<commit_before>#! /bin/bash

set -o errexit

redirectedTempFolder=tmp
cellLine=$redirectedTempFolder/Cell_Lines_Details.xlsx
doseResponse=$redirectedTempFolder/v17_fitted_dose_response.xlsx
screenedComponents=$redirectedTempFolder/Screened_Compounds.xlsx
RACS=$redirectedTempFolder/RACS_in_cell_lines.xlsx
variants=$redirectedTempFolder/WES_variants.xlsx
expression=$redirectedTempFolder/sanger1018_brainarray_ensemblgene_rma.txt.gz
expressiontmp=$redirectedTempFolder/expressiontmp.tsv.gz
dataOutFile=Gene_Expression.tsv
metadataOutFile=metadata.tsv

python3 parse.py $cellLine $doseResponse $screenedComponents $RACS $variants $expression $metadataOutFile $expressiontmp $dataOutFile 

python ../Helper/convertTallFormatToWide2.py $metadataOutFile Annotations.tsv
rm -f $metadataOutFile
<commit_msg>Change expressiontmp file to normal text file in GDSC_Expression<commit_after>#! /bin/bash

set -o errexit

redirectedTempFolder=tmp
cellLine=$redirectedTempFolder/Cell_Lines_Details.xlsx
doseResponse=$redirectedTempFolder/v17_fitted_dose_response.xlsx
screenedComponents=$redirectedTempFolder/Screened_Compounds.xlsx
RACS=$redirectedTempFolder/RACS_in_cell_lines.xlsx
variants=$redirectedTempFolder/WES_variants.xlsx
expression=$redirectedTempFolder/sanger1018_brainarray_ensemblgene_rma.txt.gz
expressiontmp=$redirectedTempFolder/expressiontmp.tsv
dataOutFile=Gene_Expression.tsv
metadataOutFile=metadata.tsv

python3 parse.py $cellLine $doseResponse $screenedComponents $RACS $variants $expression $metadataOutFile $expressiontmp $dataOutFile 

python ../Helper/convertTallFormatToWide2.py $metadataOutFile Annotations.tsv
rm -f $metadataOutFile

{'fraction_non_alphanumeric': 0.07454545454545454, 'fraction_numerical': 0.009696969696969697, 'mean_word_length': 10.626760563380282, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, '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': '7624866', 'n_tokens_mistral': 563, 'n_tokens_neox': 532, 'n_words': 74}