From b200eb141f631404563aeacb1453cd3b59d3853e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?=
 <lecorguille@users.noreply.github.com>
Date: Thu, 22 Oct 2020 14:59:38 +0200
Subject: [PATCH] Fix naming issue in CDS Search

https://github.com/abims-sbr/adaptsearch/issues/50
---
 .../S03_remove_site_with_not_enough_species_represented.py    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/05_CDS_search/S03_remove_site_with_not_enough_species_represented.py b/scripts/05_CDS_search/S03_remove_site_with_not_enough_species_represented.py
index 62f6b56..4594e5f 100644
--- a/scripts/05_CDS_search/S03_remove_site_with_not_enough_species_represented.py
+++ b/scripts/05_CDS_search/S03_remove_site_with_not_enough_species_represented.py
@@ -176,7 +176,7 @@ def remove_position_with_too_much_missing_data(bash_aa, bash_nuc, MIN_SPECIES_NB
         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" %fasta_name[0:3])
             OUTnuc.write("%s\n" %seq_nuc)
         OUTnuc.close()
     else:
@@ -188,4 +188,4 @@ def remove_position_with_too_much_missing_data(bash_aa, bash_nuc, MIN_SPECIES_NB
 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 ""
\ No newline at end of file
+print ""