def get_chromosome_lengths(rerence_multifasta):
''' Get chromosome lengths.
@param rerence_multifasta: multifasta file with chromosomes
@return: dictionary chr name -> chr length
'''
print "Read reference genome"
chrs = {}
for seq_obj in sc_iter_fasta(rerence_multifasta):
chrs[seq_obj.seq_gi] = seq_obj.seq_length
print chrs
#!/usr/bin/env python # -*- coding: utf-8 -*- # #@created: 10.10.2013 #@author: Aleksey Komissarov #@contact: [email protected] import sys from trseeker.seqio.fasta_file import sc_iter_fasta import argparse if __name__ == '__main__': parser = argparse.ArgumentParser(description='Parse multi fasta.') parser.add_argument('-i','--input', help='Fasta input', required=True) parser.add_argument('-o','--output', help='Output prefix', required=True) args = vars(parser.parse_args()) fasta = args["input"] output = args["output"] for i, seq_obj in enumerate(sc_iter_fasta(fasta, lower=False)): name = seq_obj.header.split()[0] print name with open("%s.%s.fa" % (output, name), "w") as fh: fh.write(seq_obj.fasta)
jf_path = args["jf"]
use_new = bool(args["new"])
k = int(args["k"])
c = int(args["cutoff"])
fh = open(args["output"], "w")
if jf_api and use_new:
jf_api = jellyfish.QueryMerFile(jf_path)
kmer2freq = Kmer2tfAPI(jf_api)
for sid, seq_obj in enumerate(sc_iter_fasta(input_fasta)):
print seq_obj.header, "Length:", seq_obj.length
sequence = seq_obj.sequence.upper()
n = len(sequence)
kmers = set()
for i in xrange(n-k+1):
kmer= sequence[i:i+k]
tf = kmer2freq[kmer]
if tf > 0:
print i, tf
raw_input("Next item?")
# kmers.add()
# kmers.add('A' + sequence[i:i+k-1])
# kmers.add('C' + sequence[i:i+k-1])
settings = {
"index_prefix":
"/mnt/guatemala/akomissarov/Boechera_spatifolia/raw.23.L3",
"aindex_prefix":
"/mnt/guatemala/akomissarov/Boechera_spatifolia/raw.23.L3",
"reads_file":
"/mnt/guatemala/akomissarov/Boechera_spatifolia/raw.reads",
"gene_fasta": "/mnt/guatemala/akomissarov/Boechera_spatifolia/apr1.fa",
}
k = 23
index = load_aindex(settings)
used_reads = set()
results = []
for seq_obj in sc_iter_fasta(settings["gene_fasta"]):
for i in xrange(seq_obj.length - k + 1):
kmer = seq_obj.sequence[i:i + k]
tf = index[kmer]
if not tf:
continue
print i, kmer, tf
hits = []
for data in get_reads_se_by_kmer(kmer, index, used_reads):
start, next_read_start, subread, pos, spring_pos, was_reversed, poses_in_read = data
used_reads.add((start, spring_pos))
hits.append([pos, 0, subread, poses_in_read, was_reversed])
if not hits:
#!/usr/bin/env python # -*- coding: utf-8 -*- # #@created: 10.10.2013 #@author: Aleksey Komissarov #@contact: [email protected] import sys from trseeker.seqio.fasta_file import sc_iter_fasta import argparse if __name__ == '__main__': parser = argparse.ArgumentParser(description='Check presence of adapter kmers.') parser.add_argument('-i','--input', help='Fasta input', required=True) parser.add_argument('-o','--output', help='Fixed output', required=True) args = vars(parser.parse_args()) fasta = args["input"] output = args["output"] with open(output, "w") as fh: for i, seq_obj in enumerate(sc_iter_fasta(fasta)): print i, "fix", seq_obj.seq_head seq_obj.seq_head = ">%s\n" % i fh.write(seq_obj.fasta)