<commit_before>
juncFilesDir="~/scailscratch/splicing/processed/*.junc"
juncFiles="junc_files.txt"
outPrefix="~/scailscratch/splicing/gtex_final"

#juncFiles="../run/intron_files/*.junc"
#outPrefix="../run/GEUVADIS"

mkdir outPrefix

maxIntronLen=100000
minReadsClu=50

echo "Checking junction files..."
#eval "ls $juncFilesDir > $juncFiles" 
#eval "python check_files.py $outPrefix\_chrom $juncFiles"

echo "Sorting junction files..."
#eval "python sort_junc.py $outPrefix $juncFiles"

echo "Pooling individuals to identify intron clusters..."
#eval "python get_intron_splicing_pooled.py $outPrefix $maxIntronLen $juncFiles"

echo "Spliting intron clusters..."
#eval "python refine_intron_splicing.py $outPrefix $minReadsClu"

echo "Getting per individuals counts..."
#eval "python merge_junc.py $outPrefix"

echo "Assigning genes to clusters..."
eval "python get_cluster_gene.py $outPrefix\_perind.counts.gz"
<commit_msg>get numerators in RData format<commit_after>
juncFilesDir="~/scailscratch/splicing/processed/*.junc"
juncFiles="junc_files.txt"
outPrefix="~/scailscratch/splicing/gtex_final"

#juncFiles="../run/intron_files/*.junc"
#outPrefix="../run/GEUVADIS"

mkdir outPrefix

maxIntronLen=100000
minReadsClu=50

echo "Checking junction files..."
#eval "ls $juncFilesDir > $juncFiles" 
#eval "python check_files.py $outPrefix\_chrom $juncFiles"

echo "Sorting junction files..."
#eval "python sort_junc.py $outPrefix $juncFiles"

echo "Pooling individuals to identify intron clusters..."
#eval "python get_intron_splicing_pooled.py $outPrefix $maxIntronLen $juncFiles"

echo "Spliting intron clusters..."
#eval "python refine_intron_splicing.py $outPrefix $minReadsClu"

echo "Getting per individuals counts..."
#eval "python merge_junc.py $outPrefix"

echo "Assigning genes to clusters..."
eval "python get_cluster_gene.py $outPrefix\_perind.counts.gz"

echo "Creating $outPrefix\_perind_numers.counts.gz"
eval "python get_numers.py $outPrefix\_perind.counts.gz | gzip > $outPrefix\_perind_numers.counts.gz"

echo "Creating $outPrefix\_perind_numers.RData"
eval "Rscript convert_to_RData.R $outPrefix\_perind_numers.counts.gz $outPrefix\_perind_numers.RData"


{'fraction_non_alphanumeric': 0.12534562211981568, 'fraction_numerical': 0.007373271889400922, 'mean_word_length': 6.118032786885246, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 6, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4978521', 'n_tokens_mistral': 810, 'n_tokens_neox': 766, 'n_words': 165}