacaatgtcactgccagaccagccacataacacagggctctccagggctgcagggacagctgatagcacaacgtgtgcagtatccgcgaaaaggcgaagatccggaaatgccaaagggccacctcagtcgacggcgacgtcagtacgtaaaggaaaccaatcagcacgaaagggggaatgttctccatgtcatgtcatcagatcggcaatgttcttttccaggtcatcaattctgtgtcccatgtcatctattcttgtgataacttggtcggacatgttctggaatttatcctgcatctgctgtaaaaggttttgcacatattgtgttagatcctgtatgtctttaggatcggcactgttggtgataaaaaagaagcctaatatttttccacccaaatgttttcgtcttgcctcttcatggtccataatcccacctgatgttgtgagcacaatgtacccaaactgtcttgatggcagtaggttagttgtccatttctccatgtctctgatgcaaacatcaaaccttggacttatcacaccacacttgttcagtcttcctgtcaaattaacaacaatttttcctgctctgtggtcatcaatgatctcaaactcaccaatgaaaagtgtgcggtatatgttccttcctaattttgtcctaaactggatgtatgcctctggatcatccttttctggatcttttgttgtatctgtgagaactgcttccatttcagcctctttttcttcctccttgctcataatttctgctctaaccttatcaagcaaggcatactgtgacatctgctgtatgatgacaggagctggtggtggactgtgcagactggccatgccagccagactcgtcatgcttgctgaaccattcatcatttgctgctgttgctgctgtgttagctgctgtggtttaactttgcacacattgctatggtccagttcattcttgttactggtgtttagatctgatgaggacatcacagacgtggcactctgtgcagaggtaatattttctgtgaggttcttcatgagttcggtaagtttgctagtcagatcttcatctggctgctttgccgacgttgttggtatcgttggtcgttcatgtgatgtagtcggcagatgttctgatttcgtgttctgcgctgtcgttggacttggtaaggactgggtcggtggcgccgcggtgccgtcgcggccaagactgcagtcatcagagtccgatgttagtgtgaacgtggctgggcaggaaacacgcagaccaattgacctcagtgagccatccagcggagaactgacacctggacaaggatccgaggctcggggatctacaacacgaggggctgaagctaagggatccacacccagagattctgaggtcataacatggatggggtcgacattgccaagcttcttggtgtgtgttttcagtggcagtggtggtggtggtgttgatttcactggtgactgtgcaggactcgagtctcctattgatgtgtcctcctcaataatgccctcatccgtgtgttcagcatctgcaggaagtggattggcagttatgcgtatgctgcactcggatcctttaaaccacagtgattcccattccagggaggcagatgccgtttccatggattcagacacatttagtgttgatggtagcagacgtttgaagtcaatcgtttgcttgcctcatgacagacaacagaacatctctgatgatgaattgaactccaaacatacgaagaaatcacataaattgaagaaagtgaaaagacatcaaaagagaaaaaagaaatcttccattttgggcgaatcaggatcttgcacaagtggtgattcagtggactctggagaggcggtcgcttccggcatctcttcagtgttgtcaggatctgtgatgtcttgtacaagaggttcattagatatatcctctattattgtatccgagggatccgtaacatgggcgaagtgccatctaatgccatcgttactgcctcttttaaatcggaacaagaaagagaaatctactggacgctcatcaactatgctcagcagttctttgcctctgataacaatgaagattttgccatgttttcttcaccaatgcttgaatacaaagactcagcctctttgtcatcagctggtttgtcttccacagtttcagtttccattggttcctcctcatcctctttggatgcctcctcagcagcagcctctgtacgtatcttttcctctgcctccttggcagcccttcttccacttcttcttctgggactttcatcttcctcctgttccttggcactggaccttccctttctggttgctttgcgaggcgatggtgttttcaactttttcacttcctcttcctctggctggtactcctcttcctcttcctcctcttcaccctgtgattttcgtccttgacctctcctgccacgtgaactccggccagcacctcgaccagtgcctctgccacgtggctttgactgtgagcacccatcttatcatttgcatgacatacggcacaactcttttcgtaatcctcctgacctggagctaccgtatccttcttcttagggaggtctcgaacttcgctaaatggtggattgacatcggttcgtgggtctttcaccacaaccaacttagccccatcatcttcacaatctttcatacatcgcttcccaattgctccaatattcttgccatccagtgtatgtgtgtgaaagcatgtgtagaactggtactgccagccaaatcacagcatcgtttagaagatgcccacgccgtctacgtggtgggagtccacacacacacacacgtactaaggactaagttcatagagatgctatactcaacaagaaaaagtcactatcatacagtgattacccatcacttagtgcagacaaacacatcaccattacattttccatcaacaacagtccatggatttacagattttgtcttagttgcgactttcctactgtttttagtaattctgcccgactgcatgctgcccactggttttaggtttaccttggctgttgatttgtacgattgcttacgtggcgctggaagtgttttggcgtcactggctggcaggttgttttcatctcttgttgtaagcggagcacgcaatttcttgctggagttatgcctcggtaccggcacgtcagccagcctatcagggacggatgttttgctgacgtcaccaaggcttgccgatgagcggcgttttgattcgctgctgcgtcgattccttccggaactgccgacagacgaatcggccaatgacgtcaacgaactgggacggctgctcgtacttccggcgcgcgactgcggcctctggttgctgaataatgaactacttccattcatgtgggcatcaagcttaggccctttctgtgacagtctctccagcgtgtcgtcgctgacagtctcgtttgcctctttttctaactccaaccgaaatatatatctcgtgctgcccttcttaatatcagtaacgtttacgctgtattggccttccagtgagctgtccttgagtacatcctctgttagtttagtaaatgttgccgcttcctttatgtacttacacactctagctatatcttcacatgatgcaccatattccattgctaaggcagcctcattaataagttctccagcaaccgaagcaacaatatgtacaccaagaactctgtccgactctttatctccaataacttttaccaagccatctgtatcattgttagtttttgcccgactgtttgctgccaaaggaaactttcca---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Pu
+cctgcggcaacatcgcctgttcacgtcgaacccgaagctggactgctgcccgacgataaccgagctgacccagcgggcggcgggcatcaacccgcagggcctgctcctcgagctcttccacacgcccaacttcacacagacgttctacgagacggcctgccacccggcgatcaagggccggccgtgccagttcatcgaccgccagtacgcggcgtacagcaagtgcatacagcagtactcgtacgtgtacgcgctcgggcggacgtacgg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Am
+aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaag------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Ap
+tctgatccatccataatggctgcatccatctggacttctcctttggcatttagggctgatccagtacctgcatcaaacacagagttgttctccatatccatgacagccaattccacaacatctagagcagatccaccatttaataagagctttaaccctttaagtgcagcctttttaaccccttgtctgttttgcatggccatgctgtctgggatggcccaagctccacca---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Pf
+tgtagcattaccatgtattggcattccactctccgtcatgttgacaaccaccgttccggcgagtccaaaatcatcttcaaagatataatctggtattgttatgttaatgtcatagagagtcggaaagtgattttcagttttatactgatgcgtgtatattttgccgtatccatgcacctctattgtccaccatccgtgtttacaaggatgatgttgttgtatcgttccctcgagataaccatttctaacttgttgttcgcgccatctcttcacgtactggccggcgccatctcgaaggtatatgtccacagcgccatgtgg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Pg
+gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Ph
+cgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Ps
+acatggagtagcattggtcgaccacgagtcaatggcaagcttgagatgacaaggagtatcggtgatgttgcggtgtcggcatgcggtggctccctcatggtggcaacaaggagaactacagctctgctcgaaactgatgatatattcaaacacaaagatgtgatatgtttaggtgtaatattttgtatgatattcttggtgaccttgcttcttgtggcagcgaccttcacctcacgaccattgagcgcagactttctgtcatcttcaaggaagacaaaatgtgtcatggcatggatactcgcgtatcccattgtaatcatctttttcgtttatatacgttactaccaagacgaggattgcatagatctgacaccttatattatacctcaggttgacaagacttattgtggtgctaatcttgatgacttctataaaaagtccatgttgacatttgaagcttatgtcattgccctggttggtgctgtactagtagtcttaagtatgttccatctgatgcacactgcagccaattacattcagatccacgaatctgggccgacgaattacgatatttataagaacgaagtggccaataaacatccatcgggatca------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Pp
+acacagaaggaagcacagagggcctaccaagaagaactaaagagacagattgaggagcagaagctgataaaacaaagggaaaaggaagagagagaaagatacgataagaagctagatgacgaaattaggaactatgacccctttggacgaggtggtggaggagcaccaatggatggtgaatcgtttgctagaggtggtcatggtatctttggtgaaccattgtctgatgct---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Pa
+gagctgtcctttgtgctgtcatctttaacatttatagccacatttctgtttgcatcacttgccatgaagaattaccatggcaacaagtatccaccaatttggtttcctagtgatggtggcttcacctatcatgtgataagtacagcgtctgagtggataatgggatgtagaaaatggtacgactatgcctgtaagccaatggattattacacagaaacaaaaatcttgcaagaaaagattgtcctagaagccaatagtgatgacttttttacagtagctatccgtccacatggaatctttggcccacgtgacccgcacatggtgcccactactgtacgcactgccaaggcaggaaaaatgaagttcaaaataggcgatgggaaaaatattgtggatttcacttttgtggaaaatgttgttcatggtcacatt------------------------------------------------------------------
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_3sp_2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_3sp_2.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,6 @@
+>Pg1Pg2_ContigI_295
+YGLYKQATVGEINTDRPGMLDFKGKAKWDAWE
+>Pp_2630_2/3_0.667_949
+YGLYKQVTVGDVNAARPGMLDFKGKAKWDAWE
+>Ap3661_1/2_1.000_1488
+YGLYKQATVGDVNTDRPGMLDFKGKAKWDAWE
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_3sp_7.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_3sp_7.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,6 @@
+>Ac10784_3/3_0.600_925
+DLRSNLSNYKLQLQQVEAALALDQENEDLKKLQKD
+>Pf1355_1/1_1.000_940
+DLRTNLSNYKLQLQQVEAALALDQENEDLKKLQKD
+>Ap11551_1/2_1.000_2287
+DLRSNLSNYKLQLQQVEAALALDQDNEDLKKLQKD
