#traitement gp pour amaizing
#chargmeent des fichiers et parsing des xml
/gorgone/pappso/moulon/users/Olivier/gp-read-olivier.py *.xml -e 0.01 |bzip2 -z -c >amaizing_total.bz2
#analyse du fdr 
bzip2 -d -c amaizing_total.bz2 | gp-fdr-peptide.py 
#Flag of decoy is :'reversed'
#Normal Peptide  20306817
#Decoy Peptide   6725
#FDR %   0.0331169577192
bzip2 -d -c amaizing_total.bz2 | gp-grouping --peprepro 10 --pepbyprot 2 --fasta /gorgone/pappso/moulon/database/contaminants_standarts.fasta | bzip2 -c -z > amaizing_total_group.bz2
#New peprepro : 10
#New pepbyprot : 2
#Set Fasta file filtering : /gorgone/pappso/moulon/database/contaminants_standarts.fasta
#Finish reading parameter
#Begin reading data
#Finish loading data
#Begin Peptide Reproductibility filter : 31783
#End Peptide Reproductibility filter : 17070
#Begin Minimun Peptide By Prot filter : 13625
#End Minimun Peptide By Prot filter : 5798
#Remove protein contaminants from fasta file : 5778
#Begin Grouping
#End subgroup creation : 2220
#Search non informative subgroup
#Index and Order group result
#End group creation : 1593
#Begin Export
#Finish Export
bzip2 -d -c amaizing_total.bz2 | gp-grouping --peprepro 2 --pepbyprot 2 --fasta /gorgone/pappso/moulon/database/contaminants_standarts.fasta | bzip2 -c -z > amaizing_total_group.bz2
#New peprepro : 2
#New pepbyprot : 2
#Set Fasta file filtering : /gorgone/pappso/moulon/database/contaminants_standarts.fasta
#Finish reading parameter
#Begin reading data
#Finish loading data
#Begin Peptide Reproductibility filter : 31783
#End Peptide Reproductibility filter : 25523
#Begin Minimun Peptide By Prot filter : 13625
#End Minimun Peptide By Prot filter : 7079
#Remove protein contaminants from fasta file : 7043
#Begin Grouping
#End subgroup creation : 2832
#Search non informative subgroup
#Index and Order group result
#End group creation : 1962
#Begin Export
#Finish Export
cat amaizing_total_group.bz2 | bzip2 -c -d | gp_output_protien-list.py > list_total_prot.tsv
bzcat amaizing_total_group.bz2 | gp-output-masschroqml.py > amaizing_total.masschroqML
