Opis
HTSeq je Python paket za analizu podataka sekvenciranja visoke propusnosti.
Dostupne verzije
| Verzija | Modul | Supek | Padobran |
|---|---|---|---|
| 2.0.5 | scientific/HTSeq/2.0.5 |  |  |
Službena dokumentacija
Primjer korištenja
- Podaci za primjer: https://github.com/simon-anders/htseq/tree/master/example_data
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