Mercurial > repos > devteam > fasta_compute_length

annotate utils/fasta_to_len.py @ 5:7d37cfda8e00 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 34a6c9f94a5722bb7d2f887618aafa410a770e91"
author devteam
date Mon, 02 Mar 2020 06:46:51 -0500
parents e12f68d2cc4e
children
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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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11 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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12 keep_first_char = int(keep_first_char)
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13 fasta_title = ''
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14 seq_len = 0
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15
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16 # number of char to keep in the title
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17 if keep_first_char == 0:
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18 keep_first_char = None
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19 else:
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20 keep_first_char += 1
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22 first_entry = True
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23 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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24 for line in in_fh:
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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25 line = line.strip()
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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26 if not line or line.startswith('#'):
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27 continue
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28 if line[0] == '>':
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29 if first_entry is False:
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30 if keep_first_word:
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31 fasta_title = fasta_title.split()[0]
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32 out_fh.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
e12f68d2cc4e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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33 else:
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34 first_entry = False
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35 fasta_title = line
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36 seq_len = 0
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37 else:
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38 seq_len += len(line)
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40 # last fasta-entry
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41 if keep_first_word:
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42 fasta_title = fasta_title.split()[0]
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43 out_fh.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
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46 if __name__ == "__main__":
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47 compute_fasta_length(sys.argv[1], sys.argv[2], sys.argv[3], True)