Sakyamuni Buddha was born in the land of the India as a human. He was awakened to his original nature through ascetic sufferings and practice and attained Buddhahood. He expounded his teachings of the Dharma to the beings in the human world on the basis of the doctrine of cause and conditions and transmigration. He departed this world after having revealed the truth of the universe to the world through his disciples for over forty-five years. After the passing of Sakyamuni Buddha, various kinds of Buddhist sects have appeared in the name of Buddha, various kinds of Buddhist sects have appeared in the name of Buddhism in this world. They told us the truth of the world and ways of the seekers of enlightenment, then, disappeared. Great Monk Jajae Manhyon who renounced a worldly life to become a practitioner, due to his questions on life and death in his twenties, entered a Samadhi, a high level of meditative concentration in selflessness through recitation of Buddha's name. He has clearly seen the ways of the Threefold Great Thousand World Systems and their movements and is now sharing this with others.

"The reward of the Buddhas are absolutely in existence. Buddha in the Dharma Body abides in the absolute realm as an immeasurable light that shines all over the world. The pure Dharma Vairochana Buddha is the Dharma Body of Sakyamuni. Buddha embraces all the pure Dharma bodies of all Buddhas in the body."

The Buddha that Monk Jajae Manhyon has revealed is one that is a being that has the three bodies, namely, the Dharma Body, the Reward Body and the Transformation Body. The Dharma Body is the origin of the Reward and Transformation Bodies. The Buddha Body made of immeasurable light is the essential element to become a Buddha. Monk Jajae Manhyon says that there must be a decision made by Sakyamuni Buddha for a Buddha to be born in this Saha-world.

"I see immeasurable light - a clear, bright and lucid light - during my practice. Then I pass another gateway, meet with many Buddhas in deep samadhi who have come to see me and listen to their Dharma talks directly. I listen to the Dharma of Buddhas, receive their guidance on my practice and as I practice as a Buddha, I enter deeper into samadhi."

Even to Buddhist disciples, the remarks that the Great Monk has made are not usual. It is because books written by past Great Master Monks or those of the Seon Sect seldom speak of these things. At first glance, one with no connection with Buddhism will have difficulty understanding this state which Great Monk Jajae Manhyon refers to.

"It was January 2001. While practicing chanting the sacred name of a Buddha he entered the samadhi. Buddha said to him :"

The Buddha does neither abide outside nor inside of the mind.
The Buddha abides in an 'Absolute Realm in selflessness.'
The mind does not have an inside or on outside.
As it neither goes nor comes and does not move,
Buddha abides in that way, too.
Only humans say whether it exists or it does not exist,
but the Buddhas abide in an 'Absolute Realm in Selflessness'.

At that time, he realized the fact that he himself had accomplished hardship in a past lifetime and that he had been Ananda, one of the ten noble disciples who attended to the Buddha at his side at the time of the Spirit Mountain of Sakyamuni Buddha at his side at the time of the Spirit Mountain of Sakyamuni Buddha. The Great Monk heard and experienced much regarding the Realms of Bodhisattvas and Buddhas in the state of deep samadhi that he reached through recitation of Buddha’s name. The state of his being able to see Sakyamuni Buddha supervising the Threefold Great Thousand World Systems and various stages of Bodhisattvas was not been realized in a day. He attained Buddhahood because he already broke through his Hwadu a long time ago. He chose to practice meditation by chanting Buddha’s name with a thirst for seeking the truth of the universe and also practiced recitation.

In the book <<The 21st Century Buddha’s Message>>, published in 2005, the Great Monk revealed the song of bliss that he had composed in samadhi in selflessness in 2002.

Empty, empty,
the Threefold Great Thousand World Systems
are empty.
The empty realm
where
no dust
and no particle
exists.
Clear, clean,
and pureness itself.
Bliss, bliss,
it is bliss

At that time, Great Monk Jajae Manhyon passed through samadhi and attained his Buddhahood approved by the Buddha.

From ECOVIEW 2008-4

 

'Buddhism ' 카테고리의 다른 글

Yongsan Buddhism  (0) 2012.12.24
Posted by 옥탑방람보
,

Yongsan Buddhism

Buddhism 2012. 12. 24. 17:36
Receiving approval of the Dharma from the Buddha in samadhi, the Great Monk Jajae Manhyon rose from his seat of a practitioner and made up his mind to propagate the true Dharma of the Buddha across the world. Having renounced a worldly life to become a monk of the Jogye Buddhist Order, awakening his original nature through Hwadu - a head phrase for meditation investigation, the Great Monk established Yongsan Buddhism. This is seen as the correct method of becoming a Buddha based on his experience of receiving empowerment from the Buddha through recitation of Buddha's name and of attaining Buddhahood.

