In [1]:

    

ls


    

    




0yeast_gene_list/       12homology-PPI/        2tf-binding/          5essentiality/         8nature-compare-sequence/        Batch_feature_summary_ExtractWrapper.pl  train-set/
10mips-phenotype/       13domain-interaction/  3gene-ontology/       6HighExp-PPI/          9mips-pclass/                    Investigating qi_evaluation_2006.ipynb
11sequence-similarity/  1gene-expression/      4protein-expression/  7genetic-interaction/  Batch_feature_ExtractWrapper.pl  README

In [2]:

    

cat README


    

In [8]:

    

%%bash
head -n 40 ./Batch_feature_ExtractWrapper.pl


    

    




######################################################################3
#
# copyright @ Yanjun Qi , qyj@cs.cmu.edu
# Please cite: 
# Y. Qi, Z. Bar-Joseph, J. Klein-Seetharaman, "Evaluation of different biological data and computational classification methods for use in protein interaction prediction", PROTEINS: Structure, Function, and Bioinformatics. 63(3):490-500. 2006
# Y. Qi, J. Klein-Seetharaman, Z. Bar-Joseph, "A mixture of feature experts approach for protein-protein interaction prediction", BMC Bioinformatics 8 (S10):S6, 2007 
# Y. Qi, J. Klein-Seetharaman, Z. Bar-Joseph, �Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple source�, Pacific Symposium on Biocomputing 10: (PSB 2005) Jan. 2005. 
# 
######################################################################3


# This program is a yeast PPI feature extraction wrapper 
# perl command inputPairlist


use strict; 
die "Usage: command inputPairFile \n" if scalar(@ARGV) < 1;
my ($inputPair ) = @ARGV;


print "\n--------------------------- 1gene-expression ----------------------------------------\n"; 

# -------------------   1gene-expression   ------------------------------

my $cmdPre = "perl ./1gene-expression/get_gene_expression.pl  "; 
my $cmdPro = "./1gene-expression/YeastGeneListOrfGeneName-106_pval_v9.0.txt ./1gene-expression/all_expression_fixed_s4_csv.txt  ./1gene-expression/expressionYanjunSplit.txt 0.6 "; 

my $cmd = $cmdPre." ".$inputPair." ".$cmdPro." ".$inputPair.".genexp" ; 
print "$cmd\n"; 
system($cmd); 



print "\n-------------------------------------------------------------------\n"; 

# -------------------   2tf-group-binding  ------------------------------

# perl -d get_tfGroupBinding.pl ./lists/sciencesubset.txt pvalbygene_nature04.txt 204_pvalbygene_nature04_TFs.groupIndex 0.05 ./lists/sciencesubset.tfgroup

my $cmdPre = "perl ./2tf-binding/get_tfGroupBinding.pl  ";