Part of series:Bioinfo
maf 格式转换
maf 格式转换
由来
全基因组比对，各个软件有各自的输出格式，如 MAF、SAM、PAF、delta 等，总体而言，我认为 MAF (Multiple Alignment Format) 格式是最能体现全基因组比对的特点的，但是其下游操作，比如结构变异的鉴定、可视化等，需要其他格式，所以对其进行格式转换比较有必要。目前暂时还没发现有现成的工具，而且实现起来也比较简单，就自己写了一个。不过仅限于两个基因组的比对结果。
用法
python3 maf-convert.py --maf your.maf --out your_out_prefix输出：
- your_out_prefix.sam
- your_out_prefix.paf
- your_out_prefix.delta
依赖
基本都是自带的包，无需额外安装
可能需要安装 rich 来做日志和进度条展示，pip 安装即可
pip3 install rich ## 老牌包，闭着眼睛装代码
#!/usr/bin/env python3
# -*- encoding: utf-8 -*-
'''
@文件 :maf-convert.py
@说明 :Convrt FUCKING maf to other fmts
@时间 :2022/11/11 17:04:28
@作者 :wjwei
@版本 :0.01
@邮箱 :wjwei9908@gmail.com
'''
from collections import defaultdict
from dataclasses import dataclass
import gzip
import logging
import math
from itertools import groupby
import argparse
import re
from rich.progress import track
from rich.console import Console
from rich.logging import RichHandler
console = Console ()
logging.basicConfig (level=logging.DEBUG,
format='%(asctime) s - %(message) s',
datefmt='% Y-% m-% d % H:% M:% S',
handlers=[RichHandler (rich_tracebacks=True,
console=Console (stderr=True))])
def get_args ():
# define arguments
parser = argparse.ArgumentParser (
description=__doc__, prog='maf-convert.py',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
# required arguments
required_parser = parser.add_argument_group ('required arguments')
required_parser.add_argument ('-m', '--maf', action='store',
type=str, dest='maf',required=True,
help='maf path')
required_parser.add_argument ('-o', '--out', action='store', dest='out', type=str, required=True,
help='output prefix')
# options arguments
optional_parser = parser.add_argument_group ('optional arguments')
optional_parser.add_argument ('-p','--prefix', nargs='+', dest='prefix', help='prefix of maf file, a list, exp: Zm-B73v5 Zx-TEO09', default=None)
return parser.parse_args (), parser.prog
def mapqFromProb (probString):
mapqMaximum = 100
try:
p = float (probString)
except ValueError:
raise Exception ("bad probability:" + probString)
if p < 0 or p > 1:
raise Exception ("bad probability:" + probString)
if p == 0:
return mapqMaximum
phred = -10 * math.log (p, 10)
if phred >= mapqMaximum:
return str (mapqMaximum)
return str (int (round (phred)))
def cigarCategory (alignmentColumn):
x, y = alignmentColumn
if x == "-":
if y == "-":
return "P"
else:
return "I"
else:
if y == "-":
return "D"
# elif x != y:
# return "M" ## X-->M
else:
return "M"
def cigarParts (beg, alignmentColumns, end):
if beg:
yield str (beg) + "H"
# (doesn't handle translated alignments)
for k, v in groupby (alignmentColumns, cigarCategory):
yield str (sum (1 for _ in v)) + k
if end:
yield str (end) + "H"
def get_cigar (m1, m2):
qRevStart = m2.sequence_size - m2.alignment_start - m2.alignment_size
cigar = "".join (cigarParts (m2.alignment_start, zip (m1.alignment, m2.alignment), qRevStart))
return cigar
class MAFLine:
"""A reader for :term:`MAF` format.
mode refname start algsize strand refsize alignment
::
a
s ref 100 10 + 100000 ---AGC-CAT-CATT
s contig 0 10 + 10 ---AGC-CAT-CATT
a
s ref 100 12 + 100000 ---AGC-CAT-CATTTT
s contig 0 12 + 12 ---AGC-CAT-CATTTT
The alignments are stored by pair, one item for the reference, one for the
query. The query (second line) starts at zero.