"In order to solve his doubts on the truth of birth and death and on the world after death, he investigated Hwadu, then changed his practice method to recitation, entered samadhi of deep recitation and eventually attained samadhi. He has seen the real character behind the Dharma realm of the universe by entering into a deep samadhi and seeing the Buddhas and Bodhisattvas abiding in the Absolute Realm as well as the existence of Hell, the deva realm and the Westem Paradise."

The Great Monk who not only obtained the answer to his lifetime Hwadu, but has also seen the subtle world of the Absolute Realm over the realm of emptiness through recitation of Buddha's name, has once again realized the limit of enlightenment by one's own efforts. He himself understood a new method of going beyond the limit of the practicing method of Seon Buddhism that has been taking the lead of Buddhism on this land (South Korea) for over 1000 years. His goal is to propagate this new method to all beings he encounters.

"Reciting the sacred name of Sakyamuni Buddha who perfectly possesses not only wisdom, compassion and blessed virtues, but also the Three Bodies of the Dharma, Reward and Transformation Bodies and exercises omnipotent universal ability is the best method guaranteeing rebirth in the heaven of the deva realm and the Western Paradise Pure Land."

The Great Monk established the Yongsan Buddhism Foundation in 2007. He also started to draw up the basic doctrines and code for faith and practice and systemized them.

"Human beings exist in the six realms in life and death. It is true that human beings commit countless karmic sin and exist in the Three Evil Destinies such as Hell, the animal realm, and others. They do not escape from the Three Poisons of greed, anger and ignorance. Yongsan Buddhism has shown how human beings can escape from the Three Poisons through a pure practice method and at the same time save them so that they will not fall down into the Three Evil Destinies."

Further, the important doctrines of the Yongsan Buddhism are to perform one's filial piety to their parents, respect thdir teacher, love their nation and practice loyalty and filial piety as part of their life. As a rootless tree cannot grow on the land, all living beings must observe fundamental manners and repay one's obligations and also have love toward their nation.

Besides these, Yongsan Buddhism stands on the basic doctrines of strictly observing precepts, repenting one's karmic sins in the past and loving our neighbors with endless compassion. The teachings of the Great Monk includes the idea that one must cultivate a pure mind through repentence and become a great liberated man caring for others before yourself.

"We must take refuge in the Buddha and his Dharma. We must also practice the Ten Virtues and actions fof a Bodhisattva completely. We must study the Mahayana Sutras, escape from the cycle of life and death as a recitation practitioner chanting Sakyamuni Buddha and live a life to be rebom in the Western Pure Land. The Western Paradise Pure Land exists. Hell also exists."

The Grest Monk Jajae Manhyon attaches more importance to practice than speech and exphasizes that studying scriptures steadily together with practice and establishing a systematic knowledge of the realm of the Buddhism has are the fundamentals of practice. In this connection, Yongsan Buddhism has taken the Sutras, like the Agama Sutra, the Ksitigarbha Sutra, the Diamond Sutra, the Lotus Sutra and the Avatamsaka Sutra as the basic Sutras. Whenever he has an opportunity, he stresses that practioners should not ignore the study of Sutras.

 

'Buddhism ' 카테고리의 다른 글

The Great Monk Jajae Manhyon  (0) 2012.12.24
Posted by 옥탑방람보
,
How do I work with multiple files at the same time?


vi allows for multiple files to be open at the same time. Unlike many editors, you only see one file at a time. If you start vi with multiple files on the command line they'll all be opened up.
You'll start out in the first file, and you can move to the next file by typing :n.
If you've made changes to the current file that you don't want to keep, you can go on by using :n!. Note that this will discard any changes that you've made.
If you want to save, you need to use :w first.

 

Posted by 옥탑방람보
,
Regular expressions appear to be rapidly gaining in popularity among VIM users as they discover the sheer programming power that regular expressions can provide. Historically, regular expressions have been associated with the UNIX platform and scripting languages like Perl (Practical Extraction and Report Language).

The syntax in VIM is slightly different then in Perl, but is pretty close. This makes Perl regular expression examples relevant to VIM users.