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_4sp_4.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_4sp_4.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Pg1Pg2_ContigI_830
+RHVECFTCSMRKFILFGTILPPTRLLTITPTACVTLYTRSLAMIIFVWHTFLDCSITLYIHNVTNFINFHIS
+>Pf879_1/1_1.000_626
+RHLECLTCSIRKFILLGMILPPTRLFTITPTACVTLYTRCLAMVIFVRHTFLDCSITLYIYDITNFIHFHVS
+>Ac197_2/2_1.000_643
+RHFECLTCSIRKLILLAMILPPTRLLTITPTACVTLYTRSLAMVVFVRHTFLDSSISLNIHYVTHFVHFHIG
+>Pp_589_1/1_1.000_552
+LHFECFMCSIRRLILFGMILPPTRLLTITPTACVTLYIRCLAMVIFMRHSFLDCTMTLDIHNIPYFVHFHIR
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_4sp_6.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_4sp_6.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Pg1Pg2_ContigI_1514
+PGLCLECYTCVRQDNNKDKCIKTTIQCEEYENGCYSQIRWGIPPYWKPHGDRIHFINKGCMRYERCLDWQVSKRHTCRRDWYLDWECVECCRGDMC
+>Ap3180_1/2_1.000_1116
+PGLCLECYTCVNQDNNKDKCIKTTIQCEEYENGCYSQIRWGIPPYWRPHGDRIHFINKGCMRFEKCLDWQVARRHTCRRDWYLDWECIECCRGDMC
+>Ac2018_1/1_1.000_627
+PGLCLECYTCVNQDNNKDKCIKTTIQCEEYENGCYSQIRWGIPPYWRPHGDRIHFINKGCMRFERCLDWQKSRRNTCRRDWYLDWECVECCRGDMC
+>Pf2190_1/1_1.000_917
+PGLCLECYTCVRQDNNKDKCIKTTIQCEEYENGCYSQIRWGIPPYWKPHGDRIYFINKGCMRFEKCLEWQKLKRHTCRRDWYLDWECVECCRGDMC
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_10.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_10.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Ap5723_1/1_1.000_1183
+CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPMA
+>Ac8933_1/2_1.000_1159
+CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPMA
+>PsIsotig20888_13433_1513
+CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPLA
+>Pp_2523_1/1_1.000_2145
+CFNGYEHTSDYVGKAYFGCWWIFHKEYSYVRDWIMPSWFIACQTLMTFAIVTMFITLGLFPMA
+>Pg1Pg2_ContigI_6331
+CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPMA
+>Pf1268_1/1_1.000_688
+CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPLA
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_11.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_11.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>PsContig23463_00014_509
+GDDAAQKQEILDWIEAVTGSKIPRDQPFEKILKDGVILCNLMNKIMPGSVKRINKKGGNFALMENIAAFQKAMKAYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLNKGFDGPTIGPKMAEKQEREWTEDQLREGRQGIIGLQAG
+>Pf344_1/1_1.000_2337
+GDDAAQKQEILDWIEAVIGSKIPRDQPFEKILKDGVILCNLMNKIMPGSVKRINKKGGNFALMENIAAFQKAMKDYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLNKGFDGPTIGPKMAEKHEREWTEDQLREGRQGIIGLQAG
+>Pg1Pg2_ContigI_5539
+VDDAAQKQELLDWIEAVSGSKIPRDQRFEKILKDGVILCNMMNKIVPGSVKRINKKGGNFALMENIAAFQKAMKAYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLNKGYDGPTIGPKMAEKHEREWTEDELREGRQGIIGLQAG
+>Pp_115_7/8_0.421_2349
+GDDAAQKTEILDWIEAVTGTKIPRDQPFEKILKDGVILCNLMNKITPGSVKRINKKGGNFALMENIAAFQKAMKSYGVPEEEVFQTADLFEARNVKAVVKSLNALGRTCLNKGFDGPSFGPKMAEKHERQWTEDELREGRQGIIGLQAG
+>Ac261_5/5_0.871_1061
+GDDAAQKQEILDWIEAVTGDKIPRDQPFEKVLKDGVILCNLMNKIMPGSVKKINKKGGNFALMENIAAFQKAMKAYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLAKGFDGPTIGPKMAEKQEREWTEDQLREGRQGIIGLQAG
+>Ap77_5/8_0.405_866
+GDDAAQKQEILDWIEAVTGDKIPRDQPFEKVLKDGVILCNLINKIMPGSVKKINKKGGNFALMENIAAFQKAMKAYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLAKGFDGPTIGPKMAEKHEREWTEDQLREGRQGIIGLQAG
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_16.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_16.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Ap3513_1/1_1.000_737
+KIGTVGISHYAQEALGDIVFAELPEVGSEFVKDDECGTLESV
+>Pp_7121_2/3_0.778_2103
+KIGTIGISHYAQEALGDIVFAELPEDGAEFDKDDECGTLESV
+>Pg1Pg2_ContigI_3765
+KIGTIGISHYAQEALGDIVYAELPEVGSEFNKFDECGTLESV
+>Pf199_1/1_1.000_306
+KIGTVGISQYAQEALGDIVYAELPDVGSEFNKHDECGTLESV
+>Ac4439_1/1_1.000_890
+KIGTVGISHYAQEALGDIVFAELPEAGSEFVKDDECGTLESV
+>PsIsotig06983_01306_1511
+KIGTVGISQYAQEALGDIVYAELPDVGSEFTKHDECGTLESV
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_18.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_18.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Ac3728_1/2_1.000_2558
+AMLHLMLPGTVITYYGEEIGM
+>Pp_1484_1/1_1.000_2519
+AMVHLMLPGTAITYYGEEIGM
+>Ap459_1/1_1.000_2245
+AMLHLMLPGTAITYYGEEIGM
+>Pf737_1/1_1.000_940
+AMLHLLLPGTAITYYGEEIGM
+>Pg1Pg2_ContigI_2873
+AMLHLMLPGTAITYYGEEIGM
+>PsContig14622_00221_1814
+AMLHLMLPGTAITYYGEEIGM
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_25.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_25.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Pg1Pg2_ContigI_440
+DGGGNLLVAADSYIGEKIRDLAVECGIEFDEEGTSVIDHHNYDVNDDGKHTLIVADPDNLVTAPLLTGSETHNPLLFKGVGMTADPDNPLVISILHASSSSYSFDPNSPITDYPHAVGKNTLLISGLQARNNARVLFFGSLDFFSDETFNAPVQKASGGKKYAKSGNQQLALRLSQWVFKEKGVLRVGKVTHHKKGEKEPPVAYTIMDTVEYTIEIEQFEDGKWMPLVADDVQLEFVRIDPFVRMGLRKKGGKFYAKFKIPDVYGVYQFRVDYNRIGYTHLFVTTQVSVRPLEHTQYE
+>Pf3990_1/1_1.000_914
+DGGGNLLVAADSYIGETIRDLAVECGVEFDEEGTAVIDHHNYDVKDDGKHTLIVADPENLVNAPVLTGTEKHNPLLFKGVGMTADPDNPLVISILHASSSAYSFDPDSRINDYPHAVGKNTLLISGLQARNNARVLFFGSLDFFSDETFNAPVQKAGGGQKYAKSANQELATRLSQWVFKEKGVLRVGKVTHHRKGEKEPPVAYTIMDTVEYTIEIEKKEGDKWLPLDANDVQLEFVRIDPFIRMGLRKKGGKFHAEFKIPDVYGVYQFRVDYNRIGYTHLFVTTQVSVRPLQHTQYE
+>Pp_205_1/1_1.000_1576
+DGGGNVLVAADSYIGETIRDLAGECGVEFDEEGTSVIDHLNYDVKDNGKHTLIVANPDNLVNAPMLIGSEKHNPLLFKGVGMTADPDNPLVINILHAASSAYSFDPDSRIQDYPHAVGKNTLLIAGLQARNNARVLFFGSLDFFSDETFNAPVQKSGTTQKYSKSGNQHLALRLSQWVFKEKGVLRVGKVVHHKEGEKEPPMAYTVMDIVEYSVEIEKNEDGKWMPLDAKDVQLEFVRIDPFVRMALTKKGNKFYAKFKIPDVYGVYQFRVDYNRIGYTHLFITTQVSVRPLQHTQYE
+>Ap3808_1/1_1.000_2053
+DGGGNVLVAVDSYIGETIRNLAGECGVEFDEEGTSVIDHHNYDVKDDGKHTLIVADPENLINAPLLTGNEKHNPLLFRGVGMTADPDNPLVINILHAASSAYSFDPDSRITDYPHAIGKNTLLISGLQARNNARVLFVGSLDFFSDETFNAPVQKANGGQKFSKSGNQQLATRLSQWVFKEKGVLRVGKVVHHKVGEKEPPAAYTIMDNVEYSVEIEKNEDGKWVPLDADDLQLEFVRIDPFIRMPLSKRGNQFYAKFKIPDVYGVYQFRVDYNRVGYTHLFITTQVSVRPLEHTQYE
+>Ac3918_1/1_1.000_1754
+DGGGNVLVAVDSYIGETIRNLAGECGVEFDEEGTSVIDHHNYDVKDDGKHTLIVADPENLINAPLLTGSEKHAPLLFRGVGMTADPDNPLVINILHAASSAYSFDPDSRITDYPHAVGKNTLLISGLQARNNARVLFVGSLDFFSDETFNAPVQKANGGQKFPKSGNQQLATRLSQWVFKEKGVLRVGKVVHHKVGEKEPPAAYTIMDNVEYSVEIEKNEDGKWLPLDADDLQLEFVRIDPFIRMPLTKKGNQFYAKFKIPDVYGVYQFRIDYNRIGYTHLFITTQVSVRPLEHTQYE
+>PsIsotig14896_07441_3814
+DGGGNLLVAADSFIGETIRDLAVECGIEFDEEGTSVIDHHNYDVKDDGKHTLIVADPENLVSAPMLTGTEKHNPLLFKGVGMTADPDNPLVISILHASSSAYSFDPNSRITDYPHAVGKNTLLISGLQARNNARVLFFGSLDFFSDETFNAPVQKAGGGLRYAKSGNQLLALRLSQWVFKEKGVLRVGKVTHHKKGEKVPPVAYTIMDTVEYTIEIEKNEDGKWVPLDADDVQLEFVRIDPFVRMGLHKKGDKFYAEFKIPDVYGVYQFRVDYNRIGYTHLFVTTQVSVRPLEHTQYE
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_27.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_27.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Pf1236_1/1_1.000_402
+LLWSEILRLVPFTSVELAQVRLLRLVHHCHDPC
+>PsIsotig05584_00818_503
+LLRSQILWLVLFTSVKLPQIGFLCLVHHRHDPC
+>Pp_3399_1/1_1.000_348
+LLWSQILRLVFLIFVELAQILLLRLVHHCQYTG
+>Ac363_1/1_1.000_432
+LLSPQVLWLVLFTFVKLAQVFLLCLVHHRHDSG
+>Pg1Pg2_ContigI_2596
+LLRSQVLWLVLFTTIKLSQVVLLCLMHHRHDSC
+>Ap1830_1/1_1.000_511
+LLSPQVLWLVLFTFVKLAQVFLLCLVHHCHDSG
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_30.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_30.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Pf1581_1/1_1.000_1837
+NWAVFENDMKWKPMEKRK
+>Pp_1355_1/1_1.000_1833
+NWAVFENDMKWKPMEKRE
+>Ac1659_1/1_1.000_1848
+NWAVFENDMKWKPMEKRK
+>Pg1Pg2_ContigI_3242
+NWAVFENDMKWKPMEKRK
+>PsIsotig07835_01762_1971
+NWAVFENDMKWRPMEKRK
+>Ap3485_1/1_1.000_1864
+NWAVFENDMKWKPMEKRK
