--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/S03_remove_site_with_not_enough_species_represented.py	Fri Feb 01 10:26:37 2019 -0500
@@ -0,0 +1,191 @@
+#!/usr/bin/env python
+# coding: utf8
+## Author: Eric Fontanillas
+## Modification: 03/09/14 by Julie BAFFARD
+## Last modification : 05/03/18 by Victor Mataigne
+
+## Description : find and remove indels
+
+####################
+###### DEF 2 #######
+####################
+def remove_position_with_too_much_missing_data(bash_aa, bash_nuc, MIN_SPECIES_NB):
+
+    ## 1 ## Get alignment length
+    fasta_name0 = bash_aa.keys()[0]
+    ln_aa = len(bash_aa[fasta_name0])
+
+    ln_nuc = len(bash_nuc[fasta_name0])
+
+
+    ## 2 ## Get positions keeped in aa alignment
+    LIST_POSITION_KEEPED_aa = []
+    i=0
+    while i < ln_aa:
+        site = []
+        for fasta_name in bash_aa.keys():
+            pos = bash_aa[fasta_name][i]
+
+            if pos != "-" and pos != "?" and pos != "X":
+                site.append(pos)
+        if len(site) >= MIN_SPECIES_NB:
+            LIST_POSITION_KEEPED_aa.append(i)
+        i = i+1
+
+    ## 3 ## Get positions keeped in nuc alignment
+    LIST_POSITION_KEEPED_nuc = []
+    for position in LIST_POSITION_KEEPED_aa:
+        position1 = position*3
+        position2 = position*3 + 1
+        position3 = position*3 + 2
+        LIST_POSITION_KEEPED_nuc.append(position1)
+        LIST_POSITION_KEEPED_nuc.append(position2)
+        LIST_POSITION_KEEPED_nuc.append(position3)
+
+    ## 4 ## Create entries for "filtered_bash" for aa & nuc
+    filtered_bash_aa = {}
+    filtered_bash_nuc = {}
+    for fasta_name in bash_aa.keys():
+        filtered_bash_aa[fasta_name] = ""
+    for fasta_name in bash_nuc.keys():
+        filtered_bash_nuc[fasta_name] = ""
+
+    ## 5 ## Write "filtered_bash" for aa
+    j=0
+    while j < ln_aa:
+        for fasta_name in bash_aa.keys():
+            seq=filtered_bash_aa[fasta_name]
+            pos=bash_aa[fasta_name][j]
+
+            if j in LIST_POSITION_KEEPED_aa:
+                seq = seq + pos
+                filtered_bash_aa[fasta_name] = seq
+        j = j + 1
+
+    ## 6 ## Remove empty sequence
+    for name in filtered_bash_aa.keys():
+        seq = filtered_bash_aa[name]
+        if seq == '':
+            del filtered_bash_aa[name]
+
+
+    ## 7 ## Write "filtered_bash" for nuc
+    j=0
+    while j < ln_nuc:
+        for fasta_name in bash_nuc.keys():
+            seq=filtered_bash_nuc[fasta_name]
+            #print seq
+            pos=bash_nuc[fasta_name][j]
+
+            if j in LIST_POSITION_KEEPED_nuc:
+                seq = seq + pos
+                filtered_bash_nuc[fasta_name] = seq
+        j = j + 1
+
+    ## 8 ## Remove empty sequence
+    for name in filtered_bash_nuc.keys():
+        seq = filtered_bash_nuc[name]
+        if seq == '':
+            del filtered_bash_nuc[name]
+
+    return(filtered_bash_aa, filtered_bash_nuc)
+####################################
+
+
+#######################
+##### RUN RUN RUN #####
+#######################
+import string, os, time, re, sys
+from dico import dico
