Opis

HTSeq je Python paket za analizu podataka sekvenciranja visoke propusnosti.


Dostupne verzije

VerzijaModulSupekPadobran
2.0.5scientific/HTSeq/2.0.5(error) (tick) 


Službena dokumentacija

Primjer korištenja

HTSeq-example.py
import HTSeq
import numpy
import itertools
 
fastq_file = HTSeq.FastqReader( "yeast_RNASeq_excerpt_sequence.txt", "solexa" )
 
for read in itertools.islice( fastq_file, 10 ):
    print(read)
 
read.name
read.seq
 
qualsum = numpy.zeros(len(read), int)
 
nreads = 0
for read in fastq_file:
    qualsum += read.qual
    nreads += 1
 
r =qualsum / float(nreads)
 
numpy.savetxt('qualsum.out', r, newline=" ", fmt="%f")


htseq-read.pbs
#!/bin/bash

#PBS -N htseq-read
#PBS -q cpu

cd $PBS_O_WORKDIR

module load scientific/HTSeq/2.0.5

HTSeq.sh python HTSeq-example.py