Mercurial > repos > yating-l > ucsc_trix_index_generator

annotate extractHeaders.py @ 0:3de4fbd488a1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
author yating-l
date Wed, 16 May 2018 17:33:35 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
1 #!/usr/bin/python
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
2 """ Extract headers from Fasta file and write the headers to a Tabular file """
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
3
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
4 import sys
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
5
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
6 def extractHeaders(fasta_file, tab_file):
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
7
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
8 with open(tab_file, 'w') as out:
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
9 with open(fasta_file, 'r') as f:
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
10 lines = f.readlines()
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
11 for l in lines:
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
12 if '>' in l:
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
13 l = l.split()
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
14 name = l[0].replace('>', '').rstrip()
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
15 desc = ''.join(l[1:]).rstrip()
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
16 out.write(name + '\t' + desc + '\n')
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
17
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
18
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
19
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
20 def main(argv):
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
21 input_file = argv[1]
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
22 output_file = argv[2]
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
23 extractHeaders(input_file, output_file)
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
24
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
25 if __name__ == "__main__":
3de4fbd488a1 planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
diff changeset
26 main(sys.argv)