Velocity Reviews > How does .rjust() work and why it places characters relative toprevious one, not to first character - placed most to left - or to left sideof screen?

# How does .rjust() work and why it places characters relative toprevious one, not to first character - placed most to left - or to left sideof screen?

crispy
Guest
Posts: n/a

 08-19-2012
I have an example:

def pairwiseScore(seqA, seqB):

prev = -1
score = 0
length = len(seqA)
similarity = []
relative_similarity = []

for x in xrange(length):

if seqA[x] == seqB[x]:
if (x >= 1) and (seqA[x - 1] == seqB[x - 1]):
score += 3
similarity.append(x)
else:
score += 1
similarity.append(x)
else:
score -= 1

for x in similarity:

relative_similarity.append(x - prev)
prev = x

return ''.join((seqA, '\n', ''.join(['|'.rjust(x) for x in relative_similarity]), '\n', seqB, '\n', 'Score: ', str(score)))

print pairwiseScore("ATTCGT", "ATCTAT"), '\n', '\n', pairwiseScore("GATAAATCTGGTCT", "CATTCATCATGCAA"), '\n', '\n', pairwiseScore('AGCG', 'ATCG'), '\n', '\n', pairwiseScore('ATCG', 'ATCG')

which returns:

ATTCGT
|| |
ATCTAT
Score: 2

GATAAATCTGGTCT
|| ||| |
CATTCATCATGCAA
Score: 4

AGCG
| ||
ATCG
Score: 4

ATCG
||||
ATCG
Score: 10

But i created this with some help from one person. Earlier, this code was devoided of these few lines:

prev = -1
relative_similarity = []

for x in similarity:

relative_similarity.append(x - prev)
prev = x

The method looked liek this:

def pairwiseScore(seqA, seqB):

score = 0
length = len(seqA)
similarity = []

for x in xrange(length):

if seqA[x] == seqB[x]:
if (x >= 1) and (seqA[x - 1] == seqB[x - 1]):
score += 3
similarity.append(x)
else:
score += 1
similarity.append(x)
else:
score -= 1

return ''.join((seqA, '\n', ''.join(['|'.rjust(x) for x in similarity]), '\n', seqB, '\n', 'Score: ', str(score)))

and produced this output:

ATTCGT
|| |
ATCTAT
Score: 2

GATAAATCTGGTCT
| | | | | |
CATTCATCATGCAA
Score: 4

AGCG
| | |
ATCG
Score: 4

ATCG
|| | |
ATCG
Score: 10

So I have guessed, that characters processed by .rjust() function, are placed in output, relative to previous ones - NOT to first, most to left placed, character.
Why it works like that? What builtn-in function can format output, to make every character be placed as i need - relative to the first character, placed most to left side of screen.

Cheers

crispy
Guest
Posts: n/a

 08-19-2012

Dave Angel
Guest
Posts: n/a

 08-19-2012
On 08/19/2012 12:25 PM, crispy wrote:
> <SNIP>
> So I have guessed, that characters processed by .rjust() function, are placed in output, relative to previous ones - NOT to first, most to left placed, character.

rjust() does not print to the console, it just produces a string. So if
you want to know how it works, you need to either read about it, or
experiment with it.

Try help("".rjust) to see a simple description of it. (If you're
not familiar with the interactive interpreter's help() function, you owe
it to yourself to learn it).

Playing with it:

print "abcd".rjust(8, "-") produces ----abcd

for i in range(5): print "a".rjust(i, "-")
produces:

a
a
-a
--a
---a

In each case, the number of characters produced is no larger than i. No
consideration is made to other strings outside of the literal passed
into the method.

> Why it works like that?

In your code, you have the rjust() method inside a loop, inside a join,
inside a print. it makes a nice, impressive single line, but clearly
you don't completely understand what the pieces are, nor how they work
together. Since the join is combining (concatenating) strings that are
each being produced by rjust(), it's the join() that's making this look
"relative" to you.