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_32.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_32.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>PsIsotig12291_04836_2510
+LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMKITGLPFEAELYQSEYTIEDEQLKALLATSASRKAAKKKKK
+>Pf61_1/1_1.000_1008
+LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMKITGLPFEADLYQSEHTIEDEQLKALLATSASRKAAKKKKK
+>Ac1652_1/1_1.000_2305
+LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMRITGLPLDLDIYQSEYKIEDEQIKSILATSASRKAAKKKKK
+>Ap914_1/1_1.000_2326
+LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMRITGLPLDLDLYKSEYKIEDEQIKSILATSASRKAAKKKKK
+>Pg1Pg2_ContigI_2687
+LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMKITGLPFETEIYESEHTIDDEELKTLLATSASRKAAKKKKK
+>Pp_3975_1/1_1.000_1535
+LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMMITGLPFDPDLYQSEYSVEDEKLKGLLAMSASRKAAKKKKK
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_35.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_35.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>PsIsotig06251_01036_1545
+NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTASKFTRDLFKVTCGFSGFCLHGFWCLVFIVMGWHLC
+>Ac7666_1/1_1.000_1396
+NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTSTKFTRDLFKVACGPCCFCLHGIWSVVLVTLGWNLC
+>Pg1Pg2_ContigI_275
+NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTASKFTRDLFKVTCGSSGICIYGIRCLVPIVVGWHLC
+>Ap4162_1/1_1.000_589
+NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTSTKFTRDLFKVACGPCCFCLHGIWSVVLITLGWNLC
+>Pp_3408_2/2_1.000_676
+NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTSSKFTRDLFKVTRGTSSFCIHGIWCIISLAVGWNLC
+>Pf3031_1/1_1.000_540
+SRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTASKFTRDLFKVARSFSGFCLHGLWCIVLVVMGWYLR
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_38.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_38.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Pf4498_1/1_1.000_1098
+FGGGSRKKRSRSHTRSNSKSRSYSSQESNSSASPQHSPPAKYSKKEARDNNKYYSKEYENHYDRDYHHRDSRHEHERSKHKRRRHTPTYSPVRSYSRSPEPRSKAHKKYYKEKYRA
+>Pg1Pg2_Pg13774_1/1_1.000_1948
+FGGGSRKKRSRSHTRSNSKSRSYSSQESNSSASPQHSPPAKYSKKEARDNNKYYSKDYENHYDRDYHHRDSRHDHERSKHKRRRHTPTYSPVRSYSRSPEPRSKTHKKYYKEKYRA
+>Pp_3267_1/2_1.000_1460
+FVGGTRKKRSRSRTRSNSKSRSYSSQESNSTGSPQRSPPVKFSKKEARDNNKYYSKEYDNHYDRDYHHRDSHRDHERSKHKRRRHTPTYSPIRSYSRSPEPRSKTHKKYYKEKYRA
+>Ac4272_1/2_1.000_2412
+FGGGSRKKRSRSHTRSNSKPRSYSSQESNSTASPQHSPPAKYSKKEARDNNKYYSKEYDNHYERDYHHRDSHHDHERSKHKRRRHTPTYSPLRSYSRSPEPRSKTHKKYYKEKYRA
+>Ap3418_1/1_1.000_1919
+FGGGSRKKRSRSHTRSNSKTRSYSSQESNSTASPQHSPPAKYSKKEARDNNKYYSKEYDNHYERDYHHRDSHHDHERSKHKRRRHTPTYSPLRSYSRSPEPRSKTHKKYYKEKYRA
+>PsIsotig12297_04842_646
+FGGGSRKKRSRSHTRSNSKSRSYSSQESNSSVSPHRSPPVKYSKKEARDNNKYYSKEYENHYDRDYHHRDSRHDHERSKHKRRRHTPTYSPVRSYSRSPEPRSKAHKKYYKEKYRA
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_39.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_39.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>PsIsotig10643_03194_2284
+ITHVLNITAHVPFHFEAEGIVYKRLPATDSGHQNLKQYFEDAFKFIEERFRR
+>Pp_6073_1/1_1.000_1725
+ITHVLNVTGHVPLHFEAQGIIYKRLPATDSGQQNLKQYFEDAFKFIEEKLWR
+>Pf4635_1/1_1.000_231
+ITHVLNITAHVPFHFEAEGIVYKRLPATDSGHQNLKQYFEDAFRFIEERFKR
+>Ac2807_1/1_1.000_2307
+ITHVLNVTAHVPFHFEEQGIIYKRLPATDSGHQNLKQYFEDAFTYIEEKFKW
+>Pg1Pg2_ContigI_3109
+ITHVLNVTSHMPFHFEAQGITYKRLPATDSGHQNLKQYFEDAFKFIEETFRR
+>Ap5088_1/1_1.000_2170
+ITHVLNVTAHVPFHFEEQGIKYKRLPATDSGHQNLKQYFQDAFTFIEETFRW
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_40.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_40.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Ac1381_1/2_1.000_1229
+MHSFELPLMHSYEEMYVSPDMWQATLKKEADRTSQMEKNLMRKLKKKGIPGKFIARGGGKPGEAIISAADDEDADMIVMATRGRGRLMRVLLGSVS
+>Pp_1351_1/1_1.000_1516
+MHSFELPLMHSYEEMYVSPDMWQATLKKEADRTAQMEKALMRKLKIKGTPGKFITRGGGKPGEAILSAADDEDVDMIIMATRGRGKLMRVLLGSVS
+>Ap2493_1/2_1.000_1233
+MHSFELPLMHSYEEMYVSPDMWQATLKKEAERTSQMEKNVMRRLKKKGIPGKFIARGGGKPGEAIVSAADDEDVDMIVMATRGRGRLMRVLLGSVS
+>PsIsotig15400_07945_928
+MHCFELPLMHSYEEMYVSPEMWQATLKKEADRTSHMEKALMKKLKIKGIPGKFIARGGGKPGEAILSAAEDENVDMVVMGTRGRGKLMRVLLGSVS
+>Pf1400_1/1_1.000_761
+MHCFELPLMHSYEEMYVSPEMWQATLKKEADKTAQMEKTLMRKLKIKGISGKFIARGGGKPGEAILSAAEDEDVDMIVMGTRGRGKLMRVLLGSVS
+>Pg1Pg2_ContigI_142
+MHSFELPLMHSYEEMYVSPDMWQATLKKEADRTTHMEKVLMKKLKLKGVPGKFIARGGGKPGEAILSAAEDENVDMIVMGTRGRGKLMRVLLGSVS
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_41.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_41.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Pf645_1/1_1.000_1413
+NSDLDTMTALGSRIRWITRRLGFLSRRVSTTSIVARTVFVALKSAFLQNSPSICSQGLAFSRTICMHVE
+>Pg1Pg2_ContigI_3539
+NSDLDTITALGSRIRWITRRLGFLSRSVSTTSIVARTVFVALKSAFLQNSPSICSQGFAFSRTICMHVE
+>Ap5964_2/2_1.000_2574
+NSDLDTMTALGSRIKWMTRRLGFLSSSVSTTSIVARTVFVALKSAFLQNSPSICSHGLAFSRTICIQVE
+>Pp_3400_2/2_1.000_2104
+NSDLDTMTALGSRIRWITLRLGFLSSSVSTTAMVARTVFVALKSAFLQNSPSICSQGFAFSLTICIQVE
+>Ac3315_3/4_0.828_2597
+NSDLDTMTALGSRIRWITRRFGFLSSSVSTTSIVARTVFVALKSALLQNSPNICSHGLAFSRTICMQVE
+>PsIsotig06401_01089_2384
+NSDLDTITALGSRIRWITLRLGFLSSSVSTTSIVARTVFVALKSAFLQNSPNICSQGFAFSLTICMHVE
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_46.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_46.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Pp_882_1/1_1.000_2312
+FKFGLTKVFFRPGKFAEFDQIMKSDPENLALLIKKVKVWLIKSRWRKAQWGTLSVIKLKNKIIYRRQLLIYENINKEMDKTLSEIKKLLEKQKVADEQEKLRRIQEERERERKKKEEEERKQREEEEQKKLKAEMET
+>PsIsotig15436_07981_1677
+FKFGLTKVFFRPGKFAEFDQIMKSDPENLAALIKKVKVWLIKSRWRKAQWGTLSVIKLKNKIIYRRQLLIYESINKEMDKTLAEIKKLLEKQKVAEEQERLRRIQEERERERKKKEEEERRKREEEEQKRLKAEMEA
+>Pf127_1/1_1.000_1072
+FKFGLTKVFFRPGKFAEFDQIMKSDPENLAALIKKVKIWLIKSRWRKAQWGVLSVIKLKNKIIYRRQLLIYEGINKEVDKTLVEIKKLLEKQKVAEEEERLRRIQEERERERKKKEEEERRKREEEEQKKLKAEMEA
+>Ap1670_3/5_0.667_5194
+FKFGLTKVFFRPGKFAEFDKIMTSDPENLATLIKKVKVWLIKSRWRKAQWGTLSVIKLKNKIIYRKQLLIYEGINKEMDKTLAEIKKLLDKQKVAEEQERMRRIQEERERERKRKEEEERKKREEEERLRLKAEMEA
+>Ac2574_1/1_1.000_4696
+FKFGLTKVFFRPGKFAEFDKIMTSDPENLATLIKKVKIWLIKSRWRKAQWGTLSVIKLKNKIFYRRQLLIYEGINKEMDKTLAEIKKLLDKQKVAEEQERMRRIQEERELERKRKEEEERKKQEEEERLRLKAEMEA
+>Pg1Pg2_ContigI_2586
+FKFGLTKVFFRPGKFAEFDQIMKSDPENLALLIKKVKLWLIKSRWRKAQWGALSVIKLKNKIIYRRQLLIYESVNKEMDKTLTDIRKLLEKQKVAEEQERMRRIQEERERERKRKEEEERQKREEEEQKRLKVEMEA
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_47.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_47.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Pg1Pg2_ContigII_47
+QKDVKDGKYSQILSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK
+>Ac120_1/1_1.000_522
+QKDIKDGKYSQVLSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK
+>Ap1431_4/4_0.500_851
+QKDIKDGKYSQVLSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHMKTTGRRGRTVGVSKKK
+>Pp_11407_1/1_1.000_522
+QKDVKDGKYGQILSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK
+>Pf74_1/1_1.000_506
+QKDVKDGKYSQILSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK
+>PsContig17553_00005_681
+QKDVKDGKYSQILSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_50.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_50.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Ac2592_1/1_1.000_1693
+ERAMAPAGDGAFTIGKGVLAGASAVGLGMLCYYGLGMSNQVGAIDRAAIWPEEVRQRIKDTYMYFGGSLIFTAASAVAVSRSPVMMRLVMRNGWLTIIGTMAAMIGSGMVVRSLPYKKGFGAKQIAWMVHSGIVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIYRAENHPVYALQPYDPINNSVGIYLDTINIFIRIATILAGG
+>Pf687_1/1_1.000_1628
+ERAMAPAGDGAFTVGKGMLAGVSAVGLGMLCYYGLGMSNQVGAIDRAAIWPNIVRQRIKDTYMYFGGSLIFTAASAVAASRSPFMMRLVMRNGWLTIIGTMAAMIGSGMIVRSLPYKEGFGAKQIAWMVHSGIVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIYRAENHPVYAVQPYDPINNSVGIYLDTINIFIRIATILAGG
+>PsContig29267_00170_1133
+ERAMAPAGDGAFTAGKGMLAGVSALGLGMLCYYGLGMSNQVGAIDRAAIWPNIVRQRVKDTYMYFGGSLIFTAASAVAASRSPVMMRLVMRNGWMTLIGTMAAMIGSGMIVRSLPYKEGFGAKQIAWMIHSGIVGAVIAPITLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIYRAENHPVYAVQPYDPINNSVGIYLDTINIFIRIATILAGG
+>Pp_2968_1/1_1.000_1595
+ERAMAPAGDGAFSIGKGLVAGMSAVGLGMLCYYGLGMSNQVGAIDRAAIWPDIVRQRVKDTYMYFGGSLMFTAASAVAASRSPMVMNLVMRNGWLALIGTMAAMIGSGMIVRSLPYKEGFGAKQIAWMVHSGVVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAVCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGLYSVAMYGGLALFGAFLLYDTQKIIHRAENHPVYANQPYDPVNNSVGIYLDTINIFIRIAMIMGGG
+>Ap2039_1/1_1.000_1819
+ERAMAPAGDGAFTIGKGVLAGASAVGLGMLCYYGLGMSNQVGAIDRAAIWPDVVRQRIRDTYMYFGGSLIFTAASAVAVSRSPVMMRLVMRNGWLTIIGTMAAMIGSGMVVRSLPYKEGFGSKQIAWMVHSGIVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIYRAENHPVYALQPYDPVNNSVGIYLDTINIFIRIATILAGG
+>Pg1Pg2_ContigI_3254
+ERAMAPAGDGAFTLGKGMLAGVSAVGLGMLCYYGLGMSNEVGAIDRAAIWPNVVRQRVKDTYMYFGGSLVFTAAAAVAASRSPMVMRLVMRNGWLALIGTMAAMIGSGMVVRALPYKEGFGSKQMAWIVHSGIVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSIGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIHRAENHPVYAMQPYDPINNSVGIYLDTINIFIRIATILAGG
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_53.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_53.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>PsIsotig04438_00541_1468
+SWLLGKWRSEDGQGIYPTIKDFKYIEELEFFQVGQPNIQFNFYAFNAETKKPMHREVGFIRVTPDLSKVALVSAQNTGLADIEEGTYNDKEKELRVESCALGRMSFGKLPETKIARIFR
+>Ac19848_1/1_1.000_822
+SWLLGKWRSEEGAGHYPTIKDFKYIEEVEFFQVGQPNIQFSFYAFNAETKKPMHREVGFIRVKPDLSKVAFISAQNTGLAEVEEGTYNDKDKELRFESHTIGRLTFGKPPETKIARIFR
+>Pf5916_1/1_1.000_798
+SWLLGKWRSEDGHGHYPTIKDFKYIEELEFFHVGQPNIQFSFYAFNAETKKPMHREVGFIRVTPDLSKVAFVSAQNTGLAEVEEGTYNDKEKELRFESHTVGRLTFGKPPETKIARIFR
+>Pg1Pg2_ContigI_2557
+SWLLGKWRSEDGQGHYPTIKDFKYIEELEFIQVGQPNIQFSFYAFNAETKKPMHREVGFIRVTPDLSKVAFISAQNTGLAEVEEGTYNEKEKELRFESHTVGRLTFGKPPVTKIARIFR
+>Ap4677_1/1_1.000_1142
+SWLLGKWRSEEGAGHYPTIKDFKYIEEVEFFQVGQPNIQFSFYAFNAETKKPMHREVGFIRVKPDLSKVAFISAQNTGLAEVEEGTYNDKDKELRFESHTIGRLTFGKPPETKITRIFR
+>Pp_619_3/4_0.500_1588
+SWLLGKWRSEDGSGQYPTIKGFKYIEELEFFHVGQPNIQFSFYAFNAETKKPMHREVGFIRVTPDLSKVAFVSAQSTGLAEVEEGTYNDKEKELKFESHTVGRLTFGKPPVTKIARIFR
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_57.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_57.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Pp_4624_1/1_1.000_408
+NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHILYLGGVYRGGHDVLVRAKLALTDSGVTMQITVRSTDSSAAEVIASAVG
+>Ap20_1/1_1.000_3490
+NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVYRGGHDVLVRAKLALTESGVTMQITVRSTDASAAEVIASAVG
+>Pf2182_1/1_1.000_391
+NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVFRGGHDVLVRAKLALTDNGVTMQITVRSTDSSAAEVIARAVG
+>Pg1Pg2_ContigI_4321
+NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVFRGGHDVLVRSKLALTENGVTMQITVRSTDSSAAEVIARAVG
+>Ac769_1/1_1.000_3492
+NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVYRGGHDVLVRAKLALTESGVTMQITVRSTDASAAEVIASAVG
+>PsIsotig22043_14588_2117
+NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVFRGGHDVLVRAKLALSENGVTMQITVRSTDASAAEVIARAVG
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_58.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_58.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>Pf3163_1/1_1.000_300
+SSSDSDSHSRSSSSDSSSSSGSSSSGTSRSSSSSSSSSSKSRSRGRNRSVSRGR
+>Ac5819_1/1_1.000_1087
+SSTDSDSHSRSSSSDSSSSSGSSSSGSSRSSSTSSSSSSKSRGRARNRSISRGR
+>Pp_5864_1/2_1.000_1207
+SSSDSDSHSRSSSSDSSSSSGSSSSGSSRSSSSSSSTSSKSRNRGRNRSASRGR
+>Pg1Pg2_ContigI_943
+SSSDSDSHTRSSSSDSSSSSGSSSSGSSRSSSSSSSTSSKSRSRGRNRSPSRGH
+>Ap10018_1/1_1.000_1141
+SSSDSDSHSRSSSSDSSSSSGSSSSGSSRSSSTSSSSSSKSRGRARNRSISRGR
+>PsIsotig05647_00837_2779
+SSSDSDSHSRSSSSDSSSSSGSSSSGTSRSSSSSSSSSSKSRSRGRNRSVSRGR
diff -r 000000000000 -r acc3674e515b test-data/sep_aa/locus_6sp_60.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_aa/locus_6sp_60.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,12 @@
+>PsIsotig13857_06402_734
+ERFFGGGARRNDFSISDCLVTAENSSS
+>Ap1982_1/2_1.000_2775
+ERFFGGGALRKDFSISDCLVTAENSSS
+>Pp_26038_1/1_1.000_265
+ERFFGGGALRKDFSISDCLVTAENSSS
+>Ac6601_1/2_1.000_1710
+ERFFGGGALRKDFSISDCLVTAENSSS
+>Pg1Pg2_ContigI_6747
+DRFFGGGARRKDFNISDCLGTAENSSS
+>Pf3398_1/1_1.000_178
+ERFFGGGARRNDFSISDCLVTAENSSS
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_109_with_3_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_109_with_3_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,6 @@
+>Lf38763_1/1_1.000_387
+aaggccttgcgccggaacattgcggtgaactgctcgctgatgcgcttgaagagttcctggatggccgtgctgttgccgatgaaagtgccagacatcttgaggccgcgcggcgggatgtcgcagacagcggtcttgacgttgttcgggatccactcgacgaag
+>Bj1919_1/1_1.000_456
+aaggccttacgacggaacatggcagtgaactgctcactgatgcgcttgaacagctcttggatggcggtgctgttgccgatgaaggtgcctgacatcttgaggccacgtggtgggatgtcacagacggctgtcttgacattgttgggaatccattcaacgaag
+>Bs30874_1/1_1.000_304
+aaggccttgcggcggaacatggcagtgaattgctcagagatgcgcttgaagagctcttggatggcagtgctgttaccgacaaatgtaccggacatcttgaggccacgaggagggatgtcacaaacagcagtcttgacattgttggggatccattcgacgaag
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_113_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_113_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Bs16883_1/1_1.000_765
+caggagttcaaagaagccttcacaatgattgaccagaacagagacggcttcattgacgagagtgacctggcctccatgttccagcagaccggtcgcgaggctgagcccaaacagctgaaggagatgttggctgaggctcccggcacgctcaactttactaacttcctcacgctcttcggcgagaagctgcacggaactgaccccgagaggaccctgcttgatgccttcaagatgttcgacgttgaacgcaagggtatcctgtctgaagaatacctgaaggacctcctggtgaacgttggtgaccagttctccaaggatgagatcaaacaaacatgg
+>Lf12022_1/1_1.000_613
+caggagttcaaggaggcgttcacgatgatcgaccagaaccgggacggcttcatcgacgagaacgacctggccgccatgttccagcagaccggacgcgaggctgagcccaagcaactgagagagatgttggccgaggcgccagggaccctcaacttcaccaacttcctcaccttgttcggcgaaaaacttcacgggactgacagcgagcgcaccctgacagacgccttcaagatgtttgacgaggccgggaaaggttacatttcagaggagtaccttaaggacctcctggttaacgttggtgaccagtactctaaggatgagattaaacagacgtgg
+>Ha10806_1/1_1.000_456
+caggagttcaaggaagccttcaccatgatcgaccagaacagagatggcttcatcgatgagaacgacctggcttctatgttccaacagaccggtcgtgaggctgaacccaagcagctgaaggaaatgctggccgaggcgcccggcacgctcaacttcactaacttcctcaccttgttcggtgagaagttgcacggtactgacccggagaggacgctcctcgatgccttcaagatgttcgatccggaaggcaaaggggtcctggcggaagaatacttaaagactctcctggtggaagttggtgaccagttctccaaggacgagatcaaacagacgtgg
+>Bj297_1/1_1.000_561
+caggagttcaaggaagccttcaccatgatcgacacgaaccgtgacggttttattgacgagtctgatctcgctgctatgtttcagcagaccggtaaggaagccgacccgaaaacgctgaaggagatgattgctgaggcacctggaaccttgaatttcaccaatttcctcacactctttggtgagaagcttcatggaaccgactctgagcgcaccctcattgacgccttcaagatgtttgacgatgagggcaagggtgtgctagcggaagattacctcaaggacctactggtggaggttggtgaccagtttaacaaggatgagcttaagcagacgtgg
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_253_with_2_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_253_with_2_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,4 @@
+>Ha10499_1/1_1.000_784
+ttctggatcagctgggatcgtggcctggtgcgagtcggggagggcacgcgccgcaaccaccagcccttcctcgtgtggaacgtccccgagaacaagcagcacggggtcaactgcatcgccgtctcctccgggcctgggtcggagggcgagtgggagttc
+>Bj32890_1/1_1.000_2739
