Mercurial > repos > devteam > fasta_filter_by_length

annotate fasta_filter_by_length.py @ 4:8cacfcf96a52 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
author devteam
date Sun, 01 Mar 2020 07:24:42 -0500
parents e626b3ff9922
children
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1 #!/usr/bin/env python
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2 """
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3 Input: fasta, minimal length, maximal length
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4 Output: fasta
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5 Return sequences whose lengths are within the range.
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6 """
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7
4
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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8 import sys
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9
4
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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10 assert sys.version_info[:2] >= (2, 4)
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8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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13 def stop_err(msg):
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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14 sys.exit(msg)
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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15
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17 def __main__():
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18 input_filename = sys.argv[1]
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19 try:
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8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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20 min_length = int(sys.argv[2])
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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21 except Exception:
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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22 stop_err("Minimal length of the return sequence requires a numerical value.")
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23 try:
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8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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24 max_length = int(sys.argv[3])
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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25 except Exception:
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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26 stop_err("Maximum length of the return sequence requires a numerical value.")
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27 output_filename = sys.argv[4]
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8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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28 tmp_size = 0 # -1
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29 tmp_buf = ''
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30 at_least_one = 0
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8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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31 with open(output_filename, 'w') as output_handle, open(input_filename, 'r') as input_handle:
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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32 for line in input_handle:
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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33 if not line or line.startswith('#'):
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34 continue
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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35 if line[0] == '>':
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36 if min_length <= tmp_size <= max_length or (min_length <= tmp_size and max_length == 0):
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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37 output_handle.write(tmp_buf)
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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38 at_least_one = 1
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39 tmp_buf = line
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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40 tmp_size = 0
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41 else:
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42 if max_length == 0 or tmp_size <= max_length:
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43 tmp_size += len(line.rstrip('\r\n'))
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44 tmp_buf += line
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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45 # final flush of buffer
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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46 if min_length <= tmp_size <= max_length or (min_length <= tmp_size and max_length == 0):
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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47 output_handle.write(tmp_buf.rstrip('\r\n'))
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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48 at_least_one = 1
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49 if at_least_one == 0:
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50 print("There is no sequence that falls within your range.")
8cacfcf96a52 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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51
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52
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53 if __name__ == "__main__":
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54 __main__()