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import os.path
import sys
instances = [os.path.basename(s[:len(s)-4]) for s in os.listdir('mfa') if s.endswith('.mfa')]
rule all:
input: ['fisher/%s.pairs.gz'%s for s in instances] + ['ph/%s.ph'%s for s in instances]
rule extract_mismatch_counts:
input: 'mfa/{instance}.mfa'
output: 'fisher/{instance}.pairs.gz'
message: 'Extracting number mismatches for each pair of sequences from {input}'
shell: 'sleep 2; touch {output}'
rule create_tree:
input: 'mfa/{instance}.mfa'
output: 'ph/{instance}.ph', 'ph/{instance}.ph.log'
message: 'Running CLUSTALW to compute NJ tree from {input}'
shell: "sleep 2; touch {output[0]}; touch {output[1]}"
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