https://github.com/sandyjmacdonald/blast_parser

Parses .xml formatted blast results files and returns query and hit IDs.
https://github.com/sandyjmacdonald/blast_parser

Last synced: about 2 months ago
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Parses .xml formatted blast results files and returns query and hit IDs.

• Host: GitHub
• URL: https://github.com/sandyjmacdonald/blast_parser
• Owner: sandyjmacdonald
• License: mit
• Created: 2014-08-29T16:06:04.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2015-01-12T13:55:11.000Z (almost 10 years ago)
• Last Synced: 2024-04-21T04:04:58.124Z (9 months ago)
• Language: Python
• Size: 176 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
blast_parser.py

============

Takes a .xml formatted BLAST results file as input and prints the query ID, hit ID, percentage identity, query length, alignment length and e value for sequences passing the thresholds passed via the command line arguments.

### Dependencies

Requires [Biopython](http://biopython.org) for parsing of BLAST .xml files.

### Usage

```bash

python blast_parser.py -i  -e 1e-20 -p 97 -a 100 > parsed_results.txt

```

> ##### Arguments

> `-i` The BLAST results file (in .xml format) that you want to parse.

> `-e` e value threshold. Can be a float or integer value.

> `-p` Percentage identity cutoff. Can be a float or integer value between 0 and 100.

> `-a` Minimum alignment length cutoff. Can be a float or integer value.

> `-h` Displays help.