Mercurial > repos > devteam > fasta_compute_length

annotate fasta_compute_length.py @ 6:96c921261e41 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
author devteam
date Thu, 03 Oct 2024 12:11:43 +0000
parents 79cd53e23207
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env python
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2 """
6
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
devteam
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3 Input: fasta, int
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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4 Output: tabular
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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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
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9
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79cd53e23207 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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10
6
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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11 def compute_fasta_length(fasta_file, out_file, keep_first_char, keep_first_word=False):
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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12 keep_first_char = int(keep_first_char)
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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13 fasta_title = ''
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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14 seq_len = 0
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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15
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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16 # number of char to keep in the title
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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17 if keep_first_char == 0:
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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18 keep_first_char = None
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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19 else:
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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20 keep_first_char += 1
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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21
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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22 first_entry = True
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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23 with open(fasta_file) as in_fh, open(out_file, 'w') as out_fh:
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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24 for line in in_fh:
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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25 line = line.strip()
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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26 if not line or line.startswith('#'):
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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27 continue
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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28 if line[0] == '>':
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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29 if first_entry is False:
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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30 if keep_first_word:
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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31 fasta_title = fasta_title.split()[0]
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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32 out_fh.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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33 else:
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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34 first_entry = False
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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35 fasta_title = line
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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36 seq_len = 0
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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37 else:
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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38 seq_len += len(line)
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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39
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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40 # last fasta-entry
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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41 if keep_first_word:
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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42 fasta_title = fasta_title.split()[0]
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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43 out_fh.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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44
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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45
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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46 if __name__ == "__main__":
96c921261e41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2
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47 compute_fasta_length(sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4] == 'id_only')