+ttctgggtgagctgggaccgcggctcggtgcgggttggcgaggggtcgcgccgcactcaccagcccttcctggtgtggaacgtgcccgagaacaagcagcacagcgtcaactgcatagcagtctcctccgggcccggctccgagggcgagtgggagttc
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_283_with_2_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_283_with_2_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,4 @@
+>Ha1337_1/1_1.000_1215
+gacttcttgatcttctcttcgaacagatcctttttgttgaggaaaagaatgatagaggtatcggtgaaccatttgttgttacagatcgagtcgaacagcttc
+>Bs2095_1/1_1.000_1167
+gacttcttgatcttctcttcgaataaatccttcttattaaggaagagaataatagaggtgtccgtgaaccatttgttattacaaatagagtcgaacagcttc
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_299_with_2_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_299_with_2_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,4 @@
+>Bj17018_1/1_1.000_567
+tgcttcccgtccaaccaggaagttttctcggtacagatgaaaaactgtgatccgtttgtgttagggccagcgttcgccatcgacagcataccaggccctgtgtgcttcaaagtgaaattttcatcagcaaac
+>Bs1426_1/1_1.000_513
+tgcttcccgtccagccagtcggtcttgacggtacagaggaagaactgcgacccgttggtgttggggccggcgttggccatggagaggataccgggtccagtgtgctttagggtgaagttctcgtcagcgaac
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_301_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_301_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Ha10118_1/1_1.000_897
+gaggatgatgaggaacaggtagacgatgtccaagtagagctgcagcgctccgaacacgtggtcctccggggacagctcgaacttcttgcctccgatcagcatctgtgtgtcgtaagccaggaacatggagaa
+>Lf311_1/1_1.000_384
+gaggatgatgagaaagaggtagatgatgtcgaggtagagctgaagtgctccgaacacgtggtcctctggcgacagtcggtacttcttgttgcccatcagcatctgggtgtcatacgccaggaacatagagaa
+>Bs27070_1/1_1.000_699
+gaggatgatgatgaagaggtagacgatgtccaggtacagctggagcgcaccgaacacgtgatcctccggggagagctcatgcttcttaccgccaaccagcatctgggtgtcgtacgccaggaacatagagaa
+>Bj17798_1/1_1.000_1215
+gaggaagatgaggaagaggtagactatgtccaggtacagctggagcgcaccgaacacatggtcctctggggagagctcatacttcttaccgccaatcagcatctgggtgtcatatgcgaggaacatagagaa
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_316_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_316_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Bs27803_1/1_1.000_1664
+gtgaacgcgccccctgtcccctcctctcgcgacactgcgctcaccatcgccgcagacaagggccactaccgctttgtggaactgctcctctccagaagcgctgccgtagacgtgaagaacaagaaggggaactctcctctgtggttggcttgcaacggtgggcacctggatgtggtgcagttactcgtgaacgccaaggcggatatcgacagccaggacaaccgcaaggtgtcgtgcctcatcgcggccttccgcaaaggtcacgtgaaggttatcaaatggatggtgaagcatgtggcacagttcccttcggaccaggagtgcatgcgatacatctcaaccatcacggataaggagctgctgaaaaaatgccatcaatgcatggagatcattgtgagcgccaaggaccggcaggcagcggaggcgaaccggcacgcctctatcctcctggaacagttggaccgcgagaagagcctggaggagagcaagaaggcggccgcagcccgcaagcgcgagaagcgacgccggaagaagaaggagaagcaggagcaggcgaacaacaaaaaccaggcacacaagcgaagtcggaacactgaggtgagctcgaacagcagcagtagcagcgagtcgaatggcaagacgaagagcaagaagagcaagaaggccgagcgc
+>Bj26780_1/1_1.000_2698
+gtgaatgcgccccccgttccctcctctcgcgacactgcgctcaccattgccgcagacaagggccactatcgctttgtggagctgctcctctcgagaagtgcggccgtagacgtaaagaacaaaaaggggaactctcctctatggttggcttgcaacggtgggcacttggacgtcgtgcagttattagtgaacgccaaggctgacattgacagtcaggacaaccgcaaggtatcatgcctcattgcggctttccgcaaaggtcacgtcaaggtgatcaaatggatggtgaagcacgtggcacagttcccttcagaccaggagtgcatgcgatacatctcaaccattacggacaaggagctgctgaaaaaatgccatcaatgcatggagatcattgtgagcgccaaggaccggcaggcagcggaggctaaccgccacgcttccattctcctggagcagctggaccgtgagaagagcttagaggagagcaagaaggcagcggccgcccgcaagagggagaaacgacgccgcaagaagaaggagaagcaggaacaggcgaacaacaaaaaccaggcgcacaagcggagtcgtaacaccgaggtgagctcgaacagcagcagtagcagcgaatcaaatggcaagacgaagagtaagaagagcaagaaggctgagcgc
+>Ha1883_1/1_1.000_5577
+gtgaacgcgccacccgtgccctcttcacgtgacaccgccctcaccatcgccgcagacaagggccactaccgcttcgtcgagctgctcctctcccgcagtgctgccgttgatgttaagaacaagaagggcaactcgccgctctggttagcctgcaacgggggtcacctggatgtggtgcagctgttggtgaatgctaaggcagacatcgacagtcaggacaaccgtaaggtgtcgtgcctcatcgccgccttccgtaaggggcatgtcaaggtcatcaagtggatggtgaagcatgtggcccagttcccgtcagaccccgagtgcatgcgctacatctcgaccatcactgacaaggagctgctgaagaaatgccaccagtgcatggagattatcgtcagtgccaaggaccggcaagcagccgaggccaaccgccacgcatctatcctactagagcagctcgaccgagagaagagcctagaggagagcaagaaagccgccgcagcccgcaagagggagaagcggcggcgaaagaagaaggagaaacaggagcaggcaaataacaaaaaccaagcccacaagcggagtcgcaatttggaagtgagcagcaatagtagcagtagcagcgagtccaacggcaagaccaagagcaagaagagcaaaaaggccgagcgg
+>Lf1892_1/1_1.000_9654
+gtgaacgcgccgcctgtgccgtcatcccgcgacaccgcgctcaccatcgccgctgacaaggggcactaccgctttgtggagctgcttctctccaggagtgctgctgtggatgtaaagaacaagaagggaaactctcctctctggctggcctgtaatggtgggcacctggacgtggtgcaattattggtgaacgccaaggcggacatcgacagccaggacaaccgcaaggtgtcgtgtctgattgcagctttccgcaaaggtcatgtgaaggtcatcaagtggatggtgaagcatgtggcccagttcccgtcggaccaggagtgcatgcgctacatctcgaccatcacagataaggagctgcttaagaaatgccatcaatgcatggagatcattgtgagcgccaaggaccggcaagcagcagaggcgaaccggcatgcgtcaattctcctggagcagctcgaccgcgagaagagtctggaggagagtaagaaggccgcagccgcccgcaagcgggagaaacgtcggcggaagaagaaggagaagcaggaacaggcaaacaacaaaaaccaggcccacaaacgaagtcgtaacactgaggtgagctccaacagtagcagcagcagcgagtcaaacggcaagaccaagagcaagaaaagcaagaaggcggagcgg
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_335_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_335_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Lf1038_1/1_1.000_963
+gcgccgcatggcgacggtcgagtagttgcagtgcgcgccagcgccgttccagtctcccggcatcggcttcgggtcgaagctgacgacgatcccgaagtcctcagcgacacggtgcaggacgtagcgcgccatccacaggtcgtcgcccatctggatgccctcacacggacccacctggaactcccactgtcccggcatcacctcggcgttcgtgccggcgatcttgatgtcggcgta
+>Bs16552_1/1_1.000_1152
+ctccctcatggccagcgtcgagaagttggtgtgtgccccggcaccgttccagtctccgggcattggcttggggtcgaaactgacgacgatgccaaagtcttcggcgactctgtgcaggatgaatctggccatccagaggtggtcgcccatgctgattccctcacagggtcccacttggaactcccactgggcaggcatcacctcagcgttggtaccggcgatcttgacgccggcgta
+>Bj389_1/1_1.000_1311
+ttctctcatggcttgtgtggagtagttggtgtgtgcacctgcgccgttccagtctccgggcatgggtttggggtcaaaggtgacgatgactccgaagtcctctgcgactctatgcagcaagtagcgggccatccagaggtggtctcccatctcaatgcccaggcacgggccaacctggaactcccactggccgggcatgacctcggcgttggttccggctattttgactcctgcgta
+>Ha2081_1/1_1.000_1176
+ctccctcatggccttggtggagtagtttgtgtgtgcaccggcaccattccagtctccgggcatgggtttggggtcgaaggtgacgatgacaccgaagtcctctgctacacggtgcagcaggtagcgggacatccacaggtggtcgcccatgtcgatacccaggcacggccctacctggaactcccactgggcaggcatgacctcagcattagtaccagagatgttgacccctgcgtg
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_343_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_343_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Ha10325_1/1_1.000_531
+ccccgtactgggtgccccacgctgaccgcatccactacatctctaaggactgtgagagggactggttcaacgactgggagtgtatggagtgctgcaacggagatctctgcaactactatgtca
+>Bs3268_1/1_1.000_471
+ccccctactgggtgccccacgctgaccgcatctactacatctccaagaactgcgagcgcgactggttcaacgactgggagtgcatggagtgttgcaacggcgacctgtgcaactactacgtca
+>Lf56088_1/1_1.000_447
+ccccttactgggtgccctacggagaccgcgcctacttcgtctccaagaactgcgagcgcgactggttcgacgactggggctgtgtggagtgctgctcgggcgacctgtgcaactactacgtca
+>Bj5017_1/1_1.000_456
+ccccctactgggtgccccatgctgaccgcatctactacatctccaagaactgcgagcgggactggttcaacgactgggagtgcatggagtgttgtaacggcgacctgtgtaactactacgtca
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_368_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_368_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Lf51152_1/1_1.000_999
+aggcggatggtgtttgagaagaacatgatgttcatccgagaccacaacatggaggctgaccttggacacaagtccttccgggttggggtcaagaaccaggcacaatgtggatcctgctgggcgttctccgccattggggccctggaaggtcaacacttcaggaagacaggggatctcgtctctctatctgagcagaacctggtcgactgctcaacaacagaagga
+>Ha12847_1/1_1.000_855
