annotate lib/block.py @ 0:757f2a1f8732
Initial commit with the lib modules
| author |
Boris Burkov <BurkovBA@gmail.com> |
| date |
Fri, 21 May 2010 20:30:40 +0400 |
| parents |
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| children |
bbf3a797cc67 |
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line source |
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1 #!usr/bin/python |
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2 |
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3 import sys |
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4 |
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5 import configure |
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6 import project |
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7 import sequence |
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8 import monomer |
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9 import rooted_tree |
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10 from Lgamma import Lgamma |
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11 |
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12 class Block(object): |
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13 """ |
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14 Mandatory data: |
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15 * self.project -- project object, which the block belongs to |
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16 * self.sequences - list of sequence objects, that contain monomers |
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17 and/or gaps, that constitute the block |
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18 * self.positions -- positions of the project.alignment that are |
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19 included in the block |
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20 |
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21 How to create a new block: |
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22 >>> import project |
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23 >>> import block |
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24 >>> proj = project.Project(open("test.fasta")) |
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25 >>> block1 = block.Block(proj, proj.sequences, range(len(proj.alignment[proj.sequences[0]]))) |
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26 |
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27 """ |
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28 |
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29 def __init__(self,project,sequences,positions): |
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30 self.project=project |
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31 self.sequences=sequences |
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32 self.positions=positions |
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33 |
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34 def to_fasta(self,file): |
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35 """writes the block as an alignment in fasta-format into the file. |
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36 |
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37 No changes in the names, descriptions or order of the sequences |
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38 are made. |
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39 |
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40 """ |
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41 for sequence in self.sequences: |
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42 file.write(">%s %s\n"%(sequence.name,sequence.description)) |
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43 string_index=0 |
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44 for position in self.positions: |
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45 if string_index>=60: |
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46 file.write("\n") |
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47 string_index=0 |
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48 if self.project.alignment[sequence][position]==None: |
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49 file.write("-") |
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50 string_index+=1 |
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51 else: |
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52 file.write(self.project.alignment[sequence][position].code) |
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53 string_index+=1 |
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54 file.write("\n") |
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55
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