How to use coordinates to Extract sequences in Fasta File

[1] bedtools (HTTPS://GITHUB.COM/ARQ5X/BEDTOOLS2)

Here is also Bedtools (HTTPS://GITHUB.COM/ARQ5X/BEDTOOLS2) Getfasta. It uses Erik ' s code under the hood.

$ cat test.fa>chr1AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG$ cat test.bedchr1 5 10$ bedtools getfasta -fi test.fa -bed test.bed -fo test.fa.out$ cat test.fa.out>chr1:5-10AAACC

Docs:http://bedtools.readthedocs.org/en/latest/content/tools/getfasta.html

And it is wrapped in pybedtools as well:http://pythonhosted.org/pybedtools/autodocs/pybedtools. Bedtool.sequence.html?highlight=fasta

https://code.google.com/p/bedtools/

[2] samtools faidx feature

Faidx samtools faidx <ref.fasta> [Region1 [...] Index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. If no region is specified, FAIDX would index the file and create <ref.fasta>.fai on the disk. If regions is speficified, the subsequences would be a retrieved and printed to stdout in the FASTA format.

You'll have a to first create the Fasta indexes of the reference genome Fasta file and then use this command.

[3] python implementation of Faidx to GitHub.

Https://github.com/mdshw5/pyfaidx

[4] UCSC Twobittofa

Use UCSC twobittofa in http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

See also http://genome.ucsc.edu/goldenPath/help/twoBit.html

[5] UCSC DAS

Python script to fetch sequences from UCSC DAS server:
http://genome.ucsc.edu/cgi-bin/das/h...r4:35654,35695

[6] Ensembl Biomart

REF:

https://www.biostars.org/p/81087/

Http://stackoverflow.com/questions/23089388/a-fast-way-to-get-human-genome-sequence-by-coordinate

http://seqanswers.com/forums/showthread.php?t=42463

How to use coordinates to Extract sequences in Fasta File