+aggcggatgatcttcgagaagaacatgaacttcatccgtgaacacaacatggcagctgatcttggccacaagaccttccgtgtcggtgtcaagaaccagatgcaatgtggatcatgctgggccttctccgctactggctcccttgaaggtcaacatttcaagaagacaggaaagctggtctccctttcagaacagaatcttgttgactgttcccaagctgaagga
+>Bs1045_1/1_1.000_633
+aggcgaatggtgttcgagaagaacatgatgttcatccgggaccacaacatggaagctgaccttgggcacaaatccttccgggtcggagtcaagaaccaggaacaatgtggttcctgctgggccttctctgcaactggctcactggaggggcagcacttcaagaagacaggcaagcttgtctccctgtcagagcagaacctggttgactgctcccaggccgaagga
+>Bj108003_1/1_1.000_523
+aggcgaatggtgtttgagaagaacatgatgttcatccaggaccacaacatggaggctgacctggggcacaagtccttccgggttggaatcaagaaccagggggcttgtggctcctgctgggctttctctgcaactgggtcgctcgagggacagcacttcaagaagactggtaaccttgtctccctgtcagaacagaacctggttgactgttctaaggctgaagga
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_404_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_404_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Lf14756_1/1_1.000_456
+gtcagcctttccatcacggttgctgtcaagtttgtcggcgagtccgtctttgttctggtc
+>Ha5212_1/1_1.000_491
+gtcctccttgccatcacggttgctgtccagcttgtcagctactccatcgttgttctggtc
+>Bj16996_1/1_1.000_378
+gtccttcttgccatcacggttgctgtcaaatttgtctgcgagcccatcgttgttttggtc
+>Bs10543_1/1_1.000_387
+gtccttcttgccatcgcggttgctgtcaagcttgtcagcgagcccatcgttgttctggtc
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_442_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_442_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Bj29526_1/1_1.000_478
+acacacaatgaaggagttggcatctccagcatagtagaagccataattatagccagaagcgcagtcaccctcaaaatgtccgaggtagtaaaactggccagctccaacatgaactgggtaggctcccaaagtgcggtagttgaactcattgttgaaaccaaatccttctccatatccata
+>Bs16935_1/1_1.000_456
+acatacgatgaaggagttggcatctccagcatagtagaatccatagttgtagccagaggcgcaatcaccattgaaatgtccaaggtagtagaactggccagctccaacatgaactgggtaggctccaaaggtacgatagttgaactcattgttgtagccaaatcctactccatatccata
+>Ha22482_1/1_1.000_398
+acacacaatgaaggagtcagcatttccagcaaagtagaagccataattgtatccaccagcacagttaccattgaactgcccaaggtagtagaactggccatttcctacatgaactgggtaggcaccaaatcctcggtagttgtactcattgttgaagccataccctactccagcaccaga
+>Lf10136_1/1_1.000_570
+gcacacgatgaaggagttagcatcctcagtgtagtagaagccgtaattgtagccattggcgcagttaccattgaagtttccaaggaaatagaactgcccagctgcaatattgaaaggatatgctccgaatccatgatagttgaactcattgttatagccatatcctactccatatccata
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_487_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_487_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Bj104219_1/1_1.000_544
+ggcttctgggacaagttgatccttgagccttacggccggcagcgggacatagtctac
+>Lf26378_1/1_1.000_6633
+ggcttctgggacaagctgatactggaaccatacggccggcagcgagacattgtctac
+>Ha278_1/1_1.000_2763
+ggcttctgggacaagttgatcctggagccgtacgggcggcagcgtgacgtggcctac
+>Bs54896_1/1_1.000_618
+ggtttctgggacaagctgatccttgagccttatgggcggcagcgggacatcgtctac
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_508_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_508_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Bj115168_1/1_1.000_390
+tcctcctcctcctccgagctgctgacgtcaccaaatatgtcttcctccaggaatttgctaatgttctccgatgcggctgcgttctcgaccttcttggcctccgatgagttcagtggattgaacacgtccccg
+>Lf36714_1/1_1.000_1599
+tcctcctcttcctcggagctgctcacgtcgccgaagatatcctcctccaggaatttgctgatgttctccgaggcggctgcgttctccaccttcttagcttcggaggaattcagcgggttgaaaacatcgccg
+>Bs6083_1/1_1.000_337
+tcctcttcctcctcagagctgctcacatcaccaaagatatcctcctccaggaatttgctgatgttctccgacgcggctgcgttctcgaccttcttggcttcagatgagttgagcgggttgaacacatccccg
+>Ha18272_1/1_1.000_681
+tcctcctcctcttctgagctgctcacgtcgccgaagatatcctcctctaagaatttgcttatgttttcagaggcggcagcattttccactttcttggcctctgatgagttaagtgggttgaagacgtctccg
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_544_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_544_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Bj19203_1/1_1.000_2676
+gaactgaagcgagcagacttcaagctgatcggcaagggcaagtctgacccctactgcaagatctacatcgggtcccagatgtacaagacacgagtgatcgaaaacaccattaacccagtctggaacagctacttcgaggcggttgttgaccaaaaacatggccaatttgcggagcttgaggtacttgaccaggatcctggggaggatgacgaactgggaacggcaagtattgatattgagaacgtggcagtaaagggctcattggacacgtggctccctcttgagaatgtcgagaccggcatggtgcacatccgggcaatatggcttcacctcagcaagaaccctaaagacctg
+>Lf110082_1/1_1.000_1416
+gaactgaagagagccgacttcaaactggtcggcaagggcaagtccgacccctactgcaagatctacatcggtgctcagatgtacaagacgaaggtaattgagaacacgatcaacccggtctggaacagctacttcgaggcggttgttgaccagaagcacggtcaatttgcggagctcgaggtacttgacaaagatccgggtgatgatgacgagttgggcacagcgagtatcgacatcgagaatgttggcgacaagggcacattggacacgtggctgccgctggagaacgtggagacgggtatggtacacatccgtgccatatggctgcacctgagtaaggacccggccgacctg
+>Ha37107_1/1_1.000_642
+gaactgaagcgggccgacttcaaactggtggggaaaggcaaatcggacccctactgcaaaatatacattggcgcacagagcttcaagaccaaagtgatagaaaacactatcaatcctgtatggaacagctactttgaggcggtagtggaccagaagcatggacaattcgctgaactggaagtgctcgatcaggatcctggagaagatgacgaacttggaacggcgagtgtggacatccagaatgtaggtgaacatggctcaattgacacgtggctccccctggagaatgtggacactggcatggtgcacatccgtgctatgtggctgcacctgagtaaggaccccgctgatctg
+>Bs13030_1/1_1.000_2652
+gaactgaaacgggcagacttcaaactggtcgggaagggcaagtcggacccctactgcaagatctacatcggcgcccagatgtacaagacgaaagtcatcgaaaacaccattaacccagtctggaacagctacttcgaggcggttgttgaccaaaaacatggtcaatttgcggagcttgaggtacttgaccaggatcccggtgaagatgacgaactgggcacagcaagtattgacattgaggacgtgggtgcaaaaggctcactggacacgtggcttcccctggagaacatcgaaactggcatggtgcacgtccgggccatctggctccacctcagcaaggacccgaacgacctg
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_546_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_546_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Ha41649_1/1_1.000_527
+ctcaccccggtacctgtagacgaacccgctcacacctgtacactacattcacgctacacctgcctcattaag
+>Lf11086_1/1_1.000_2517
+ctcaccccagtacctgtggacgagccggcacacacgtgcaccctccatgcacgctacacgtgtctcgtgaag
+>Bs41282_1/1_1.000_485
+ctgagcccggtgcctgaagacgagccagcacacacatgcactctgcatgcacgctacacgtgcctggtgaag
+>Bj19624_1/1_1.000_1584
+ctgagcccggtgcctgtagacgagcctgcccacacgtgcacccttcatgcacgctacacgtgtctggtgaag
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_588_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_588_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Bj3220_1/1_1.000_3147
+agtttggagaccgagtgcccgccgacgtgcgcgttagctcatggatttaaggtggacaactcctcgctgactggggaatctgagcctcagactagaaccgcagagttcacgaatgataacccgctcgagaccaagaacctcgccttcttctcaacaaatgctgttgaaggcacgtgtcgcgggattgtagtgagcactggggaccgcaccgttatgggccggatcgccaacctggcatccggactcgagatgggccagactccgatcgcacgtgagatcgaacatttcatccacatcattactggtgtcgctgtattcctcggcgtagccttctttatcgtcgctttcatccttggttactactggcttgatgctgtcatcttcctcatcggtatcattgtcgccaatgtgcccgaaggtctgctggctaccgtcacggtgtgcctgactctgaccgctaagcgcatggcgtccaagaactgtctcgttaagaacctggaggccgtggaaacacttggctccacatccacaatctgctccgataaaacgggaactctcactcagaaccgtatgactgtcgctcacatgtggttcgacaaccgcatcattgaggcggacaccactgaggatcagtcagcagatgcgggctgtgacgcggcatctgccacttggcaaagtttggcgcgtattgccatgttatgtaaccgcgctgagttcaagatgggacaggagaaccttcctgtactaaaaagggaatgtaacggcgacgcctccgagtctgcgctgctgaagtgcgcagagctatctatcggcaaggtgagagagttccgcgcaaagcacaagaaagcagttgaaattccattcaactcaaccaataaatatcaggtctctgtgcatgagatgccggacgatccgcgctacctgcttgtaatgaagggcgcccctgagcgcatcctggaccgctgcactaccatcctcattaatggcgaagagaaacccgtgtctcccgagtggaaggaggccttcgaacattcctacatggagttgggaggccttggagagcgcgtactcggattctgtgactacatccttgatgttgcaaaattcccacgtggctatccgtttgactcggaggaagagaacttccccctgaccggcctgcgcttcgttggtcttatgtccatgatcgaccctccacgagccgccgtgccggatgccgtgggcaaatgtcgcagtgctgggattaaggtgatcatggtgacgggcgaccatcccatcaccgccaaggccatcgcgaagggcgttggcatcatctctgagggaaatgaaactgtagaggacatcgctgcacggctcaacatacccgtcagtgaagtcaaccccagggacgctatggcatgtgttgtacacggctctgacctgcgtgatatgacccctgctcaaatagacgacatcctcagcaaccacacggagattgtattggcacgtacttcaccgcaacagaaactcatcattgtcgagggctgccaacgtcaaggcgccattgttgctgtcacaggcgatggggttaacgactcccctgccctaaagaaagccgatatcggagttgccatgggcattgctggcagcgacgtgtcgaaacaagcggctgacatgattcttctcgacgacaacttcgcatctattgtaactggtgtagaagagggccgtctgatcttcgacaacctcaagaagtcgatcgcctacaccctcacctcgaacatccccgaaatctctcccttccttctcttcatcctggccgatgtgccactgcccctgggaaccatcaccatcctgtgcattgatctcgggaccgaccttgtcccagcgatctccttggcctacgagcaggctgaaagtgacatcatgaaacgccagccccgtgatcctctccacgacaagctcgtgaacaacaggctgatcggcatggcctacgggcaggtcggtatgatccaggcatcggccgggttcttcgtctacttcgtcatcctcgccgagaatggcttcttgccatcacggcttctcggcatccgggaaagttgggactcgaaggctatcaacgacgagctcttatggtcaggagtggacatacgcccagcg
