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1 #!/usr/bin/env python3
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2 '''
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3 wrapper for last program
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4 run last with BlastTab+ output and return mgblast like formated output
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5 last BlastTab+ output column order:
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6 1 query name
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7 2 reference name
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8 3 percent identity
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9 4 alignment length
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10 5 mismatches
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11 6 gap opens
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12 7 query start
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13 8 query end
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14 9 reference start
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15 10 reference end
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16 11 e-value
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17 12 bitscore
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18 13 length of query
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19 14 length of reference sequence
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20 (accordin lastal manual - more column may be added in future)
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21
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22 Needed mgblast order:
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23
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24 qseqid 1 -> 1
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25 qlen 2 -> 13
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26 qstart 3 -> 7
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27 qend 4 -> 8
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28 sseqid 5 -> 2
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29 slen 6 -> 14
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30 sstart 7 -> 9
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31 send 8 -> 10
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32 pident 9 -> 3
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33 bitscore 10-> 12
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34 evalue 11-> 11
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35 sstrand 12-> must be evaluated!
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36
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37 '''
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38 import subprocess
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39 import sys
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40 last_command = " ".join(["lastal"] + sys.argv[1:])
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41 p = subprocess.Popen(last_command, shell=True, stdout=subprocess.PIPE)
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42 for j in p.stdout:
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43 line = j.decode()
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44 if line[0] != "#":
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45 items = line.split("\t")
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46 strand = "+" if int(items[6]) < int(items[7]) else "-"
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47 out = "\t".join([items[i - 1]
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48 for i in [1, 13, 7, 8, 2, 14, 9, 10, 3, 12, 11]
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49 ]) + "\t" + strand + "\n"
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50 print(out, end="")
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