<commit_before>biopython>=1.61
boto>=2.34.0
Cython>=0.19
ipython>=2.0.0
ipython-cluster-helper>=0.4.3
Logbook>=0.6.0
lxml>=3.3.5
msgpack-python>=0.4.0
nose>=1.3.0
pandas>=0.14.1
progressbar>=2.3.0
pybedtools>=0.6.8
pysam>=0.8.2.1
pyzmq>=2.2.0
PyYAML>=3.10
toolz>=0.7.1
tornado>=3.1.0
# soft dependencies -- not required for bcbio-nextgen-vm
arrow>=0.4.4
arvados-python-client>=0.1.1405019228.4a7ca04
awscli>=1.7.14
bioblend>=0.4.3
chanjo>=2.0.2
click>=3.3
cnvkit>=0.3.4
cutadapt==1.4.2
cyvcf>=0.1.11
fabric>=1.7.0
gffutils>=0.8.4rc1
HTSeq >= 0.5.4p5
joblib>=0.8.4
openpyxl>=1.6.1,<2.0.0
path.py>=7.0
psutil>=1.2.0
pythonpy>=0.3.6
python-dateutil>=2.1
PyVCF>=0.6.7
sh>=1.07
tabulate>=0.7.3
scikit-learn>=0.15.2
seaborn>=0.5.0
bcbio-nextgen==0.8.9<commit_msg>add fadapa to requirements<commit_after>biopython>=1.61
boto>=2.34.0
Cython>=0.19
ipython>=2.0.0
ipython-cluster-helper>=0.4.3
Logbook>=0.6.0
lxml>=3.3.5
msgpack-python>=0.4.0
nose>=1.3.0
pandas>=0.14.1
progressbar>=2.3.0
pybedtools>=0.6.8
pysam>=0.8.2.1
pyzmq>=2.2.0
PyYAML>=3.10
toolz>=0.7.1
tornado>=3.1.0
# soft dependencies -- not required for bcbio-nextgen-vm
arrow>=0.4.4
arvados-python-client>=0.1.1405019228.4a7ca04
awscli>=1.7.14
bioblend>=0.4.3
chanjo>=2.0.2
click>=3.3
cnvkit>=0.3.4
cutadapt==1.4.2
cyvcf>=0.1.11
fadapa>=0.3.1
fabric>=1.7.0
gffutils>=0.8.4rc1
HTSeq >= 0.5.4p5
joblib>=0.8.4
openpyxl>=1.6.1,<2.0.0
path.py>=7.0
psutil>=1.2.0
pythonpy>=0.3.6
python-dateutil>=2.1
PyVCF>=0.6.7
sh>=1.07
tabulate>=0.7.3
scikit-learn>=0.15.2
seaborn>=0.5.0
bcbio-nextgen==0.8.9
{'fraction_non_alphanumeric': 0.23621025308241403, 'fraction_numerical': 0.18883841661258924, 'mean_word_length': 4.298969072164948, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 82, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 2, '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': '6839592', 'n_tokens_mistral': 926, 'n_tokens_neox': 879, 'n_words': 99}