+>Bs118_1/1_1.000_3114
+agttcggggaccgggtgcctgccgacgtgcgtgtcagcgcacggcttcaaggtggacaactcctccctgaccggagagtccgagcctcagacgaggaccgccgagtttactaacgacaacccgctcgagactaagaatctcgccttcttctccacgaatgctgttgaaggcacgtgccgcggcgtcgtggtgagcacgggtgaccgcacggtgatggggcgcatcgccaacctggcctccgggctcgagatgggccagacgccgatcgcgcgcgagatcgaacacttcatccacatcatcacgggcgtggccgtgttcctcggcgtcgccttcttcatcgtcgccttcatcctcggctactactggctcgacgcagtcatcttccttatcggaatcattgtcgcgaacgtgcccgaaggtctgctggccaccgtcacggtgtgcctgactctgaccgctaagcgcatggcgtcgaagaactgcctcgtcaagaacctggaggctgtcgaaactctgggctccacgtccaccatctgttctgacaagaccggaaccctcacccagaaccgaatgactgtcgcccatatgtggttcgacaaccgcatcgtcgaagccgacaccactgaggaccagtcagcagatgcatgctacgactccaagtctgccacatggatatgtctggcgcgtattgccatgttgtgtaaccgcgccgagttcaaaatgggacaagagaatgtccccgtactgaagagagagtgtaacggtgatgcctcggaatctgcgctgctcaaatgtgtcgaactgtccatcggtaaggtgaccgagttccgtgccaaacacaagaaggctgtagaaattccattcaactcaaccaacaaataccaggtatccgtgcacgagatccctgacgacccgcgctacctgctcgtcatgaagggcgcccccgagcgcatcctcgaccgctgctccaccatcctcatcaacggcgaagagaagccgatgagcgaagactggaaggaagcctttgaacaatcctatatggagctcggagggcttggcgagcgcgtccttggattctgcgactacatcctcgatgctgcacagtacccccatggctatcccttcgactccgaagaggagaacttccccctgaccggtctgcgctttgtgggtctcatgtcgatgatcgaccctccacgtgccgctgtgcctgatgccgtgggaaaatgtcgcagcgctggaattaaagtgatcatggtgactggtgatcatcctatcactgccaaggctattgccaaaggtgtcggaatcatctccgaaggcaatgaaactgtcgaagacatcgctgcacgcctcaatattcctgtgagcgaagtcaaccctagagatgccaaggcttgcgttgtccatggctccgacctgcgcgatatgacgccagcacaaattgatgacatcctcgttaatcacattgagatcgtgttcgcacgaacctcacctcagcagaaactcatcattgtcgagggctgccaacgtcaaggcgccattgtcgctgtcaccggtgacggcgtcaatgattcacccgcgcttaaaaaagccgacataggcgttgccatgggcattgctggcagcgacgtgtcgaaacaagcggccgacatgatcctgctcgacgacaactttgcctccatcgtcactggtgtcgaagaaggtcgtctgatcttcgacaacctgaagaagtcgatcgcctacaccctgacctcgaacatccctgaaatctcgcccttcctcctcttcatcttggccgacgtgcccctgcccctgggaaccatcaccatcctgtgtattgatctcgggaccgaccttgtccccgccatctccttggcctacgaacaggctgagagcgacattatgaaacgccagccccgtgatcctctccacgacaagctcgtgaatcacaggctgatcggcatggcctatgggcagatcggcatgatccaggcctcggccggcttcttcgtctacttcgtcatcctcgctgagaacggcttctggccgtcgcatctgcttggtctgcgcaagcgttgggattccaaagccgtgaatgacgagctcctatggacaggagtggacatatgcccaacg
+>Ha3202_1/1_1.000_3108
+agttcggggacagggttccggctgacgtgcgtgtcagcacacggtttcaaggtcgacaactcctccctgactggtgaatccgagccgcagacaagaactgctgagttcaccaacgaaaaccctctagaaaccaagaacctggcattcttctcaaccaatgccgtcgaaggtacctgccgtggtgttgtcatcagcaccggtgacagtaccgtcatgggccgtattgccaacctggcctccggtctcgagatgggccagactccgattgcccgcgagatcgagcatttcatccacatcattactggggtagccgtcttcctgggcatatcattctttgtcatcgccttcatcctcggctattactggctcgatgccgtcatcttccttatcggtatcatcgtcgccaacgtgcccgaaggtctgctcgccaccgtcacggtgtgcctgaccctgactgccaagcgtatggcgtccaagaactgtctggtgaagaacctggaagccgtggagaccctcggctccacctccaccatctgctccgacaagaccggcacactcacccagaaccgtatgaccgtcgcccacatgtggttcgacaaccgcatcgtcgaggctgacaccactgaggaccagtcagcagacgcatgctacgactcctcctccccgacttggttggccctggcctgcatcgctatgctctgtaaccgtgctgagttcaagatgggccaagaatctgtacctgtactaaagagggaatgtaacggtgatgcctcggagtccgctctgctgaagtgcgttgagctgtccatcgggaaggtggtcgagttccgtgccaggcacaagaaggccgtagaaattccattcaactcaaccaacaaataccaggtgtctgtacacgaggtaccagatgatcctcgctacctgctggtgatgaagggagcccccgagcgtatcctggaccgctgctccactatcctgatcaacggcgaggagaagcccctctcggatgagtggagggaggccttcaaccaggcctacctcgagttgggaggcctcggagagcgtgtgcttggattctgtgactactaccttgacgccgctcagtacccccatggctaccccttcgactctgaggaagaaaacttccctctaactggactccgcttcgtcgggcttatgtccatgattgaccccccacgtgctgctgtgcctgatgctgtcggcaaatgccgcagcgcaggcatcaaagttatcatggttaccggcgaccaccccatcactgccaaggctatcgccaaaggtgtcggaattatctccgagggcaacgagaccgtggaagacatcgctgccaggcttaacattcccgtcagcgaagtcaacccaagggatgcgaaggcttgcgttgttcacgggtccgacctacgcgatatgaccccggctcagattgatgatatcctcgccaaccacaccgaaatcgtgtttgcacgtacctcaccccagcagaaactcatcattgtagaaggttgccagcgccaaggagccattgtggctgtcactggtgacggtgtgaacgactcaccggccctcaagaaggctgacatcggtgttgccatgggcatcgctggtagcgacgtgtccaaacaggccgccgacatgattctgctggatgacaacttcgcctctattgttacaggcgtggaggaggggcgtctgatctttgacaacctgaagaaatcgatcgcctacactctgacctcgaacatcccagagatctcccccttcctcctcttcatcctggctgacgtcccacttcctctcggaactatcaccatcctgtgtattgatctcgggaccgaccttgtccctgctatctcccttgcctacgagcaggcggagagcgatattatgaagcgccagccccgtgatcctcttcacgacaagctcgtgaaccacaggctgatcggcatggcttatggccaaattggcatgattcaggccactgccggcttcttcgtttacttcgtcatcttggccgagaatggcttctggccatcccgtcttctcggcatccggatgcgttgggattcgaaagcggtgaacgacgagctcctatggacaggagtggacctacgcccagcg
+>Lf11686_1/1_1.000_3102
+agttcggggaccgcgtcccggccgacgtcagggtcagcccacggctttaaggttgacaactcatcactgaccggagaatctgaacctcagtcaagaactgccgagtttaccaacgagaatccactcgagaccaagaaccttgctttcttctccacgaatgctgttgaaggtacgtgccgtggcgtcgtggtcggcacgggggaccgcaccgttatggggcggattgcaaacctggcgtctggcctcgaagttggtcagactccaatcgcacgagagatcgagcatttcatccacatcatcacgggcgtggccgtgttcctcggtgtcgccttcttcatcgtcgccttcatccttggctactactggctcgatgcagtcatcttcctcattggtatcattgtcgctaatgtccccgaaggtctgcttgctactgtcacagtatgcctgacactgaccgccaagcgcatggcgtccaagaactgtctcgttaagaaccttgaggctgtcgagacgctcggatctacctccaccatctgctccgacaagactggcaccctcacccagaaccgcatgacggtcgcccacatgtggttcgacaaccacatcgtggaagccgacacgaccgaagaccagtccacggaggccgggtgcgactctgcatcccccacatggcagtgtctgatccgcgttgctatgttatgtaaccgtgccgagttcaaaatgggacaagataaattccctgtactgaaaagggaatgtaatggcgatgcttctgaatctgccttgttgaagtgtgccgaactctccattggcaaagtaattgagttccgtgccaaacacaagaaagccattgaaattcccttcaactcaaccaacaaatatcaggtgtctatacatgagctgccagatgacccacgctacctgctcgtaatgaagggcgcccctgagcgcatcctggaccgttgtgccaccatcctcataaatggggaggagaagccgatgagtgaggaatggaaagaggcatttgagcagtcctacatggagctgggcgggctcggcgagcgcgtgctcggattctgcgacttcattctggatgctgaaaagtttccccggggctatccattcgatgctgacgaggagaacttcccactgacagggctgcgctttgtggggctcatgtcgatgatcgaccccccgcgtgctgctgtcccagacgcggtcggcaaatgccgcagcgctggaatcaaagtcatcatggtaactggggaccacccgatcactgccaaggccatcgctaagggtgttggcattatctctgagggcaatgaaactgtagaggatatcgccgcacggctcaacatacccctcagccaggtcaagcccagtgatgcgaaagcttgtgtcattcatggctctgacctccgtgatatgacacctgctgaaatagatgacatgctccgaaaccacactgaaatagtgatggcgcggacctcgccccagcagaaactcatcattgtggagggctgccagcggcagggcgccattgtagctgtcacgggtgacggtgtgaatgattcacccgccctaaagaaagcagatattggagttgccatgggcatcgctggtagcgacgtgtcaaaacaagcggccgacatgatccttcttgatgacaactttgcatctattgtcactggcgtagaagagggacgtctgatcttcgacaacctgaagaaatcgattgcttacactcttacttcaaacatcccggaaatttccccattccttctgttcatcctggctgatgtgccactgcctctgggaaccatcaccatcctgtgtattgatcttgggacggatctcatccccgccatctcactcgcatacgagcaggctgaaagcgacatcatgaagcgccagccccgtgaccctctccacgacaagctcgtcaacaaccggctcatcggcatggcctatgggcagattggcatgattcaggcctctgccggcttctttgtttactttgtgattcttgcagagaatggctttttaccgtgggatctgtttggcatccgtcaaaactgggattccagggctgtaaacgataagctcctatggacaggagtggacgtacgcccagcg