"""
def __init__(self, line, prefix=""):
self._items = line.split ()
self.prefix = prefix
assert self._items [0] in "aspq", self._items
@property
def name (self):
if self.prefix:
return self.prefix+'.'+self._items [1]
return self._items [1]
@property
def sequence_size (self):
return int (self._items [5])
@property
def mode (self):
return self._items [0]
@property
def strand (self):
return self._items [4]
@property
def alignment_start (self): # alignment start
return int (self._items [2])
@property
def alignment_size (self):
return int (self._items [3])
@property
def alignment (self):
return self._items [6]
def get_alignment_length (self):
return len (self._items [6].replace ("-", ""))
@dataclass
class Header:
pg: str ## program
vn: str ## version
cl: str ## command line
@dataclass
class Prefix:
ref_pre: str ## reference prefix
query_pre: str ## query prefix
class MAF:
"""A reader for :term:`MAF`format."""
def __init__(self, filename, header: Header, prefix: Prefix, outfile=None,):
self.filename = filename
self.outfile = outfile
self.header = header
self.prefix = prefix
def count_insertions (self, alnString):
"""return length without insertion, forward and reverse shift"""
gaps = alnString.count ("-")
forwardFrameshifts = alnString.count ("\\")
reverseFrameshifts = alnString.count ("/")
letters = len (alnString) - gaps - forwardFrameshifts - reverseFrameshifts
return letters, forwardFrameshifts, reverseFrameshifts
# @SQ SN:NC_002929 LN:4086189
# @PG ID:bioconvert VN:?? CL:bioconvert input.maf output.sam
def to_sam (self):
# identifier flag ref start qual cigar * 0 0 sequence_ref qual NM: MD:
# AS XS RG ....
fout = open (self.outfile, "w")
fout.write ("@HD\tVN:1.3\tSO:unsorted\n")
msg = "maf2paf found q starting a new line."
with console.status ("[bold green] Writing Header for sam...") as status:
with open (self.filename, "r") as fin:
# scan once to get sequence name and length.
# only reference is of interest
names = set ()
top = True
fin_total = 0
for line in fin:
fin_total += 1
if len (line.strip ()) == 0 or line.startswith ("#"):
top = True
continue
m = MAFLine (line) if not self.prefix.ref_pre else MAFLine (line, self.prefix.ref_pre)
if m.mode == "s" and top is True:
if m.name not in names:
names.add (m.name)
fout.write (f"@SQ\tSN:{m.name}\tLN:{m.sequence_size}\n")
top = False
fout.write (
"@PG\tID:{0}\tPN:{0}\tVN:{1}\tCL:{2} \n".format (self.header.pg, self.header.vn, self.header.cl)
)
with open (self.filename, "r") as fin:
for line in track (fin, description="[bold green] Converting maf to sam...", total=fin_total):
# skipping empty lines
if line.strip ()== ""or line.startswith ("#"):
continue
if line [0] == "a":
s = []
if "=" in line:
tags = dict (i.split ("=") for i in line [1].split ())
else:
tags = {}
elif line [0] == "s":
s.append (line)
elif line [0] == "q":
# quality ?
raise NotImplementedError (msg)
elif line [0] == "p":
raise NotImplementedError (msg)
elif line [0] == "#":
logging.warning (line)
# now that we have the two lines, save into SAM file
if len (s) > 2:
raise NotImplementedError ("mutliple alignment not implemented yet")
if len (s) == 2:
ref = MAFLine (s [0]) if not self.prefix.ref_pre else MAFLine (s [0], self.prefix.ref_pre)
query = MAFLine (s [1]) if not self.prefix.query_pre else MAFLine (s [1], self.prefix.query_pre)
if ref.strand != "+":
raise Exception ("for SAM, the 1st strand in each alignment must be +")
flag = self.get_flag (ref.alignment, query.strand)
# This is the slowest part of the code
cigar = get_cigar (ref, query)
qual = "*"
if "mismap" in tags:
mapq = tags ["mismap"]
else:
mapq = "255" # missing 254 is maximum
pos = int (ref.alignment_start) + 1 # convert to 1-based coordinate
data = [
query.name,
flag,
ref.name,
pos,
mapq,
cigar,
"*",
0,
0,
query.alignment.replace ("-", "").upper (),
qual,
]
# MD
# XS
# RG:Z:1
if "score" in tags:
data.append ("AS:i:{}".format (tags ["score"]))
if "expect" in tags:
data.append ("EZ:Z:{}".format (tags ["expect"]))
# try: mapq = mapqFromProb (maf.namesAndValues ["mismap"])
# except KeyError: mapq = mapqMissing
editDistance = sum (1 for x, y in zip (ref.alignment, query.alignment) if x != y)
# no special treatment of ambiguous bases: might be a minor bug
editDistance = "NM:i:" + str (editDistance)
data.append (editDistance)
fout.write ("\t".join ([str (x) for x in data])+ "\n")
s = []
if len (s):
raise ValueError ("Your MAf file seems truncated.")
