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1 #!/usr/bin/env python
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2 """
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3 Input: fasta, int
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4 Output: tabular
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5 Return titles with lengths of corresponding seq
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6 """
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7
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8 import sys, os
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9
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10 assert sys.version_info[:2] >= ( 2, 4 )
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11
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12 def compute_fasta_length( fasta_file, out_file, keep_first_char, keep_first_word=False ):
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13
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14 infile = fasta_file
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15 out = open( out_file, 'w')
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16 keep_first_char = int( keep_first_char )
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17
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18 fasta_title = ''
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19 seq_len = 0
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20
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21 # number of char to keep in the title
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22 if keep_first_char == 0:
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23 keep_first_char = None
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24 else:
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25 keep_first_char += 1
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26
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27 first_entry = True
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28
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29 for line in open( infile ):
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30 line = line.strip()
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31 if not line or line.startswith( '#' ):
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32 continue
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33 if line[0] == '>':
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34 if first_entry == False:
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35 if keep_first_word:
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36 fasta_title = fasta_title.split()[0]
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37 out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) )
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38 else:
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39 first_entry = False
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40 fasta_title = line
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41 seq_len = 0
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42 else:
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43 seq_len += len(line)
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44
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45 # last fasta-entry
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46 if keep_first_word:
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47 fasta_title = fasta_title.split()[0]
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48 out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) )
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49 out.close()
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50
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51 if __name__ == "__main__" :
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52 compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True ) |
