Mercurial > repos > devteam > fasta_compute_length

annotate utils/fasta_to_len.py @ 4:e12f68d2cc4e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
author devteam
date Sun, 01 Mar 2020 07:24:10 -0500
parents ece409f6573c
children 7d37cfda8e00
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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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e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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8 import sys
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9
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10 assert sys.version_info[:2] >= (2, 4)
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e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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13 def compute_fasta_length(fasta_file, out_file, keep_first_char, keep_first_word=False):
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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14 keep_first_char = int(keep_first_char)
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15 fasta_title = ''
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16 seq_len = 0
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17
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18 # number of char to keep in the title
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19 if keep_first_char == 0:
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20 keep_first_char = None
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21 else:
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22 keep_first_char += 1
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23
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24 first_entry = True
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25 with open(fasta_file) as in_fh, open(out_file, 'w') as out_fh:
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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26 for line in in_fh:
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27 line = line.strip()
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28 if not line or line.startswith('#'):
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29 continue
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30 if line[0] == '>':
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31 if first_entry is False:
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32 if keep_first_word:
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33 fasta_title = fasta_title.split()[0]
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34 out_fh.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
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35 else:
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36 first_entry = False
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37 fasta_title = line
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38 seq_len = 0
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39 else:
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40 seq_len += len(line)
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42 # last fasta-entry
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43 if keep_first_word:
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44 fasta_title = fasta_title.split()[0]
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45 out_fh.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
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47
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48 if __name__ == "__main__":
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49 compute_fasta_length(sys.argv[1], sys.argv[2], sys.argv[3], True)