fout.close ()
logging.info (f"Sueccessfuly Done in {self.outfile}")
return fin_total//4
def get_flag (self, qName, query_strand):
if qName.endswith ("/1"):
qName = qName [:-2]
if query_strand == "+":
flag = "99" # 1 + 2 + 32 + 64
else:
flag = "83" # 1 + 2 + 16 + 64
elif qName.endswith ("/2"):
qName = qName [:-2]
if query_strand == "+":
flag = "163" # 1 + 2 + 32 + 128
else:
flag = "147" # 1 + 2 + 16 + 128
else:
if query_strand == "+":
flag = "0"
else:
flag = "16"
return flag
class SAM2PAF:
"""Convert :term:`SAM`file to :term:`PAF` file
The :term:`SAM` and :term:`PAF` formats are described in the :ref:`formats`
section.
Description:
The header of the SAM file (lines starting with @) are dropped. However, the
length of the target is retrieved from the @SQ line that must be present.
Consider this SAM file with two alignements only. One is aligned on the
target (first) while the other is not (indicated by the ``*`` characters)::
@SQ SN:ENA|K01711|K01711.1 LN:15894
@PG ID:minimap2 PN:minimap2 VN:2.5-r572 CL:minimap2 -a measles.fa Hm2_GTGAAA_L005_R1_001.fastq.gz
HISEQ:426:C5T65ACXX:5:2302:1943:2127 0 ENA|K01711|K01711.1 448 60 101M * 00 CTTACCTTCGCATCAAGAGGTACCAACATGGAGGATGAGGCGGACCAATACTTTTCACATGATGATCCAATTAGTAGTGATCAATCCAGGTTCGGATGGTT BCCFFFFFHHHHHIIJJJJJJIIJJJJJJJJFHIHIJJJIJIIIIGHFFFFFFEEEEEEEDDDDDFDDDDDDDDD>CDDEDEEDDDDDDCCDDDDDDDDCD NM:i:0 ms:i:202 AS:i:202 nn:i:0 tp:A:P cm:i:14 s1:i:94 s2:i:0
HISEQ:426:C5T65ACXX:5:2302:4953:2090 4 * 0 0 * * 0 0 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAACAACCAAAAAGAGACGAACAA CCCFFDDFAFFBHJHGGGIHIJBGGHIIJJJJJJJHGEIJGIFIIIHCBGHIJIIIIIJJHHHHEF@D@=;=,0) 0&5&))+(((+((((&+(((()&&)(
The equivalent PAF file is ::
HISEQ:426:C5T65ACXX:5:2302:1943:2127 101 0 101 + ENA|K01711|K01711.1 15894 447 548 101 101 60 NM:i:0 ms:i:202 AS:i:202 nn:i:0 tp:A:P cm:i:14 s1:i:94 s2:i:0 cg:Z:101M
In brief, the sequences are dropped. The final file is therefore smaller.
Extra fields (starting from NM:i:0) can be dropped or kept using the
keep_extra_field argument. Alignement with ``*`` characters are dropped.
The first line (@SQ) is used to retrieve the length of the contigs that is
stored in the PAF file (column 6).
