<commit_before>#!/usr/bin/env python
import subprocess,glob, os

run_pipeline = []
for flu in ["H3N2", "H1N1pdm", "H1N1", "Vic", "Yam"]:
	auspice_files = glob.glob('../auspice/data/'+flu+"*json")
	input_files = glob.glob('data/'+flu+'*fasta')
	if len(input_files):
		if len(auspice_files)==0 or min([os.path.getmtime(fname) for fname in auspice_files])<max([os.path.getmtime(fname) for fname in input_files]):
			run_pipeline.append(flu)

#python_binary = '/ebio/ag-neher/share/programs/bin/python'
python_binary = 'python'

if 'H3N2' in run_pipeline:
	call = map(str, [python_binary, 'src/H3N2_process.py', '-v', 50, '-y', 3, '--skip', 'genotype_frequencies', '-r', 1.0, '--prefix', 'data/H3N2_'])
	print call
	subprocess.call(call)
if 'H1N1' in run_pipeline:
	call = map(str, [python_binary, 'src/H1N1historical_process.py', '-v', 20, '--interval', 1990, 2010, '--skip', 'genotype_frequencies', '-r', 1.0, '--prefix', 'data/H1N1_'])
	print call
	subprocess.call(call)
if 'H1N1pdm' in run_pipeline:
	call = map(str, [python_binary, 'src/H1N1pdm_process.py', '-v', 30, '-y', 6, '--skip', 'genotype_frequencies', '-r', 1.0, '--prefix', 'data/H1N1pdm_'])
	print call
	subprocess.call(call)
if 'Vic' in run_pipeline:
	call = map(str, [python_binary, 'src/Vic_process.py', '-v', 30, '-y', 6, '--skip', 'genotype_frequencies', '-r', 1.0, '--prefix', 'data/Vic_'])
	print call
	subprocess.call(call)
if 'Yam' in run_pipeline:
	call = map(str, [python_binary, 'src/Vic_process.py', '-v', 30, '-y', 6, '--skip', 'genotype_frequencies', '-r', 1.0, '--prefix', 'data/Yam_'])
	print call
	subprocess.call(call)<commit_msg>silly error in make_all...<commit_after>#!/usr/bin/env python
import subprocess,glob, os

run_pipeline = []
for flu in ["H3N2", "H1N1pdm", "H1N1", "Vic", "Yam"]:
	auspice_files = glob.glob('../auspice/data/'+flu+"*json")
	input_files = glob.glob('data/'+flu+'*fasta')
	if len(input_files):
		if len(auspice_files)==0 or min([os.path.getmtime(fname) for fname in auspice_files])<max([os.path.getmtime(fname) for fname in input_files]):
			run_pipeline.append(flu)

#python_binary = '/ebio/ag-neher/share/programs/bin/python'
python_binary = 'python'

if 'H3N2' in run_pipeline:
	call = map(str, [python_binary, 'src/H3N2_process.py', '-v', 50, '-y', 3, '--skip', 'genotype_frequencies', '-r', 1.0, '--prefix', 'data/H3N2_'])
	print call
	subprocess.call(call)
if 'H1N1' in run_pipeline:
	call = map(str, [python_binary, 'src/H1N1historical_process.py', '-v', 20, '--interval', 1990, 2010, '--skip', 'genotype_frequencies', '-r', 1.0, '--prefix', 'data/H1N1_'])
	print call
	subprocess.call(call)
if 'H1N1pdm' in run_pipeline:
	call = map(str, [python_binary, 'src/H1N1pdm_process.py', '-v', 30, '-y', 6, '--skip', 'genotype_frequencies', '-r', 1.0, '--prefix', 'data/H1N1pdm_'])
	print call
	subprocess.call(call)
if 'Vic' in run_pipeline:
	call = map(str, [python_binary, 'src/Vic_process.py', '-v', 30, '-y', 6, '--skip', 'genotype_frequencies', '-r', 1.0, '--prefix', 'data/Vic_'])
	print call
	subprocess.call(call)
if 'Yam' in run_pipeline:
	call = map(str, [python_binary, 'src/Yam_process.py', '-v', 30, '-y', 6, '--skip', 'genotype_frequencies', '-r', 1.0, '--prefix', 'data/Yam_'])
	print call
	subprocess.call(call)
{'fraction_non_alphanumeric': 0.21854714064914993, 'fraction_numerical': 0.03523956723338485, 'mean_word_length': 5.071294559099437, 'pattern_counts': {'":': 0, '<': 5, '<?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': '6161224', 'n_tokens_mistral': 1442, 'n_tokens_neox': 1390, 'n_words': 288}