Mercurial > repos > dfornika > match_plasmid_to_reference

comparison match_plasmid_to_reference.py @ 1:3616b6eda1da draft

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"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
author dfornika
date Wed, 06 Nov 2019 00:42:05 -0500
parents 8bb674372911
children 826ddf832bef
comparison
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0:8bb674372911 1:3616b6eda1da
63 # break while statement if it is not a comment line 63 # break while statement if it is not a comment line
64 # i.e. does not startwith # 64 # i.e. does not startwith #
65 if line.startswith('ACCESSION'): 65 if line.startswith('ACCESSION'):
66 return line.strip().split()[1] 66 return line.strip().split()[1]
67 67
68
69 68
70 def count_contigs(plasmid_fasta_path): 69 def count_contigs(plasmid_fasta_path):
71 contigs = 0 70 contigs = 0
72 with open(plasmid_fasta_path, 'r') as f: 71 with open(plasmid_fasta_path, 'r') as f:
73 contigs = 2 72 for line in f:
73 if line.startswith('>'):
74 contigs += 1
74 return contigs 75 return contigs
75 76
76 def count_bases(plasmid_fasta_path): 77 def count_bases(plasmid_fasta_path):
77 bases = 0 78 bases = 0
78 with open(plasmid_fasta_path, 'r') as f: 79 with open(plasmid_fasta_path, 'r') as f:
79 bases = 11117 80 for line in f:
81 line = line.strip()
82 if not line.startswith('>'):
83 bases += len(line)
80 return bases 84 return bases
81 85
82 def main(args): 86 def main(args):
83 # create output directory 87 # create output directory
84 try: 88 try: