#!/usr/bin/env
import sys
from seqio import iteratorFromExtension
from nucio import fileIterator
if not len(sys.argv) == 2:
sys.exit("sequencToLine.py in.{fa.fq}\n")
it = iteratorFromExtension(sys.argv[1])
for record in fileIterator(sys.argv[1], it):
if hasattr(record, "desc"):
print "\t".join([record.name, record.seq, record.desc, record.qual])
else:
print "\t".join([record.name, record.seq])
sys.exit("reference_segments.py in.fa")
store_table = {"A": [], "C": [], "G": [], "T": [], "N": []}
previous = 0
curr_count = 1
table = 2
accumulator = ["N", -1, store_table]
def runs(acc, nxt):
prev_letter = acc[previous]
acc[curr_count] += 1
if not prev_letter == nxt:
if acc[curr_count] > 0:
acc[table][prev_letter].append(acc[curr_count])
acc[previous] = nxt
acc[curr_count] = 0
return accumulator
for entry in fileIterator(sys.argv[1], fastaIterator):
reduce(runs, entry.seq, accumulator)
runs(accumulator, "X") # get last sequence
accumulator[previous] = "N"
accumulator[curr_count] = -1
print max(store_table["N"])
arguments = map(CLArgument._make, argument_list)
if not len(sys.argv) > 1:
sys.exit(getHelpStr(description, arguments) + "\n")
(p_arg_map, args_remaining) = parseArgs(sys.argv[1:], arguments)
if not len(args_remaining) >= 1:
sys.exit(getHelpStr(description, arguments) + "\n")
title = args_remaining[0]
infiles = args_remaining[1:]
cellnames = map(lambda f: "_".join(f.split(".")[0].split("_")[:2]), infiles)
fit_gen = lambda filename: fileIterator(filename, lineItemIterator)
file_iterators = map(fit_gen, infiles)
def getBasesFromLineArr(arr):
if not bool(arr):
return
if arr[0].startswith("n="):
return arr[6].split("=")[1]
if arr[0].startswith("#>%d" % p_arg_map["lengreater"]):
return arr[1].split("=")[1]
def getCountsFromLineArr(arr):
if not bool(arr):
return
def getRawAlignments(fn):
'''fn is the filename
returns An iterator over raw M4Records'''
itemIterator = lambda f : lineRecordIterator(f, M4Record, M4RecordTypes)
return fileIterator(fn, itemIterator)
#Downsample a library
import sys
from nucio import typeify, fileIterator
from seqio import iteratorFromExtension, recordToString, seqlen
if not len(sys.argv) == 5:
sys.exit("Usage: downsample.py genome_size desired_cov input.{fa,fq} output.{fa,fq}\n")
types = [int, float, str, str]
sysins = sys.argv[1:len(types)+1]
(genome_size, target_cov, infn, outfn) = typeify(sysins,types)
max_bases = genome_size * target_cov
total_bases = 0
with open(outfn, "w") as of:
for record in fileIterator(infn,iteratorFromExtension(infn)):
length = seqlen(record)
if "N" in record.seq:
continue
if total_bases > max_bases:
break
of.write(recordToString(record))
of.write("\n")
total_bases += length
#!/usr/bin/env python
import sys
from seqio import iteratorFromExtension, recordToString
from nucio import fileIterator
from misc import reverse_complement
if not len(sys.argv) == 2:
sys.exit("reverseComplement.py in.{fa,fq}")
f = sys.argv[1]
for record in fileIterator(f,iteratorFromExtension(f)):
print recordToString(record._replace(seq=reverse_complement(record.seq)))
ref = itemgetter(7)
pos = lambda r : int(itemgetter(8)(r))
strand = itemgetter(9)
if not len(sys.argv) == 3:
sys.exit("filterpairs.py read1.novo read2.novo\n")
names_eq = lambda name1,name2: name1.split("/")[0] == name2.split("/")[0]
filenames = sys.argv[1:3]
#filter out header lines
headfilt = lambda x : not x.startswith("#")
