#!/usr/bin/env python
##Converts a fasta file
#To fastq by just using 'I' for quality
import sys
from seqio import fastaIterator, FastqRecord, fastqRecordToString
QUAL_STR = "I"
if not len(sys.argv) == 2:
sys.exit("fastaToFastq.py in.fa \n")
fn = sys.argv[1]
with open(fn) as fh:
for record in fastaIterator(fh):
fqr = FastqRecord(record.name, record.seq,
"", QUAL_STR * len(record.seq))
print fastqRecordToString(fqr)
#!/usr/bin/env python
##Clears the fastq description
import sys
from seqio import fastqIterator, fastqRecordToString
if not len(sys.argv) == 2:
sys.exit("clearFastqDescription.py in.fq\n")
with open(sys.argv[1]) as fh:
for record in fastqIterator(fh):
clean_rec = record._replace(desc="")
print fastqRecordToString(clean_rec)
#!/usr/bin/env python
##Clears the fastq description
import sys
from seqio import fastqIterator, fastqRecordToString
if not len(sys.argv) == 2:
sys.exit("clearFastqDescription.py in.fq\n")
with open(sys.argv[1]) as fh:
for record in fastqIterator(fh):
clean_rec = record._replace(desc="")
print fastqRecordToString(clean_rec)
#!/usr/bin/env python
##Converts a fasta file
#To fastq by just using 'I' for quality
import sys
from seqio import fastaIterator, FastqRecord, fastqRecordToString
QUAL_STR = "I"
if not len(sys.argv) == 2:
sys.exit("fastaToFastq.py in.fa \n")
fn = sys.argv[1]
with open(fn) as fh:
for record in fastaIterator(fh):
fqr = FastqRecord(record.name, record.seq, "",
QUAL_STR * len(record.seq))
print fastqRecordToString(fqr)
