Mercurial > repos > galaxyp > fasta_merge_files_and_filter_unique_sequences

comparison fasta_merge_files_and_filter_unique_sequences.py @ 1:74144834b0bd draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 9f9eba8df62b4db1ef35718d880a1bcda7457b99
author galaxyp
date Fri, 16 Dec 2016 05:19:27 -0500
parents 2904d46167da
children 379c41d859aa
comparison
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0:2904d46167da 1:74144834b0bd
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 import sys,os 2 import os
3 import sys
3 4
4 #====================================================================== Classes
5 class Sequence: 5 class Sequence:
6 ''' Holds protein sequence information ''' 6 ''' Holds protein sequence information '''
7 def __init__(self): 7 def __init__(self):
8 self.header = "" 8 self.header = ""
9 self.sequence = "" 9 self.sequence = ""
54 for protein in fa_reader: 54 for protein in fa_reader:
55 if protein.sequence in seen_sequences: 55 if protein.sequence in seen_sequences:
56 pass 56 pass
57 else: 57 else:
58 seen_sequences.add(protein.sequence) 58 seen_sequences.add(protein.sequence)
59
60 out_file.write(protein.header) 59 out_file.write(protein.header)
61 out_file.write(os.linesep) 60 out_file.write(os.linesep)
62 out_file.write(protein.sequence) 61 out_file.write(protein.sequence)
63 out_file.write(os.linesep) 62 out_file.write(os.linesep)
64 out_file.close() 63 out_file.close()