The 12 compulsary PAF fields are:
====== ======== ===========================================
Col Type Description
====== ======== ===========================================
1 string Query sequence name
2 int Query sequence length
3 int Query start (0-based)
4 int Query end (0-based)
5 char Relative strand: "+" or "-"
6 string Target sequence name
7 int Target sequence length
8 int Target start on original strand (0-based)
9 int Target end on original strand (0-based)
10 int Number of residue matches
11 int Alignment block length
12 int Mapping quality (0-255; 255 for missing)
====== ======== ===========================================
For developesr:
Get the measles data from Sequana library (2 paired fastq files)::
minimap2 measles.fa R1.fastq > approx-mapping.paf
You can ask minimap2 to generate CIGAR at the cg tag of PAF with:
minimap2 -c measles.fa R1.fastq > alignment.paf
or to output alignments in the SAM format::
minimap2 -a measles.fa R1.fastq > alignment.sam
The SAM lines must contains 11 positional element and the NM:i and nn:i
fields (see example above).
"""
#: Default value
_default_method = "python"
def __init__(self, infile, outfile, total_line):
""".. rubric:: constructor
:param str infile: input SAM file
:param str outfile: output PAF filename
:reference: This function is a direct translation of
https://github.com/lh3/miniasm/blob/master/misc/sam2paf.js (Dec.
2017).
"""
self.infile = infile
self.outfile = outfile
self.total_line = total_line
def convert (self, *args, **kwargs):
"""Internal method"""
pattern = r"(\d+)([MIDSHNX=])"
extra_fields = kwargs.get ("extra_fields", "SAM")
# TODO: what is this ?
pri_only = kwargs.get ("pri_only", True)
skipped = 0
reference_lengths = {}
with open (self.infile, "r") as fin:
with open (self.outfile, "w") as fout:
for lineno, line in track (enumerate (fin.readlines ()),description="[bold green] Converting maf to sam...", total=self.total_line):
if line.startswith ("@"):
if line.startswith ("@SQ"):
match = re.findall (r"\tSN:(\S+)", line)
name = match [0] if len (match) else "unknown_reference"
match = re.findall (r"\tLN:(\d+)", line)
if len (match) == 1:
reference_lengths [name] = int (match [0])
else:
raise ValueError (
"Could not parse SQ line to extract the length" "(LN: field missing maybe ?)"
)
continue
t = line.split ()
flag = int (t [1])
if t [9] != "*" and t [10] != "*" and len (t [9]) != len (t [10]):
raise ValueError (
"ERROR at line"
+ str (lineno)
+ ":inconsistent SEQ and QUAL lengths -"
+ str (len (t [9]))
+ "!="
+ str (len (t [10]))
)
if t [2] == "*" or (flag & 4):
skipped += 1
continue
# if flag is 256 and pri_only, we skip the alignment
if pri_only and (flag & 0x100):
continue
# Get the reference length for this alignment
if t [2] in reference_lengths:
tlen = reference_lengths [t [2]]
else:
raise KeyError ("can't find the length of contig {}".format (t [2]))
# The reference is known but the length is not
if tlen == -1:
raise ValueError (
"ERROR at line" + str (lineno) + ": can't find the length of contig" + str (t [2])
)
# TODO explain what are the nn and NM tags
match = re.findall (r"\tnn:i:(\d+)", line)
if match:
nn = int (match [0])
else:
nn = 0
match = re.findall (r"\tNM:i:(\d+)", line)
if match:
NM = int (match [0])
have_NM = True
else:
NM = 0
have_NM = False
NM += nn
# See sequana.cigar for more information
clip = [0, 0]
I = [0, 0] # Insertion
D = [0, 0] # Deletion
M, N = 0, 0 # Matches