filt_lii = partial(lineItemIterator, filter_func=headfilt)
filt_fits = map( lambda fn : fileIterator(fn, filt_lii), filenames)
failrepeat = 0
failmapq = 0
failsameref = 0
total = 0
passed = 0
insertNotRF = []
insertRF = []
for read1,read2 in izip(*filt_fits):
total += 1
if not names_eq(name(read1), name(read2)):
sys.exit("Error: %s not equal to %s\n" % (name(read1),name(read2)))
["miny", "miny", int, 0, "minimum y axis value"],
["maxy", "maxy", int, -1, "maximmum y axis value"],
[
"out", "out", str, "out.pdf",
"output file name (default out.pdf)"
], ["title", "title", str, "", "Title for graph"]]
arguments = map(CLArgument._make, argument_list)
(p_args, args_remaining) = parseArgs(sys.argv[1:], arguments)
if not len(args_remaining) == 1:
sys.exit(getHelpStr(description, arguments) + "\n")
conv = lambda (i, j): (int(i), int(j))
(x, y) = zip(*imap(conv, fileIterator(args_remaining[0], lineItemIterator)))
pp = PdfPages(p_args["out"])
plt.plot(x, y)
(minx, maxx) = plt.xlim()
(miny, maxy) = plt.ylim()
minx = p_args["minx"] if p_args["minx"] > minx else minx
maxx = p_args["maxx"] if p_args["maxx"] > 0 else maxx
miny = p_args["miny"] if p_args["miny"] > miny else miny
maxy = p_args["maxy"] if p_args["maxy"] > 0 else maxy
plt.xlim((minx, maxx))
plt.ylim((miny, maxy))
plt.xlabel("Kmer Coverage")
#!/usr/bin/env python
import sys
from itertools import imap
from seqio import iteratorFromExtension
from nucio import fileIterator
##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 fileIterator(fn, iteratorFromExtension(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
argument_list = [["span","span", argflag, False, "Only alignments that span the region"]]
arguments = map(CLArgument._make, argument_list)
(p_arg_map, args_remaining) = parseArgs(sys.argv[1:], arguments)
if not len(args_remaining) == 2:
sys.exit(getHelpStr(description,arguments) + "\n")
inm4 = args_remaining[0]
(chrom, rest) = args_remaining[1].split(":")
(start,end) = map(int,rest.split("-"))
it = lambda fh : lineRecordIterator(fh, M4Record, M4RecordTypes)
cond = lambda r : r.tname == chrom and not r.tend < start and not r.tstart > end
if p_arg_map["span"]:
cond = lambda r : r.tname == chrom and r.tstart < start and r.tend > end
filt_records = ifilter(cond,fileIterator(inm4, it))
for r in imap(recordToString, filt_records):
print r
["minx","minx", int, 0,"minimum x axis value"],
["maxx", "maxx", int, -1,"maximum x axis value"],
["miny","miny", int, 0,"minimum y axis value"],
["maxy","maxy", int, -1,"maximmum y axis value"],
["out","out", str, "out.pdf", "output file name (default out.pdf)"],
["title","title", str, "", "Title for graph"]]
arguments = map(CLArgument._make, argument_list)
(p_args, args_remaining) = parseArgs(sys.argv[1:], arguments)
if not len(args_remaining) == 1:
sys.exit(getHelpStr(description, arguments) + "\n")
conv = lambda (i,j) : (int(i),int(j))
(x,y) = zip(*imap(conv,fileIterator(args_remaining[0], lineItemIterator)))
pp = PdfPages(p_args["out"])
plt.plot(x,y)
(minx,maxx)=plt.xlim()
(miny,maxy)=plt.ylim()
minx = p_args["minx"] if p_args["minx"] > minx else minx
maxx = p_args["maxx"] if p_args["maxx"] > 0 else maxx
miny = p_args["miny"] if p_args["miny"] > miny else miny
maxy = p_args["maxy"] if p_args["maxy"] > 0 else maxy
plt.xlim((minx,maxx))
plt.ylim((miny,maxy))
plt.xlabel("Kmer Coverage")
