def iterator_over_file_from_extension(filename):
import gzip
openers = {"gz" : gzip.open}
ext = filename.split(".")
opener = openers.get(ext[-1], open)
i_o_f = iterator_over_file(filename, opener)
if "fa" in ext or "fasta" in ext:
from jbio.fasta import record_iterator as fasta_iterator
return fasta_iterator(i_o_f)
elif "fq" in ext or "fastq" in ext:
from jbio.fastq import record_iterator as fastq_iterator
return fastq_iterator(i_o_f)
else:
raise Exception("Unknown File Extension \'%s\'" % ext[-1])
if not len(sys.argv) == 3:
print "gene_fasta.py input.fa input.gff"
sys.exit(1)
#FIELDS = ["ID","Alias","orf_classification","gene","Note"]
FIELDS = ["ID","Note"]
fa_fn,gff_fn = sys.argv[1:3]
#read fasta records into memory
def fasta_clean_getter(fasta_entry):
name = fasta_entry.name.split()[0]
return (name, fasta_entry.seq)
fasta_records = dict(imap(fasta_clean_getter,fasta_iterator(iterator_over_file(fa_fn))))
gene_entries = ifilter(lambda x: x.feature == "gene",
gff_iterator(iterator_over_file(gff_fn)))
for gene_record in gene_entries:
attrs = dict(map(lambda x: x.split("="), gene_record.attribute.split(";")))
header = ">" + attrs["Name"]
fields = FIELDS
field_getter_func = lambda x : unquote(attrs.get(x,"None")) if x =="Note" else attrs.get(x,"None")
field_getter = imap(field_getter_func, fields)
header += " " + " ".join(imap(lambda fv: "[%s=%s]" % fv, izip(fields, field_getter)))
start, end = gene_record.start-1, gene_record.end-1
seq = fasta_records[gene_record.seqname][start:end+1]
print header
#!/usr/bin/env python
import sys
from jbio.io.file import iterator_over_file
from jbio.fasta import record_iterator as fasta_iterator
if not len(sys.argv) == 2:
sys.exit("fasta_to_line.py in.fa")
for record in fasta_iterator(iterator_over_file(sys.argv[1])):
print "\t".join([record.name, record.seq])
sys.exit(1)
#FIELDS = ["ID","Alias","orf_classification","gene","Note"]
FIELDS = ["ID", "Note"]
fa_fn, gff_fn = sys.argv[1:3]
#read fasta records into memory
def fasta_clean_getter(fasta_entry):
name = fasta_entry.name.split()[0]
return (name, fasta_entry.seq)
fasta_records = dict(
imap(fasta_clean_getter, fasta_iterator(iterator_over_file(fa_fn))))
gene_entries = ifilter(lambda x: x.feature == "gene",
gff_iterator(iterator_over_file(gff_fn)))
for gene_record in gene_entries:
attrs = dict(map(lambda x: x.split("="), gene_record.attribute.split(";")))
header = ">" + attrs["Name"]
fields = FIELDS
field_getter_func = lambda x: unquote(attrs.get(
x, "None")) if x == "Note" else attrs.get(x, "None")
field_getter = imap(field_getter_func, fields)
header += " " + " ".join(
imap(lambda fv: "[%s=%s]" % fv, izip(fields, field_getter)))
start, end = gene_record.start - 1, gene_record.end - 1
#!/usr/bin/env python
import sys
from itertools import imap
from jbio.io.file import iterator_over_file
from jbio.fasta import record_iterator as fasta_iterator
##Create Kmers
if not len(sys.argv) == 3:
sys.exit("Usage: kmer.py k-size in.fa\n")
fn = sys.argv[2]
ksize = int(sys.argv[1])
for record in fasta_iterator(iterator_over_file(fn)):
seq = record.seq
starts = range(len(seq)-ksize+1)
kmers = imap(lambda start: seq[start:start+ksize], starts)
for kmer in kmers:
print kmer
