https://github.com/adamtaranto/quick-ortho-fetch

Take an XML formatted multiblast result, extract genbank IDs for best x hits to each query and download a non-redundant list of matching seqs from ncbi.
https://github.com/adamtaranto/quick-ortho-fetch

Last synced: about 2 months ago
JSON representation

Take an XML formatted multiblast result, extract genbank IDs for best x hits to each query and download a non-redundant list of matching seqs from ncbi.

• Host: GitHub
• URL: https://github.com/adamtaranto/quick-ortho-fetch
• Owner: Adamtaranto
• Created: 2013-11-08T01:57:14.000Z (about 11 years ago)
• Default Branch: master
• Last Pushed: 2014-01-23T06:39:26.000Z (almost 11 years ago)
• Last Synced: 2024-10-13T20:45:33.627Z (3 months ago)
• Language: Python
• Size: 155 KB
• Stars: 0
• Watchers: 5
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
Quick-Ortho-Fetch

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

What: Provides raw material for building phyogenies from paraphyletic gene families.  

How: Extracts a non-redundant list of best hits from a multi-query blast and fetches matching fasta seqs from NCBI.

Example

-------------------------

    python quickOrtho.py myMultiBlast.xml protein [email protected] -n 40 -e 1e-5 -o outputFile.fas -t -q

Takes the top 40 unique gids for each query from xml, outputs non-redundant .fas file containing sequences.

Options

-------------------------

usage: quickOrtho.py file_dir {protein,nucleotide} email [-h] [-n NUMBER_UNIQUE_GIDS] [-e E_VALUE_THRESHOLD] [-o OUTPUT_DIR] [-t table][-q quiet] 

  

	ArgNameDescription

  

  

  

	[1]file_dirDirectory to NCBI .xml file.

  

  

  

	[2]{protein,nucleotide}Which database to direct entrez query to.

  

  

	[3]emailEmail for entrez record retrieval, tells NCBI who you are.

  

  

	-eE_VALUE_THRESHOLDMaximum e-value allowed in screening, enter as decimal or in scientific notation (eg. 1e-20). Default = 1e-20

  

  

    -nNUMBER_UNIQUE_GIDSNumber of unique gids to extract for each query. Default = 50

  

  

    -oOUTPUT_DIRSet name of output fasta file. Default = "'input_dir'_quickOrthoResults.fas"

  

  

    -ttableCreates a new .txt table summarising top hits for each query. Writes file to "'output_dir'_summaryTable.txt". Recommend viewing this file in a text editor without text wrapping.

  

  

    -qquietRuns the program in quiet mode, with no running feedback

  

  

    -hhelpPrint help message and exit