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56
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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3
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4 import sys
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5 from Bio import SeqIO
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6
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7 fasta_file = sys.argv[1]
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8 shift_in = sys.argv[2]
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9 result_file = sys.argv[3]
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10 length = sys.argv[4]
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11 t_end = sys.argv[5]
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12
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13 shift = int(shift_in)
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14
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15 fasta_sequences = SeqIO.parse(open(fasta_file),'fasta');
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16 h = file(result_file,'w')
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17 for seq in fasta_sequences:
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18 nuc = seq.id;
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19 sequence = seq.seq.tostring();
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20 if (len(sequence)-shift)>=int(length):
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21 h.write('>'+nuc)
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22 h.write('\n')
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23 if t_end == 'three_end':
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24 h.write(sequence[0:(len(sequence)-shift)])
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25 if t_end == 'five_end':
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26 h.write(sequence[(shift):(len(sequence))])
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27 h.write('\n')
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28
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29
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30
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31
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32 h.close()
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33
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34
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35
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36
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