ql, tl, mm = (
0,
0,
0,
)
ext_cigar = False
n_cigar = 0
Zacc = ""
for count, letter in re.findall (pattern, t [5]):
l = int (count)
if letter == "M":
M += l
ql += l
tl += l
ext_cigar = False
Zacc += "{} M".format (count)
elif letter == "I":
I [0] += 1
I [1] += l
ql += l
Zacc += "{} I".format (count)
elif letter == "D":
D [0] += 1
D [1] += l
tl += l
Zacc += "{} D".format (count)
elif letter == "N":
N += l
tl += l
elif letter == "S":
clip [0 if M == 0 else 1] = l
ql += l
elif letter == "H":
clip [0 if M == 0 else 1] = l
elif letter == "=":
M += l
ql += l
tl += l
ext_cigar = True
elif letter == "X":
M += l
ql += l
tl += l
mm += l
ext_cigar = True
n_cigar += 1
prefix_msg = "at line {}:".format (lineno) + "{}"
if n_cigar > 65535:
logging.warning (prefix_msg.format (str (n_cigar) + "CIGAR operations"))
if tl + int (t [3]) - 1 > tlen:
logging.warning (prefix_msg.format ("alignment end" "position larger than ref length; skipped"))
continue
if t [9] != "*" and len (t [9]) != ql:
logging.warning (
prefix_msg.format (
"SEQ length inconsistent with CIGAR ("
+ str (len (t [9]))
+ "!="
+ str (ql)
+ "); skipped"
)
)
continue
if have_NM is False or ext_cigar:
NM = I [1] + D [1] + mm
if NM < I [1] + D [1] + mm:
logging.warning (
prefix_msg.format (
"NM is less than the total number of gaps ("
+ str (NM)
+ "<"
+ str (I [1] + D [1] + mm)
+ ")"
)
)
NM = I [1] + D [1] + mm
# extra information to store in the PAF after the 12
# extra field from original code. The insert and
# deletions (io/in and do/di) and mm is the number of other
# substitutions ? NM -I [1] -D [1]
extra = [
"mm:i:" + str (NM - I [1] - D [1]),
"io:i:" + str (I [0]),
"in:i:" + str (I [1]),
"do:i:" + str (D [0]),
"dn:i:" + str (D [1]),
]
match = M - (NM - I [1] - D [1])
blen = M + I [1] + D [1]
qlen = M + I [1] + clip [0] + clip [1]
# What does flag 16 means ?
if flag & 16:
qs = clip [1]
qe = qlen - clip [0]
else:
qs = clip [0]
qe = qlen - clip [1]
ts = int (t [3]) - 1
te = ts + M + D [1] + N
## WARNING: difference with sam2paf.js : we add and substract nn
## from match and blen to agree with the output SAM file
## generated by minimap2
# The 12 compulsary fields to have a valid PAF format
a = [
t [0],
qlen,
qs,
qe,
"-" if flag & 16 else "+",
t [2],
tlen,
ts,
te,
match + nn,
blen - nn,
t [4],
]
# cast to string and save in file
a = [str (x) for x in a]
# What extra fields do we want to add ?
# original fields found in the SAM file ?
if extra_fields == "SAM" and len (t) > 11:
fout.write ("\t".join (a) + "\t" + "\t".join (t [11:]) + "\tcg:Z:{}\n".format (Zacc))
elif extra_fields == "summary":
fout.write ("\t".join (a) + "\t" + "\t".join (extra) + "\n")
elif extra_fields is None:
fout.write ("\t".join (a) + "\n")
self.skipped = skipped
logging.info (f"Sueccessfuly Done in {self.outfile}")
class Alignment:
def __init__(self, in_r_start, in_r_end, in_q_start, in_q_end, in_cigar, in_strand, in_num_matches, in_aln_len):
self.r_start = int (in_r_start) + 1
self.r_end = int (in_r_end)
self.q_start = int (in_q_start) + 1
self.q_end = int (in_q_end)
self.cigar = in_cigar
self.strand = in_strand
self.num_matches = int (in_num_matches)
self.aln_len = int (in_aln_len)
self.parsed_cigar = []
self._parse_cigar ()
if self.strand == "-":
# self.parsed_cigar = self.parsed_cigar [::-1]
self.q_start, self.q_end = self.q_end, self.q_start
def _parse_cigar (self):
"""Given a CIGAR string, create a list of with each CIGAR operation as its own element."""