> What builtn-in function can format output, to make every character be placed as i need - relative to the first character, placed most to left side of screen.

If you want to randomly place characters on the screen, you either want
a curses-like package, or a gui. i suspect that's not at all what you want.

if you want to randomly change characters in a pre-existing string,
which will then be printed to the console, then I could suggest an
approach (untested)

res = [" "] * length
for column in similarity:
res[column] = "|"
res = "".join(res)

--

DaveA

Dennis Lee Bieber
Guest
Posts: n/a

 08-19-2012
On Sun, 19 Aug 2012 09:25:03 -0700 (PDT), crispy <(E-Mail Removed)>
declaimed the following in gmane.comp.python.general:

<snip>

> So I have guessed, that characters processed by .rjust() function, are placed in output, relative to previous ones - NOT to first, most to left placed, character.
> Why it works like that? What builtn-in function can format output, to make every character be placed as i need - relative to the first character, placed most to left side of screen.
>

str.rjust(x) will right justify "str" in a field of "x" width. This
is done by adding enough spaces to the left to make the length of the
result string (spaces + "str") equal to the specified width. The method
works on strings, not on output lines.

Make sure your display is using fixed width fonts, not variable.

>>> strs = ["1", "to", "two", "long term", "short"]
>>> for s in strs:

.... print s.rjust(, s.rjust(10), s.ljust(, s.ljust(10),
s.center(10)
....
1 1 1 1 1
to to to to to
two two two two two
long term long term long term long term long term
short short short short short

(Note that xjust doesn't trim a long string, which is why the line of
"long term" does not align)

>>> for s in strs:

.... print s[:8].rjust(, s.rjust(10), s[:8].ljust(, s.ljust(10),
s.center(10)
....
1 1 1 1 1
to to to to to
two two two two two
long ter long term long ter long term long term
short short short short short

In the above samples, I have specified an output line containing 5
"fields" of sizes 8, 10, 8, 10, 10, and using right, right, left, left,
centered justification.

If you need to layout a whole line, where some positions are being
set based on indexes, you need to do that as one array, not a collection
of substrings.

>>> match = [2, 7, 9, 13, 14, 24, 4]

dummy data, note that order doesn't matter

>>> buffer = [" "] * max(match)

build empty array sized to needed output

>>> print repr(buffer)

[' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', '
', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ']
>>> for m in match:

.... buffer[m - 1] = "|"
....
replace space with pipe for each position in match (match is
presumed to count from 1, but Python indexes from 0)

>>> print repr(buffer)

[' ', '|', ' ', '|', ' ', ' ', '|', ' ', '|', ' ', ' ', ' ', '|', '|', '
', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', '|']
>>> output = "".join(buffer)

join the position contents together to make the final output line

>>> print repr(output)

' | | | | || |'
--
Wulfraed Dennis Lee Bieber AF6VN
http://www.velocityreviews.com/forums/(E-Mail Removed) HTTP://wlfraed.home.netcom.com/

crispy
Guest
Posts: n/a

 08-19-2012
W dniu niedziela, 19 sierpnia 2012 19:31:30 UTC+2 użytkownik Dave Angel napisał:
> On 08/19/2012 12:25 PM, crispy wrote:
>
> > <SNIP>

>
> > So I have guessed, that characters processed by .rjust() function, are placed in output, relative to previous ones - NOT to first, most to left placed, character.

>
>
>
> rjust() does not print to the console, it just produces a string. So if
>
> you want to know how it works, you need to either read about it, or
>
> experiment with it.
>
>
>
> Try help("".rjust) to see a simple description of it. (If you're
>
> not familiar with the interactive interpreter's help() function, you owe
>
> it to yourself to learn it).
>
>
>
> Playing with it:
>
>
>
> print "abcd".rjust(8, "-") produces ----abcd
>
>
>
> for i in range(5): print "a".rjust(i, "-")
>
> produces:
>
>
>
> a
>
> a
>
> -a
>
> --a
>
> ---a
>
>
>
> In each case, the number of characters produced is no larger than i. No
>
> consideration is made to other strings outside of the literal passed
>
> into the method.
>
>
>
>
>
> > Why it works like that?

