# ========================================= #
# 			Get OTU Main Sequence			#
# ========================================= #

This program treats files generated by mothur (http://www.mothur.org/wiki/454_SOP or http://www.mothur.org/wiki/MiSeq_SOP).
The aim of this programm is to return a fasta file listing the highly representative sequence of a given OTU for each samples.

---------------------------
Included Files and Folders
---------------------------

- get_otuMainSeq.pl: The program to launch
- lib: The folder containg the homemade libraries
	--> File: The folder containing the libraries to handle files
		--> Fasta.pm: The librarie to handle fasta files

---------------------------
Command Line Arguments
---------------------------

Example: ./get_otuMainSeq.pl input.list input.fasta input.names input.groups label otu

Input: 
- input.list: List file generated by mothur containing the list sequences for each label
	(file obtain after cluster.split)
- input.fasta: Fasta file generated by mothur
- input.names: Names file generated by mothur
- input.groups: Groups File generated by mothur
- label: The chosen label (distance cutoff used to form OTU)
- otu: The otu selected for analysis 
	!!! Do not write the 0 at the begining of otu number (for otu "00014" enter "14")
 
---------------------------
Output
--------------------------- 

- A fasta file with, for each sample, the higly representative sequence for the selected OTU
Each sequences are named according to this nomenclature:
>[sample name]_[Highly representative sequence name]_MO=[XXX]_S=[YYY]_US=[ZZZ]

Here is an example (see the test file below)
- BB10189bis: 
	The name of the sample
- M00842_94_000000000-AACJM_1_1103_9388_15633: 
	The ID of the unique sequence find as the highly representative one for the sample BB10189bis
- MS (17): 
	The number of copies of the Main Sequence of the OTU into the ongoing sample
- S (22): 
	The number of Sequences associated to the ongoing sample (all sequences regardless of the OTU)
- US (5):
	The number of Unique Sequences associated to the OTU into the ongoing sample


---
mainsequence_otu[XXX].fasta

>BB10189bis_M00842_94_000000000-AACJM_1_1103_9388_15633_MO=17_S=22_US=5
GAC--GG-AG-GGG--GCT-A-G--C-G--T-T--GT-T-CGG-AA--TT-A-C-T--GG
-GC---GT--A---AA-GG-GC-GC---G-TA-G-G-C-G--G--T-TT-A-A-T-----
-AA----G-T-T-A--G-G-A--G--TG--A-AA-TC--C-C-AG-G-G---CT-T-AA-
---C-C-C-T-G-G-A--A-C--T-G--C-T--T--C--T--AA-A-A--C-T--G-T--
TG--G-A-C-T-A-G-A-G-T-G---T-GG---TA-G-G-----G-G-A-T---GA-T--
>BB10026bis_M00842_94_000000000-AACJM_1_1103_9388_15633_MO=90_S=96_US=5
GAC--GG-AG-GGG--GCT-A-G--C-G--T-T--GT-T-CGG-AA--TT-A-C-T--GG
-GC---GT--A---AA-GG-GC-GC---G-TA-G-G-C-G--G--T-TT-A-A-T-----
-AA----G-T-T-A--G-G-A--G--TG--A-AA-TC--C-C-AG-G-G---CT-T-AA-
---C-C-C-T-G-G-A--A-C--T-G--C-T--T--C--T--AA-A-A--C-T--G-T--
TG--G-A-C-T-A-G-A-G-T-G---T-GG---TA-G-G-----G-G-A-T---GA-T--
>BB10189_M00842_94_000000000-AACJM_1_1103_9388_15633_MO=7_S=7_US=1
GAC--GG-AG-GGG--GCT-A-G--C-G--T-T--GT-T-CGG-AA--TT-A-C-T--GG
-GC---GT--A---AA-GG-GC-GC---G-TA-G-G-C-G--G--T-TT-A-A-T-----
-AA----G-T-T-A--G-G-A--G--TG--A-AA-TC--C-C-AG-G-G---CT-T-AA-
---C-C-C-T-G-G-A--A-C--T-G--C-T--T--C--T--AA-A-A--C-T--G-T--
TG--G-A-C-T-A-G-A-G-T-G---T-GG---TA-G-G-----G-G-A-T---GA-T--
---