cigar_chars = {
'M',
'I',
'D',
'N',
'S',
'H',
'P',
'=',
'X'
}
this_field = ''
for char in self.cigar:
this_field += char
if char in cigar_chars:
self.parsed_cigar.append (this_field)
this_field = ''
def write_delta (in_alns, in_r_lens, in_q_lens, outfile):
with open (outfile, 'w') as f:
f.write ('file1 file2\n')
f.write ('NUCMER\n')
# Iterate over each reference-query header pair
for r_header in in_alns.keys ():
for q_header in in_alns [r_header].keys ():
f.write ('>% s % s % r % r\n' % (r_header, q_header, in_r_lens [r_header], in_q_lens [q_header]))
for z in in_alns [r_header][q_header]:
f.write ('% r % r % r % r % r % r % r\n' % (
z.r_start,
z.r_end,
z.q_start,
z.q_end,
z.aln_len - z.num_matches,
z.aln_len - z.num_matches,
0
))
# Continue with the cigar string
offsets = []
cigar = z.parsed_cigar
if cigar [0][-1] == 'S' or cigar [0][-1] == 'H':
cigar = cigar [1:-1]
else:
cigar = cigar [:-1]
counter = 1
for code in cigar:
if code [-1] == 'M':
counter += int (code [:-1])
elif code [-1] == 'D':
offsets.append (counter)
num_I = int (code [:-1])
for i in range (1, num_I):
offsets.append (1)
counter = 1
elif code [-1] == 'I':
offsets.append (-1*counter)
num_I = int (code [:-1])
for i in range (1, num_I):
offsets.append (-1)
counter = 1
else:
raise ValueError ('Unexpected CIGAR code')
offsets.append (0)
offsets = [str (a) for a in offsets]
f.write ('\n'.join (offsets) + '\n')
logging.info (f"Sueccessfuly Done in {outfile}")
class PAF2DELTA:
def __init__(self, infile, outfile, line_total):
self.infile = infile
self.outfile = outfile
self.line_total = line_total
def convert (self):
# parser = argparse.ArgumentParser (description="Convert a PAF file to a nucmer delta file.\nPAF file must be created with a CIGAR string '-c' Minimap2 parameter")
# parser.add_argument ("paf_file", metavar="<alns.paf>", type=str, help="PAF file to convert (gziped file allowed).")
# args = parser.parse_args ()
paf_file = self.infile
alns = dict ()
# Dictionaries to store reference and query sequence lengths
r_chr_lens = dict ()
q_chr_lens = dict ()
if paf_file [-3:] == ".gz":
f = gzip.open (paf_file)
else:
f = open (paf_file, 'r')
for line in track (f, description="[bold green] Reading paf...", total=self.line_total):
if not isinstance (line, str):
fields = line.decode ("utf-8").split ('\t')
else:
fields = line.split ('\t')
# Get the reference/query sequence lengths
r_header = fields [5]
q_header = fields [0]
if r_header not in r_chr_lens:
r_chr_lens [r_header] = int (fields [6])
if q_header not in q_chr_lens:
q_chr_lens [q_header] = int (fields [1])
# Get the rest of the info and instantiate the Alignment object
cigar_string = ''
for i in fields [12:]:
if i.startswith ('cg:'):
cigar_string = i.split (":")[2]
if not cigar_string:
raise ValueError ("PAF file must contain a CIGAR string. Use 'minimap2 -c'")
x = Alignment (
fields [7],
fields [8],
fields [2],
fields [3],
cigar_string,
fields [4],
fields [9],
fields [10]
)
# Add the alignments to the nested dictionary (first key=reference header, second key=query header)
if r_header not in alns:
alns [r_header] = defaultdict (list)
alns [r_header][q_header].append (x)
f.close ()
with console.status ("[bold green] Writing delta...") as status:
write_delta (alns, r_chr_lens, q_chr_lens, paf_file + '.delta')
if __name__ == "__main__":
args, pg = get_args ()
cl = pg + ' ' + ' '.join (f'--{k} {v}' for k, v in vars (args).items ())
output_sam = args.out + ".sam" ## unsorted
Header = Header (pg, "0.1", cl)
prefix = Prefix (args.prefix [0], args.prefix [1]) if args.prefix else Prefix (None, None)
maf = MAF (filename=args.maf, outfile=output_sam, header=Header, prefix=prefix)
line_total = maf.to_sam ()
output_paf = args.out + ".paf" ## unsorted
sam2paf = SAM2PAF (output_sam, output_paf, line_total)
sam2paf.convert ()
output_delta = args.out + ".delta"
paf2delta = PAF2DELTA (output_paf, output_delta, line_total)
paf2delta.convert ()原理
除了 CIGAR 解析那里麻烦点，其他看一眼就懂了
TODO
- 选择只输出指定的格式
- 排序 SAM 和 PAF
- 分染色体多线程
当然，大概率是不会再优化了，实际上也就我一个人用，自娱自乐罢了，足矣。