Softpanorama RegEx page contain basic information about regular expressions. I would like to stress that Vim's regexp implementation is reasonably close to Perl's and skills are transferable. Among the differences between Perl and Vim we can note:

Some meta characters are different (in yellow)

# Matching # Matching
. any character except new line
\s whitespace character \S non-whitespace character
\d digit \D non-digit
\x hex digit \X non-hex digit
\o octal digit \O non-octal digit
\h head of word character (a,b,c...z,A,B,C...Z and _) \H non-head of word character
\p printable character \P like \p, but excluding digits
\w word character \W non-word character
\a alphabetic character \A non-alphabetic character
\l lowercase character \L non-lowercase character
\u uppercase character \U non-uppercase character

Many special characters need to be escaped. For example:
\+ matches 1 or more of the preceding characters...
\{n,m} matches from n to m of the preceding characters...
\= is used instead of \? (matches 0 or 1 more of the preceding characters)

Quantifier Description

* matches 0 or more of the preceding characters, ranges or metacharacters .* matches everything including empty line
\+ matches 1 or more of the preceding characters...
\= matches 0 or 1 more of the preceding characters...
\{n,m} matches from n to m of the preceding characters...
\{n} matches exactly n times of the preceding characters...
\{,m} matches at most m (from 0 to m) of the preceding characters...
\{n,} matches at least n of of the preceding characters...


Alternatives (OR) need to be escaped

Using "\
" you can combine several expressions into one which matches any of its components. The first one matched will be used.

\(Date:\
Subject:\
From:\)\(\s.*\)

will parse various mail headings and their contents into \1 and \2, respectively. The thing to remember about VIM alternation that it is not greedy. It won't search for the longest possible match, it will use the first that matched. That means that the order of the items in the alternation is important!

Tip 3: Quick mapping to put \(\) in your pattern string
cmap ;\ \(\)

Non-greed modifiers are different and more obscure then in Perl. Perl allows you to convert any quantifier into a non-greedy version by adding an extra ? after it. So *? is a non-greedy version of a special character *


Quantifier Description
\{-} matches 0 or more of the preceding atom, as few as possible
\{-n,m} matches 1 or more of the preceding characters...
\{-n,} matches at lease or more of the preceding characters...
\{-,m} matches 1 or more of the preceding characters...

Replacement rules are different

You can group parts of the pattern expression enclosing them with "\(" and "\)" and refer to them inside the replacement pattern by their special number \1, \2 ... \9. Typical example is swapping first two words of the line:

s:\(\w\+\)\(\s\+\)\(\w\+\):\3\2\1:


where \1 holds the first word, \2 - any number of spaces or tabs in between and \3 - the second word. How to decide what number holds what pair of \(\) ? - count opening "\(" from the left.

Replacement part of the S&R has its own special characters which we are going to use to fix grammar:



# Meaning # Meaning
& the whole matched pattern \L the following characters are made lowercase
\0 the whole matched pattern \U the following characters are made uppercase
\1 the matched pattern in the first pair of \(\) \E end of \U and \L
\2 the matched pattern in the second pair of \(\) \e end of \U and \L
... ... \r split line in two at this point
\9 the matched pattern in the ninth pair of \(\) \l next character made lowercase
~ the previous substitute string \u next character made uppercase


Now the full S&R to correct non-capital words at the beginning of the sentences looks like

s:\([.!?]\)\s\+\([a-z]\):\1 \u\2:g

We have corrected our grammar and as an extra job we replaced variable number of spaces between punctuation and the first letter of the next sentence with exactly two spaces.

Perl supports a more options that can be appended to the regexp, or even embedded in it.

You can also embed variable names in a Perl regular expression. Perl replaces the name with its value; this is called "variable interpolation".

The most common task is to make replacements in a text following some certain rules using VIM search and replace command (S&R) :s(substitute). For example here is how globally replace all occurrences of vi with VIM.


%s/1999/2003/g

This is a very common idiom in vi/vim. Like in Perl you can also use several modifiers

c Confirm each substitution
g Replace all occurrences in the line (without g - only first).
i Ignore case for the pattern.
I Don't ignore case for the pattern

 

Posted by 옥탑방람보
,

reference site: http://samtools.sourceforge.net/
manual : http://samtools.sourceforge.net/SAM1.pdf

The Samtools is an essential tool to handle files with sam (bam) format.

