annotate lib/block.py @ 4:0905a39738f2
project.py: EXTREMELY ugly method to calculate the identity percentage of alignment columns for colouring has been added. It will be improved later.
| author |
grishin@gorilla |
| date |
Wed, 09 Jun 2010 14:43:04 +0400 |
| parents |
757f2a1f8732 |
| children |
217d83a617c3 |
| rev |
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 project |
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6 import sequence |
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7 import monomer |
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8 |
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9 class Block(object): |
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10 """ |
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11 Mandatory data: |
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12 * self.project -- project object, which the block belongs to |
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13 * self.sequences - set of sequence objects that contain monomers |
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14 and/or gaps, that constitute the block |
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15 * self.positions -- list of positions of the project.alignment that |
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16 are included in the block |
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17 |
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18 How to create a new block: |
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19 >>> import project |
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20 >>> import block |
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21 >>> proj = project.Project(open("test.fasta")) |
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22 >>> block1 = block.Block(proj, proj.sequences, range(len(proj.alignment[proj.sequences[0]]))) |
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23 |
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24 """ |
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25 |
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26 def __init__(self,project,sequences,positions): |
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27 self.project=project |
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28 self.sequences=sequences |
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29 self.positions=positions |
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30 |
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31 def to_fasta(self,file): |
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32 """writes the block as an alignment in fasta-format into the file. |
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33 |
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34 No changes in the names, descriptions or order of the sequences |
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35 are made. |
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36 |
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37 """ |
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38 for sequence in self.sequences: |
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39 file.write(">%s %s\n"%(sequence.name,sequence.description)) |
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40 string_index=0 |
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41 for position in self.positions: |
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42 if string_index>=60: |
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43 file.write("\n") |
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44 string_index=0 |
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45 if self.project.alignment[sequence][position]==None: |
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46 file.write("-") |
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47 string_index+=1 |
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48 else: |
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49 file.write(self.project.alignment[sequence][position].code) |
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50 string_index+=1 |
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51 file.write("\n") |
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52
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