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_623_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_623_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Bj55915_1/1_1.000_1497
+ctggtgcgtctgtcccagcaggagctgatcgactgctcgtggggagaggggaacaatggatgtgatggcggagacgacttcctcgcctaccagtggatttccaaacacggactggcc
+>Lf5592_1/1_1.000_1659
+ctggtacggctgtctcagcaggagctaatcgactgttcgtggggagaggggaacaacgggtgtgacgggggtgatgacttccgcgcctacaagtggattactaagcacggactggcc
+>Ha1592_1/1_1.000_1710
+ctggtgcgcctgtcccagcaggagctggtagactgttcgtggggtatgggtaacaacgggtgtgatggcggagaggacttccgtgcttaccagtggatcaccaagcacgggctggcc
+>Bs34509_1/1_1.000_1086
+ctggtgcgcctgtcacagcaggagctgatcgactgctcgtggggagaagggaacaatgggtgtgacggaggagaggactttcgtgcctaccagtggatcagcaagcacgggctcagc
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_651_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_651_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Bs8968_1/1_1.000_1776
+tgtgaagaggatgcaggaggtctgctgcagactgaatgcctgtcctcctggaagcaggacaacacgacgctggttctcgtccgccgattagacgtcagcaag
+>Ha12591_1/1_1.000_492
+tgtgaggaggatgttggaggtctgatgcaaactgaatgtctatcatcgtggaaacaggataacacgacactggtgctggtgcgccgtctcgactcccacaaa
+>Lf56294_1/1_1.000_1773
+tgtgagcaggatgctggtggtttactgcagactgagtgcctctccacgtggaaacaggacaacaccacactggttcttgtcaggcgcctagacgtcagcaag
+>Bj88046_1/1_1.000_797
+tgtgaggaggatgcgggtggtttgctgcagacagaatgtctctcctcctggaagcaggagaacacgacgctggtgctcgtccgccgtctggacgtcagcaaa
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_660_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_660_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Bj102_1/1_1.000_1566
+gcagatggtatcgtgaagacgatgcgctccaaggcaggccccagctccaaggaacttaaggccgccgacgaggtcgagaagtttatcaatggaaaagatcttgtcatcgttggcttcttcgagtctgatggcagt
+>Lf3141_1/1_1.000_1467
+tcagatgggattgtaaagacgatgcgctccaaggcgggacccacatcgatggaattaaaggctgttgacgatgttgagaaatttattggcggaaaaggtcacgtcgttgttggtttcttcaagtcggaaggcagt
+>Bs17280_1/1_1.000_360
+gcagatggtattgttaagaccatgcgtggcaaggctggcccaagctccaaggaactcaagtctggtgacgaagttgagaagtacatctcaggaaacgacattgtcttcgttggtttcttcgaggctgagggcagt
+>Ha1450_1/1_1.000_1497
+gcagatggtattgttaagaccatgcgtggcaaggctggcccaagctccaaggaactcaagtctggtgacgaagttgagaagtacatctcaggaaacgacattgtcttcgttggtttcttcgaggctgagggcagt
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_696_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_696_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Lf46816_1/1_1.000_3195
+aagctcaacgcgcagctcctaaaccacccgctcacccaccagcacttcgtccccgcactcatgaagttctacgtcgacattgagacgactggtgcgagtagcgaattctatgacaagttcacggtgcgctaccacacgtccattatcctgaagacgctgtgggaaatccctatgcaccaagcgcgcattgtggaggaggccaccggggcagtttgtccgtttcac
+>Bj11264_1/1_1.000_1503
+aagctcaactcacagctcctcaaccacccactgacgcatgagcatttcgtaccagcactcatgaagttctatgtcgacattgagacgacgggtgcaagtagtgagttttacgacaagttcacagtacggtaccacacgtccatcatcctgaagaatatgtgggacatccccatgcaccaggcacgcattgtgaaggaagcgactggggcagtttgtgcgatttac
+>Ha2853_1/1_1.000_2274
+aaactcaacactcagctactcaaccacccgctaacacatcaacactttgtacccgcactcatgaagttctacgtagacatagagacgacgggggcgagcagcgagttctatgacaagttcacggtacgctaccacatcagtatcatcctcaagaccatgtgggacatccccatccaccagggccgcatcgtacaagaagccatcgggccagtttgtgcgtttcac
+>Bs8429_1/1_1.000_306
+aagctcaactcgcagctcctcaaccacccgctcacacatgagcatttcgtaccggcactcatgaagttctacgtcgacattgagacgacgggggctagtagtgagttctacgacaagttcactgtgcgatatcacacgtccatcatcctgaagaatatgtgggacatccccatgcaccaagcacgcattgtgaaggaggcaactggagcagtttgtgcggtttac
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_707_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_707_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Ha58565_1/1_1.000_582
+tgtgtaagatctcagactttggcagctcacgggacatcgcacagagccggcagtacgagagccgcacacagaaccggttaccgatacgttggatggcgcctgagtctctgtatgattgcatgtacagtatcaagtctgacgtctggtcctttggggttctactctgggagatcgtcacac
+>Lf5218_1/1_1.000_3096
+tgtgtaagatctcggactttggcagcgcgcgggacatcgcgcagagccggcagtatgagagccgcacacagaaccgcctgcccatccggtggatggcgcccgagtcgctgtacgactgtatgtacagcgtcaagtccgacgtgtggtccttcggcgtgctgctgtgggaaattgtcacac
+>Bj116010_1/1_1.000_312
+tctgcaagatctctgactttgggagttctcgcgacatcgcacagagccggcagtatgagagtcgaacgcagaaccgccttccaatccggtggatggcgcctgagtcgctgtacgactgcatgtacagcgtcaagtcggacgtctggtccttcggggttctactctgggaggtcgtcacgc
+>Bs1374_1/1_1.000_1335
+tgtgcaagatctccgactttggaagttctcgcgacatcgcacagagccgacagtatgaaagccggacgcagaaccgccttccaatccggtggatggcgcctgagtcactgtatgactgcatgtacagcatcaagtcagacgtctggtcctacggcgttctgctgtgggagatcgtcacgc
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_727_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_727_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Lf1012_1/1_1.000_735
+tatggctgggtctaccgaaatgggcgggacttgtccggcttcatcgacggaactgagaatccggctgacgggagctacgtgattacccaacgatgggttcataacctggcgaagataaagaagacaaaagat
+>Ha1000_1/1_1.000_1200
+tacggctgggtgtaccagaatggtcgtgacttgtcagggttcattgatggtactgagaaccctgccgacggaagttacgtgatcacacaacgatgggttcacaacttggagaagatcaagaagactaaagat
+>Bs2375_1/1_1.000_555
+tacggctgggtgttccgccaggggcgcgacctgtccggcttcatcgacggcaccgagaacccggcggacggaagttacgtgatcacccagcggtgggtccatgaccttgaaaagattaaaatgacaaaagtg
+>Bj12534_1/1_1.000_1269
+tacggctgggtgttccgccagggacgcgacttgtccggcttcatcgacggcaccgagaacccggccgacggaagttacgtgatcacccagcgatgggttcataaccttcccaagatcaagaagaccaaagat
diff -r 000000000000 -r acc3674e515b test-data/sep_nuc/orthogroup_761_with_4_species.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sep_nuc/orthogroup_761_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500
@@ -0,0 +1,8 @@
+>Bs10197_1/1_1.000_1857
+cagatcggcttcacgaccgacccccgctcgtctcggtcgtcgccttactgcacggacgtggcgcgcgttgtcaacgcgcccatcttccacgtcaacgccgacgaccccgaggccgtgatgcacgtgtgcaaggtggctgccgagtaccgctccgagtggggcaaggacgtcgtcatcgacttggtctgttaccggcgtaatggtcacaacgagatagatgagcccatgttcacccagccgctcatgtacaagcgcatccatcagcagccatccatcctcaaactctactccgccaagctcatcgacgagaaagttgtttcgcaggatgagtatgagctcgaggtggcaaagtacgacaaaatctgcgaagacgcctatgtgaacgccaagaaggagacggtcacccgcaatagcctgtggctcgactcgccctggcccggcttcttcgacagt
+>Ha1458_1/1_1.000_3087
+cagattggcttcacgacagacccccgctcatcgcgctcgtcaccctactgcacggacgtggcacgtgtcgtcaatgcacctattttccacgtaaatgccgatgaccccgaggctgtcatgcacgtatgcaaggtggcagccgagtaccgtgctgagtggggcaaagatgtggtcattgacttggtgtgctaccggaagaacggccacaatgagactgacgagcccatgttcacccaaccgctcatgtacaaacgtatccaccagcagccgtccatccttaaacagtactctacgaagctcatcaccgagggcatcgtcagccaggaagagtatgaggttgaagttgcaaagtatgacaagatttgtgaggatgcctaccttaacgcaaagaaggagacggtcacacgtaacagtcagtggctagactctccatggccaggcttctttgatcgt
+>Bj16755_1/1_1.000_2085
+cagattggcttcacgactgaccctcggtcatcacggtcgtcaccgtattgcacagacgtggcacgcgtcgtgaacgcgcccatcttccacgtgaacgcggatgaccccgaagccgtcatgcatgtgtgtaaggtggctgccgagtaccgcgcagaatggggcaaggacgtcgtcattgacttggtatgctaccggcgcaatggtcacaacgagatagatgagcctatgtttacgcagccactcatgtacaagcgcatccaccagcagccgtccatccttaagctctactctgccaagctcattgatgagaaaatagtttcacaagatgaatatgaggttgaagtggcaaagtacgataaaatctgtgaagatgcttacataaatgccaagaaggagactgtcacccgcaacagtctatggctcgactcgccttggccaggattctttgactgt
+>Lf14456_1/1_1.000_2623
+cagatcggcttcacgacagacccacggtcctcccgctcgtccccatactgcacggacgtggcacgtgtcgtgaacgcacctatcttccacgtgaacgcggacgaccccgaggccgtgatgcacgtgtgtaaggtggccgccgagtaccgcgccgagtggggcaaggacgtcgtcatcgacttggtgtgttatcgccgtaacggtcacaacgagatcgacgagccgatgttcacacaaccgctcatgtacaagcgtatccaccaacagccgtccatcctcaaactgtactcggcaaaactcatcgacgagaagatcgtctcacaggaggaatacgagcttgaagtggccaagtacgacaagatctgcgaggacgcgtacctgaacgccaagaaggagacagtgacccgaaacagcctatggctcgactcaccctggcccggcttcttcgatcgt