99 (decimal) -> 1100011 (binary) : paired, proper pair, mapped, forward, mate reverse .... (Watch the number one by one by reverse order)

'Bioinformatics > Biological data analysis' 카테고리의 다른 글

[TMAP]TMAP설치  (0) 2013.02.04
[samtools] SAMtools FAQ  (0) 2012.12.24
[bam] MD tag and cigar  (0) 2012.12.24
[python] a method to reduce ID length using ascii value  (0) 2012.12.24
[python] decimal to binary  (0) 2012.12.24
Posted by 옥탑방람보
,

FROM: http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ

About SAMtools

How to convert SAM to BAM?
If your SAM file has header @SQ lines, you may get BAM by:
samtools view -bS aln.sam > aln.bam
If not, you need to have your reference file ref.fa and then do this:
samtools faidx ref.fa
samtools view -bt ref.fa.fai aln.sam > aln.bam
The second method also works if your SAM file has @SQ lines. After conversion, you would probably like to sort and index the alignment to enable fast random access:
samtools sort aln.bam aln-sorted
samtools index aln-sorted.bam

I want to call SNPs and short indels.
For a short answer, do this:
samtools pileup -vcf ref.fa aln.bam | tee raw.txt | samtools.pl varFilter -D100 > flt.txt
awk '($3=="*" && $6>=50)||($3!="*" && $6>=20)' flt.txt > final.txt
For a long answer, see SAM protocol. Please always remember to set the maximum depth (-D) in filtering.

I want to call SNPs from one chromosome only.
Index your alignment with the `index' command and:
samtools view -u aln.bam chr10 | samtools pileup -vcf ref.fa - > chr10.raw.txt
Please read [http://samtools.sourceforge.net/pipe.shtml this page] for more information.

The integer FLAG field is not friendly to eyes.
You may get string FLAG by:
samtools view -X aln.bam | less -S
For more information, please check out:
samtools view -?


Pileup output.

This is explained in the [http://samtools.sourceforge.net/samtools.shtml manual page]. Or briefly (when you invoke pileup with the -c option):
1. reference sequence name
2. reference coordinate
3. reference base, or `*' for an indel line
4. genotype where heterozygotes are encoded in the [http://biocorp.ca/IUB.php IUB code]: M=A/C, R=A/G, W=A/T, S=C/G, Y=C/T and K=G/T; indels are indicated by, for example, */+A, -A/* or +CC/-C. There is no difference between */+A or +A/*.
5. Phred-scaled likelihood that the genotype is wrong, which is also called `consensus quality'.
6. Phred-scaled likelihood that the genotype is identical to the reference, which is also called `SNP quality'. Suppose the reference base is A and in alignment we see 17 G and 3 A. We will get a low consensus quality because it is difficult to distinguish an A/G heterozygote from a G/G homozygote. We will get a high SNP quality, though, because the evidence of a SNP is very strong.
7. [http://en.wikipedia.org/wiki/Root_mean_square root mean square] (RMS) mapping quality
8. # reads covering the position
9. read bases at a SNP line (check the manual page for more information); the 1st indel allele otherwise
10. base quality at a SNP line; the 2nd indel allele otherwise
11. indel line only: # reads directly supporting the 1st indel allele
12. indel line only: # reads directly supporting the 2nd indel allele
13. indel line only: # reads supporting a third indel allele
If pileup is invoked without `-c', indel lines and columns between 3 and 7 inclusive will not be outputted.

I see `*' in the pileup sequence column. What are they?
A star at the sequence column represents a deletion. It is a place holder to make sure the number of bases at that column matches the read depth column. Simply ignore `*' if you do not use this information.


Does samtools generate the consensus sequence like Maq?

Yes. Try this:
samtools pileup -cf ref.fa aln.bam | samtools.pl pileup2fq -D100 > cns.fastq
Again, remember to set -D according to your read depth. Note that pileup2fq applies fewer filters in comparison to varFilter, and you may see tiny inconsistency between the two outputs.

I want to get `unique' alignments from SAM/BAM.
We prefer to say an alignment is `reliable' rather than `unique' as `uniqueness' is not well defined in general cases. You can get reliable alignments by setting a threshold on mapping quality:
samtools view -bq 1 aln.bam > aln-reliable.bam
You may want to set a more stringent threshold to get more reliable alignments.

In repetitive regions, SAMtools call all bases as 'A' although there are no 'A' bases in reads.
This is due to a floating underflow in the MAQ SNP calling model used by default and only happens in repetitive regions. These calls are always filtered out. However, if you are uncomfortable with this, you may use the simplified SOAPsnp model with:
samtools -avcf ref.fa aln.bam > raw.txt
The MAQ model and SOAPsnp model usually deliver very similar SNP calls.