>
>
>
> In your code, you have the rjust() method inside a loop, inside a join,
>
> inside a print. it makes a nice, impressive single line, but clearly
>
> you don't completely understand what the pieces are, nor how they work
>
> together. Since the join is combining (concatenating) strings that are
>
> each being produced by rjust(), it's the join() that's making this look
>
> "relative" to you.
>
>
>
>
>
> > What builtn-in function can format output, to make every character be placed as i need - relative to the first character, placed most to left sideof screen.

>
>
>
> If you want to randomly place characters on the screen, you either want
>
> a curses-like package, or a gui. i suspect that's not at all what you want.
>
>
>
> if you want to randomly change characters in a pre-existing string,
>
> which will then be printed to the console, then I could suggest an
>
> approach (untested)
>
>
>
> res = [" "] * length
>
> for column in similarity:
>
> res[column] = "|"
>
> res = "".join(res)
>
>
>
>
>
>
>
> --
>
>
>
> DaveA

Thanks, i've finally came to solution.

def pairwiseScore(seqA, seqB):

score = 0
bars = [str(' ') for x in seqA] #create a list filled with number of spaces equal to length of seqA string. It could be also seqB, because both are meant to have same length
length = len(seqA)
similarity = []

for x in xrange(length):

if seqA[x] == seqB[x]: #check if for every index 'x', corresponding character is same in both seqA and seqB strings
if (x >= 1) and (seqA[x - 1] == seqB[x - 1]): #if 'x' is greater than or equal to 1 and characters under the previous index, were same in both seqA and seqB strings, do..
score += 3
similarity.append(x)
else:
score += 1
similarity.append(x)
else:
score -= 1

for x in similarity:
bars[x] = '|' #for every index 'x' in 'bars' list, replace space with '|' (pipe/vertical bar) character

return ''.join((seqA, '\n', ''.join(bars), '\n', seqB, '\n', 'Score: ',str(score)))

print pairwiseScore("ATTCGT", "ATCTAT"), '\n', '\n', pairwiseScore("GATAAATCTGGTCT", "CATTCATCATGCAA"), '\n', '\n', pairwiseScore('AGCG', 'ATCG'), '\n', '\n', pairwiseScore('ATCG', 'ATCG')

crispy
Guest
Posts: n/a

 08-19-2012
W dniu niedziela, 19 sierpnia 2012 19:31:30 UTC+2 użytkownik Dave Angel napisał:
> On 08/19/2012 12:25 PM, crispy wrote:
>
> > <SNIP>

>
> > So I have guessed, that characters processed by .rjust() function, are placed in output, relative to previous ones - NOT to first, most to left placed, character.

>
>
>
> rjust() does not print to the console, it just produces a string. So if
>
> you want to know how it works, you need to either read about it, or
>
> experiment with it.
>
>
>
> Try help("".rjust) to see a simple description of it. (If you're
>
> not familiar with the interactive interpreter's help() function, you owe
>
> it to yourself to learn it).
>
>
>
> Playing with it:
>
>
>
> print "abcd".rjust(8, "-") produces ----abcd
>
>
>
> for i in range(5): print "a".rjust(i, "-")
>
> produces:
>
>
>
> a
>
> a
>
> -a
>
> --a
>
> ---a
>
>
>
> In each case, the number of characters produced is no larger than i. No
>
> consideration is made to other strings outside of the literal passed
>
> into the method.
>
>
>
>
>
> > Why it works like that?

