RefFinder: Difference between revisions
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Small fast cprogram to extract bases from a fasta file. Download here [http://popgen.dk/software/download/refFinder/refFinder.tar.gz] | Small fast cprogram to extract bases from a fasta file. Download here [http://popgen.dk/software/download/refFinder/refFinder.tar.gz] | ||
Program can either work as a standalone program, or allow for easy retrieval of reference bases by using the API. | |||
=Install= | =Install= | ||
<pre> | <pre> | ||
wget http://popgen.dk/software/download/refFinder/refFinder.tar.gz | |||
tar xf refFinder.tar.gz | |||
cd refFinder/ | |||
make | |||
cd .. | |||
</pre> | </pre> | ||
=Example= | =Stand alone= | ||
==Example== | |||
Generate samtools chr pos ref doing | Generate samtools chr pos ref doing | ||
Line 16: | Line 24: | ||
<pre> | <pre> | ||
cut -f1-2 ../angsd/test/small.sam |./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full >tst | cut -f1-2 ../angsd/test/small.sam |./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full >tst | ||
cmp tst small. | cmp tst ../angsd/test/small.sam | ||
</pre> | </pre> | ||
Line 70: | Line 78: | ||
1 13999911 g | 1 13999911 g | ||
</pre> | </pre> | ||
=API= | |||
<pre> | |||
#include "refFinder.h" | |||
perFasta *pf = init("hg19.fa"); | |||
char refbase = getchar("chr20",130224101,pf) | |||
//refbase now contains the reference base for chr20 at position 130,224,101 | |||
destroy(pf); | |||
</pre> | |||
Remember to link with refFinder.o and -lz | |||
<pre> | |||
g++ sampleProg.cpp refFinder.o -lz | |||
</pre> | |||
=bugs= | |||
# do check if reference file doesn't exist. |
Latest revision as of 14:55, 20 March 2014
Small fast cprogram to extract bases from a fasta file. Download here [1]
Program can either work as a standalone program, or allow for easy retrieval of reference bases by using the API.
Install
wget http://popgen.dk/software/download/refFinder/refFinder.tar.gz tar xf refFinder.tar.gz cd refFinder/ make cd ..
Stand alone
Example
Generate samtools chr pos ref doing
samtools mpileup -b smallBam.filelist -f /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa |cut -f1-3 >small.sam
Use refFinder to find the bases for each position in small.sam
cut -f1-2 ../angsd/test/small.sam |./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full >tst cmp tst ../angsd/test/small.sam
possible options are
- inputIsZero
- full
These are flags, so examples are
cut -f1-2 ../angsd/test/small.sam |./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa |head a g c t a c t c g g
Or if we want the chr position also
cut -f1-2 ../angsd/test/small.sam |./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full |head 1 13999902 a 1 13999903 g 1 13999904 c 1 13999905 t 1 13999906 a 1 13999907 c 1 13999908 t 1 13999909 c 1 13999910 g 1 13999911 g
Or if the positions are zero index as opposed to one indexed:
cut -f1-2 ../angsd/test/small.sam |./refFinder /space/genomes/refgenomes/hg19/merged/hg19NoChr.fa full inputIsZero |head 1 13999902 g 1 13999903 c 1 13999904 t 1 13999905 a 1 13999906 c 1 13999907 t 1 13999908 c 1 13999909 g 1 13999910 g 1 13999911 g
API
#include "refFinder.h" perFasta *pf = init("hg19.fa"); char refbase = getchar("chr20",130224101,pf) //refbase now contains the reference base for chr20 at position 130,224,101 destroy(pf);
Remember to link with refFinder.o and -lz
g++ sampleProg.cpp refFinder.o -lz
bugs
- do check if reference file doesn't exist.