bx.seq.fasta module

Classes to support FASTA files.

Author:

Bob Harris (rsharris@bx.psu.edu)

A FASTA file contains multiple sequences. Each sequence is usually DNA.

A typical FASTA file:

>mule
TAATACCCCGGATATATGTCCTCACATAGTTCGAGGTCGAGAAAAATGAC
TTCCCACCAAGTGGACTCAGCTCGAGTAAACGCCAACGATACGTCCATTA
GGTGTGTGCCgcaactagtcggacccgttgtgacggaaacaggtccccgc
caagtcacacgggcatgtcatggacTCTCGATCGTTCATCGCCTTCTTGG
GTACCGCAGCCGCAATTAAGCCGTGTCTTCTTCCCCCTTCAAACGGGAAT
CGTGTCGACTTCTTAGGAGCAGNNNNNNNNNNCTAACTCCAGAG
>donkey
TAATACCCCGGATATATGTCTTAACATAGTTCCAGGTCGAGAAGAATGAC
TTGCCACCAAGTGGACTCAGATTCAGTCAACGCGAACGATAAGTCCATTA
GGTGTGTACCgcaactagtgggacccgttgtgacggaaacaggtcaccgc
caagtcacacgtgcatgtcatgtacTCTCGATCGTTTATCGCCTTCTTGG
GTACCGCAGCCGAAATTAAGCCGTGTCTTCTTCCCACTTCAAACGGGAAT
CGTGTCGACTTTACAGGAACAGNNNNNNNNNNATAACGCCAGAG
 ... more sequences

Typical use:

for seq in bx.seq.fasta.FastaReader(sys.stdin):

print seq.name print seq.get(0,seq.length)

class bx.seq.fasta.FastaFile(file, revcomp=False, name='', gap=None, lookahead=None, contig=None)

Bases: SeqFile

class bx.seq.fasta.FastaReader(file, revcomp=False, name='', gap=None)

Bases: SeqReader

class bx.seq.fasta.FastaWriter(file, columns=50)

Bases: object

close()

write(seq)