>
>
>
> In your code, you have the rjust() method inside a loop, inside a join,
>
> inside a print. it makes a nice, impressive single line, but clearly
>
> you don't completely understand what the pieces are, nor how they work
>
> together. Since the join is combining (concatenating) strings that are
>
> each being produced by rjust(), it's the join() that's making this look
>
> "relative" to you.
>
>
>
>
>
> > What builtn-in function can format output, to make every character be placed as i need - relative to the first character, placed most to left sideof screen.

>
>
>
> If you want to randomly place characters on the screen, you either want
>
> a curses-like package, or a gui. i suspect that's not at all what you want.
>
>
>
> if you want to randomly change characters in a pre-existing string,
>
> which will then be printed to the console, then I could suggest an
>
> approach (untested)
>
>
>
> res = [" "] * length
>
> for column in similarity:
>
> res[column] = "|"
>
> res = "".join(res)
>
>
>
>
>
>
>
> --
>
>
>
> DaveA

Thanks, i've finally came to solution.

def pairwiseScore(seqA, seqB):

score = 0
bars = [str(' ') for x in seqA] #create a list filled with number of spaces equal to length of seqA string. It could be also seqB, because both are meant to have same length
length = len(seqA)
similarity = []

for x in xrange(length):

if seqA[x] == seqB[x]: #check if for every index 'x', corresponding character is same in both seqA and seqB strings
if (x >= 1) and (seqA[x - 1] == seqB[x - 1]): #if 'x' is greater than or equal to 1 and characters under the previous index, were same in both seqA and seqB strings, do..
score += 3
similarity.append(x)
else:
score += 1
similarity.append(x)
else:
score -= 1

for x in similarity:
bars[x] = '|' #for every index 'x' in 'bars' list, replace space with '|' (pipe/vertical bar) character

return ''.join((seqA, '\n', ''.join(bars), '\n', seqB, '\n', 'Score: ',str(score)))

print pairwiseScore("ATTCGT", "ATCTAT"), '\n', '\n', pairwiseScore("GATAAATCTGGTCT", "CATTCATCATGCAA"), '\n', '\n', pairwiseScore('AGCG', 'ATCG'), '\n', '\n', pairwiseScore('ATCG', 'ATCG')

Peter Otten
Guest
Posts: n/a

 08-20-2012
crispy wrote:

> Thanks, i've finally came to solution.
>
> Here it is -> http://codepad.org/Q70eGkO8
>
> def pairwiseScore(seqA, seqB):
>
> score = 0
> bars = [str(' ') for x in seqA] # ...
> length = len(seqA)
> similarity = []
>
> for x in xrange(length):
>
> if seqA[x] == seqB[x]: # ...
> if (x >= 1) and (seqA[x - 1] == seqB[x - 1]): # ...
> score += 3
> similarity.append(x)
> else:
> score += 1
> similarity.append(x)
> else:
> score -= 1
>
> for x in similarity:
> bars[x] = '|' # ...
>
> return ''.join((seqA, '\n', ''.join(bars), '\n', seqB, '\n', 'Score:

', str(score)))
>

Python has a function zip() that lets you iterate over multiple sequences

for i in xrange(len(a)):
x = a[i]
y = b[i]
...

you can write

for x, y in zip(a, b):
...

Also, you can build the bar list immediately and avoid the similarity list.

With these changes:

def pairwise_score(a, b):
score = 0
was_equal = False
bars = []
for x, y in zip(a, b):
equal = x == y
if equal:
bars.append("|")
if was_equal:
score += 3
else:
score += 1
else:
bars.append(" ")
score -= 1
was_equal = equal
print a
print "".join(bars)
print b
print "Score:", score

If you want to take this even further you can use a score matrix instead of
if ... else:

def pairwise_score(a, b):
score = 0
was_equal = False
bars = []
matrix = [[-1, 1], [-1, 3]]
for x, y in zip(a, b):
equal = x == y
score += matrix[was_equal][equal]
bars.append(" |"[equal])
was_equal = equal
print a
print "".join(bars)
print b
print "Score:", score