aqual = lambda r: int(itemgetter(6)(r))
ref = itemgetter(7)
pos = lambda r: int(itemgetter(8)(r))
strand = itemgetter(9)
if not len(sys.argv) == 3:
sys.exit("filterpairs.py read1.novo read2.novo\n")
names_eq = lambda name1, name2: name1.split("/")[0] == name2.split("/")[0]
filenames = sys.argv[1:3]
#filter out header lines
headfilt = lambda x: not x.startswith("#")
filt_lii = partial(lineItemIterator, filter_func=headfilt)
filt_fits = map(lambda fn: fileIterator(fn, filt_lii), filenames)
failrepeat = 0
failmapq = 0
failsameref = 0
total = 0
passed = 0
insertNotRF = []
insertRF = []
for read1, read2 in izip(*filt_fits):
total += 1
if not names_eq(name(read1), name(read2)):
sys.exit("Error: %s not equal to %s\n" % (name(read1), name(read2)))
if not status(read1) == "U" or not status(read2) == "U":
if not len(sys.argv) == 2:
sys.exit("reference_segments.py in.fa")
store_table = {'A': [], 'C': [], 'G': [], 'T': [], 'N': []}
previous = 0
curr_count = 1
table = 2
accumulator = ["N", -1, store_table]
def runs(acc, nxt):
prev_letter = acc[previous]
acc[curr_count] += 1
if not prev_letter == nxt:
if acc[curr_count] > 0:
acc[table][prev_letter].append(acc[curr_count])
acc[previous] = nxt
acc[curr_count] = 0
return accumulator
for entry in fileIterator(sys.argv[1], fastaIterator):
reduce(runs, entry.seq, accumulator)
runs(accumulator, 'X') #get last sequence
accumulator[previous] = 'N'
accumulator[curr_count] = -1
print max(store_table['N'])
def getRawAlignments(fn):
'''fn is the filename
returns An iterator over raw M4Records'''
itemIterator = lambda f: lineRecordIterator(f, M4Record, M4RecordTypes)
return fileIterator(fn, itemIterator)
from args import parseArgs, getHelpStr, argflag, CLArgument
description = ("Usage: m4region.py [options] input.m4 chr:start-end\n"
"Returns alignments that touch a region\n")
argument_list = [[
"span", "span", argflag, False, "Only alignments that span the region"
]]
arguments = map(CLArgument._make, argument_list)
(p_arg_map, args_remaining) = parseArgs(sys.argv[1:], arguments)
if not len(args_remaining) == 2:
sys.exit(getHelpStr(description, arguments) + "\n")
inm4 = args_remaining[0]
(chrom, rest) = args_remaining[1].split(":")
(start, end) = map(int, rest.split("-"))
it = lambda fh: lineRecordIterator(fh, M4Record, M4RecordTypes)
cond = lambda r: r.tname == chrom and not r.tend < start and not r.tstart > end
if p_arg_map["span"]:
cond = lambda r: r.tname == chrom and r.tstart < start and r.tend > end
filt_records = ifilter(cond, fileIterator(inm4, it))
for r in imap(recordToString, filt_records):
print r
if not len(sys.argv) > 1:
sys.exit(getHelpStr(description, arguments) + "\n")
(p_arg_map, args_remaining) = parseArgs(sys.argv[1:], arguments)
if not len(args_remaining) >= 1:
sys.exit(getHelpStr(description, arguments) + "\n")
title = args_remaining[0]
infiles = args_remaining[1:]
cellnames = map(lambda f : "_".join(f.split(".")[0].split("_")[:2]), infiles)
fit_gen = lambda filename : fileIterator(filename, lineItemIterator)
file_iterators = map(fit_gen, infiles)
def getBasesFromLineArr(arr):
if not bool(arr):
return
if arr[0].startswith("n="):
return arr[6].split("=")[1]
if arr[0].startswith("#>%d" % p_arg_map["lengreater"]):
return arr[1].split("=")[1]
def getCountsFromLineArr(arr):
if not bool(arr):
return
if arr[0].startswith("n="):
return arr[0].split("=")[1]
