Pipelines - Solutions
Solution to challenge #1
import sys
print sys.argv
filename = sys.argv[1]
gbk = open(filename)
for line in gbk:
if line[0:5] == 'LOCUS':
print line
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Solution to challenge #2
import subprocess
seqs = ['P00519', 'P05480', 'P12931']
for seq in seqs:
command_line = ['blastp','-query',
seq + '.fasta','-out',
seq + '_blout', '-outfmt',
'6','-db','nr.00']
subprocess.call(command_line)
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Solution to challenge #3
seqs = ['P00519', 'P05480', 'P12931']
out = open('blast_best_scores', 'w')
for seq in seqs:
first_line = open(seq + '_blout').readline()
column = first_line.split()
out.write(column[0] + '\t' + column[2] + '\n')
out.close()
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