+
+### 0 ### PARAMETERS
+MIN_SPECIES_NB = int(sys.argv[1])
+MIN_LENGTH_FINAL_ALIGNMENT_NUC = int(sys.argv[2])
+n0 = 0
+bad = 0
+good = 0
+list_new_file = []
+dicoco = {}
+list_file = []
+name_elems = ["orthogroup", "0", "with", "0", "species.fasta"]
+
+### 1 ### IN
+path_IN1 = "./07_CDS_aa/"
+L_IN1 = os.listdir(path_IN1)
+lenght = len(L_IN1)
+path_IN2 = "./07_CDS_nuc/"
+L_IN2 = os.listdir(path_IN2)
+
+## 2 ## OUT
+os.mkdir("08_CDS_aa_MINIMUM_MISSING_SEQUENCES")
+path_OUT1 = "08_CDS_aa_MINIMUM_MISSING_SEQUENCES"
+os.mkdir("08_CDS_nuc_MINIMUM_MISSING_SEQUENCES")
+path_OUT2 = "08_CDS_nuc_MINIMUM_MISSING_SEQUENCES"
+
+
+for file in L_IN1:
+    file_INaa = "%s/%s" %(path_IN1, file)
+    file_INnuc = "%s/%s" %(path_IN2, file)
+
+    dico_aa = dico(file_INaa)   ### DEF 1 ###
+    dico_nuc = dico(file_INnuc)   ### DEF 1 ###
+
+    if len(dico_aa) < MIN_SPECIES_NB :
+        list_file.append(file)
+
+if list_file == lenght :
+    MIN_SPECIES_NB == MIN_SPECIES_NB - 1
+
+
+for file in L_IN1 :
+    file_INaa = "%s/%s" %(path_IN1, file)
+    file_INnuc = "%s/%s" %(path_IN2, file)
+
+    dico_aa = dico(file_INaa)   ### DEF 1 ###
+    dico_nuc = dico(file_INnuc)   ### DEF 1 ###
+
+    ## 4.1 ## REMOVE POSITIONS WITH TOO MUCH MISSING DATA (i.e. not enough taxa represented at each position in the alignment)
+    filtered_bash_aa, filtered_bash_nuc = remove_position_with_too_much_missing_data(dico_aa, dico_nuc, MIN_SPECIES_NB)   ### DEF 2 ###
+
+    k = filtered_bash_nuc.keys()
+    new_leng_nuc = 0
+    if k != []:
+        k0 = k[0]
+        seq0 = filtered_bash_nuc[k0]
+        new_leng_nuc = len(seq0)
+
+    ## 4.3 ## Change file name for output, depending the number of species remaining in the alignment 
+    n0+=1
+    #name_elems[1] = str(n0)
+    name_elems[1] = file.split('_')[1]
+    name_elems[3] =  str(len(filtered_bash_aa.keys()))
+    new_name = "_".join(name_elems)
+
+    ## 4.5 ## Write filtered alignment in OUTPUTs
+    ## aa
+    if filtered_bash_aa != {} and new_leng_nuc >= MIN_LENGTH_FINAL_ALIGNMENT_NUC:
+        OUTaa=open("%s/%s" %(path_OUT1, new_name), "w")
+        for fasta_name in filtered_bash_aa.keys():
+            seq_aa = filtered_bash_aa[fasta_name]
+            OUTaa.write("%s\n" %fasta_name)
+            OUTaa.write("%s\n" %seq_aa)
+        OUTaa.close()
+    # nuc
+    if filtered_bash_nuc != {} and new_leng_nuc >= MIN_LENGTH_FINAL_ALIGNMENT_NUC:
+        good+=1
+        OUTnuc=open("%s/%s" %(path_OUT2, new_name), "w")
+        for fasta_name in filtered_bash_nuc.keys():
+            seq_nuc = filtered_bash_nuc[fasta_name]
+            OUTnuc.write("%s\n" %fasta_name)
+            OUTnuc.write("%s\n" %seq_nuc)
+        OUTnuc.close()
+    else:
+        bad+=1
+
+
+## 5 ## Print
+print "*************** 2nd Filter : removal of the indel ***************"
+print "\nTotal number of locus recorded  = %d" %n0
+print "\tTotal number of locus with no indels (SAVED) = %d" %good
+print "\tTotal number of locus, when removing indel, wich are empty (EXCLUDED) = %d" %bad
+print ""
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