<commit_before>#!/bin/bash
set -ex

python=/gsc/software/linux-x86_64/python-2.7.2/bin/python
#python=/gsc/software/linux-x86_64-centos6/python-2.7.8/bin/python
#cooccurrenceMajigger=/projects/jlever/megaTextProject/nounphrasePipeline/cooccurrenceMajigger/cooccurrenceMajigger_articleCode.py

HERE=`pwd`

cooccurrenceMajigger=$HERE/../text_extraction/cooccurrenceMajigger.py
wordlist=$HERE/umlsWordlist.Final.pickle

cooccurrenceMajigger=`readlink -f $cooccurrenceMajigger`
wordlist=`readlink -f $wordlist`

# Set the directories containing the MEDLINE files and the article lists
filteredMedlineDir=/projects/bioracle/ncbiData/2017/filteredMedline/
articleListDir=/projects/bioracle/ncbiData/2017/articleLists

mkdir -p $HERE/mined/abstracts
mkdir -p $HERE/mined/articles
mkdir -p $HERE/logs/abstracts
mkdir -p $HERE/logs/articles<commit_msg>Command listing takes directory as parameter<commit_after>#!/bin/bash
set -ex

medlineAndPMCDir=$1
medlineAndPMCDir=`readlink -f $medlineAndPMCDir`

python=/gsc/software/linux-x86_64/python-2.7.2/bin/python
#python=/gsc/software/linux-x86_64-centos6/python-2.7.8/bin/python
#cooccurrenceMajigger=/projects/jlever/megaTextProject/nounphrasePipeline/cooccurrenceMajigger/cooccurrenceMajigger_articleCode.py

HERE=`pwd`

cooccurrenceMajigger=$HERE/../text_extraction/cooccurrenceMajigger.py
wordlist=$HERE/umlsWordlist.Final.pickle

cooccurrenceMajigger=`readlink -f $cooccurrenceMajigger`
wordlist=`readlink -f $wordlist`

# Set the directories containing the MEDLINE files and the article lists
filteredMedlineDir=$medlineAndPMCDir/filteredMedline/
articleListDir=$medlineAndPMCDir/articleLists

mkdir -p $HERE/mined/abstracts
mkdir -p $HERE/mined/articles
mkdir -p $HERE/logs/abstracts
mkdir -p $HERE/logs/articles
{'fraction_non_alphanumeric': 0.1109846328969835, 'fraction_numerical': 0.0221969265793967, 'mean_word_length': 6.778761061946903, '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': '1997221', 'n_tokens_mistral': 699, 'n_tokens_neox': 633, 'n_words': 88}