How are SNPs and indels called and filtered by SAMtools?
By default, SNPs are called with a Bayesian model identical to the one used in MAQ. A simplified SOAPsnp model is implemented, too. Indels are called with a simple Bayesian model. The caller does local realignment to recover indels that occur at the end of a read but appear to be contiguous mismatches. For an example, see [http://samtools.sourceforge.net/images/seq2-156.png this picture].

The varFilter filters SNPs/indels in the following order:
* d: low depth
* D: high depth
* W: too many SNPs in a window (SNP only)
* G: close to a high-quality indel (SNP only)
* Q: low root-mean-square (RMS) mapping quality (SNP only)
* g: close to another indel with more evidence (indel only)
The first letter indicates the reason why SNPs/indels are filtered when you invoke varFilter with the `-p' option. A SNP/indel filtered by a rule higher in the list will not be tested against other rules.

'Bioinformatics > Biological data analysis' 카테고리의 다른 글

[TMAP]TMAP설치  (0) 2013.02.04
[samtools] samtools sam bam  (0) 2012.12.24
[bam] MD tag and cigar  (0) 2012.12.24
[python] a method to reduce ID length using ascii value  (0) 2012.12.24
[python] decimal to binary  (0) 2012.12.24
Posted by 옥탑방람보
,
10A5^AC6

REF:         ATCGTAGCTAATTTGGACATCGGT
READ:        ATCGTAGCTATTTTGG--ATCGGT
MD TAG:      10        A5   ^AC6
CIGAR:       16M             2D6M
READ:        atcGTAGCTATTTTGGATA..GGT (ATCGTAGCTATTTTGGATAAAGGT)
MD TAG:      17               C1TC3
CIGAR:       3S 16M             2N3M
READ:        ATCGTAGCTAATTTGGACATCGGT (ATCGTGGAGCTAATTTGGACATCGGT)
CIGAR:       5M   2I19M




MD TAG
The MD eld aims to achieve SNP/indel calling without looking at the reference. For example, a string `10A5^AC6' means from the leftmost reference base in the alignment, there are 10 matches followed by an A on the reference which is di erent from the aligned read base; the next 5 reference bases are matches followed by a 2bp deletion from the reference; the deleted sequence is AC; the last 6 bases are matches. The MD eld ought to match the CIGAR string.

CIGAR

M     alignment match (can be a sequence match or mismatch)
I     insertion to the reference
D     deletion from the reference
N     skipped region from the reference
S     soft clipping (clipped sequences present in SEQ)
H     hard clipping (clipped sequences NOT present in SEQ)
P     padding (silent deletion from padded reference)
=     sequence match
X     sequence mismatch

H can only be present as the rst and/or last operation.
S may only have H operations between them and the ends of the CIGAR string.
For mRNA-to-genome alignment, an N operation represents an intron. For other types of alignments, the interpretation of N is not de ned.
Sum of lengths of the M/I/S/=/X operations ought to equal the length of SEQ.

 

Posted by 옥탑방람보
,
def asciiID(i,one,two,three,four,five):
   if one >= len(chrtb): one=0;two+=1
   if two >= len(chrtb): two=0;three+=1
   if three >= len(chrtb): three=0;four+=1
   if four >= len(chrtb): four=0;five+=1
   pk = chrtb[five]+chrtb[four]+chrtb[three]+chrtb[two]+chrtb[one]
   one+=1
   return pk,one,two,three,four,five

chrtb=[]
for ch in range(33,127): chrtb.append( chr(ch) )
one=0;two=0;three=0;four=0;five=0

for inputInteger in range(1,3000000000):
   pk,one,two,three,four,five = asciiID(inputInteger,one,two,three,four,five)
   print inputInteger,pk


When a ID is formatted with sequencial interger, it is able to convert to characters based on ascii code. Only 5 characters are able to present 7.3 billon IDs (33~126: 94, 94*94*94*94*94).

 

Posted by 옥탑방람보
,
def decimalToBinary(i):
   b = ''
   while i > 0:
      j = i & 1
      b = str(j) + b
      i >>= 1
   return b

 

Posted by 옥탑방람보
,
def subsets(x):  
    if x == []:
        return [[]]
    else:
        s = [x]
        for elem in x:
            tmp = x[:]
            tmp.remove(elem)
            new_sub = subsets(tmp)
            for y in new_sub:  # <-- can't just make it a set(), because lists aren't hashable.
                if y not in s:
                    s.append(y)
        return s
>>> s = [1,2,3]
>>> subsets(s)
[[1, 2, 3], [2, 3], [3], [], [2], [1, 3], [1], [1, 2]]


from http://www.daniweb.com/forums/thread89048.html

 

Posted by 옥탑방람보
,