92 lines
2.9 KiB
Markdown
92 lines
2.9 KiB
Markdown
---
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author: einar
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comments: true
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date: 2007-04-25 14:26:07+00:00
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layout: page
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slug: databases
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title: Databases
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wordpress_id: 237
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categories:
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- Linux
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- Science
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header:
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image_fullwidth: banner_other.jpg
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---
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As I've been working to get some results done for my Ph.D. thesis, I've stumbled across the problem of having different data obtained through different software. Even if it's just a matter of text files, the fields are all different and even if dealing with the same data, trying to infer relationships is a pain.<!-- more -->
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Therefore I decided to create a small database to host the data of my work and query it accordingly. I didn't want to run a database server, so I settled for [SQLite](http://sqlite.org), a lightweight file-driven database, I don't handle enormous amount of data so it should be ok. Up to now I've inserted parts of the Entrez Gene database. First of all I downloaded the gene_info.gz from NCBI's FTP, which contains data such as gene name, gene symbol, and so on. Then it was a matter of filtering out non-human entries, and to do so I wrote a small script called taxon_filter.py:
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[code lang="python"]
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#!/usr/bin/env python
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import gzip
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import sys
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import csv
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"""Filters NCBI annotation files by human taxon (9606). Works directly from the source
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gzipped file and outputs a tab-delimited file."""
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class ncbi:
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delimiter = '\t'
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quotechar = '"'
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escapechar = None
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doublequote = True
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skipinitialspace = False
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lineterminator = '\n'
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quoting = csv.QUOTE_NONE
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def __init__(self):
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# Dialect registration
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csv.register_dialect("ncbi", self)
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ncbi()
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if len(sys.argv) < 3:
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print "Not enough command line arguments"
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sys.exit(0)
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try:
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compressed_file = gzip.open(sys.argv[1])
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except IOError:
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print "Could not open file!"
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sys.exit(-1)
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delim = csv.reader(compressed_file,dialect="ncbi")
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try:
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destination_file = open(sys.argv[2],"wb")
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except IOError:
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print "Can't open destination file!"
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sys.exit(-1)
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write_delim = csv.writer(destination_file,dialect="ncbi")
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write_delim.writerow(delim.next())
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for row in delim:
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if row[0] == "9606":
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write_delim.writerow(row)
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print "Complete!"
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compressed_file.close()
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destination_file.close()
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sys.exit(0)
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[/code]
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(apologies, tabs are messed up)
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That filtered the file for entries belonging to taxon 9606 (_Homo sapiens) . _Then I had to keep only the interesting bits in the file, so I cut the leading comment and selected only the correct fields:
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[code lang="bash"]
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sed '1d' gene_info_human | cut -f2,9,3,7-8 > entrez_gene.txt
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[/code]
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SQLite has Python bindings (officially part of Python since 2.5) but those don't allow the direct import of text files, so I fired up the command line sqlite3 command and created the relevant table, called entrez_gene, and imported the data:
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[code lang="bash"]
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.separator "\t"
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.import datafiles/File_NCBI/entrez_gene.txt entrez_gene
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[/code]
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Done! This is the first step, then I'll work on creating tables for my own data.
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