I have to find all initializations (captial letter words, such as SAP, JSON or XML) in my plain text files. Is there any ready-made script for this? Ruby, Python, Perl - the language doesn't matter. So far, I've found nothing.
Regards,
Stefan
Here you go:
perl -e 'for (<>) { for (m/\b([[:upper:]]{2,})\b/) { print "$1\n"; } }' textinput.txt
Grabs all all-uppercase words that are at least two characters long. I use [[:upper:]] instead of [A-Z] so that it works in any locale.
A simpler version of Conspicuous Compiler's answer uses the -p flag to cut out all that ugly loop code:
perl -p -e 'm/\b([[:upper:]]{2,})\b/' input.txt
A regular expression like /[A-Z]{2,}/ should do the trick.
Here's a Python 2.x solution that allows for digits (see example). Update: Code now works for Python 3.1, 3.0 and 2.1 to 2.6 inclusive.
dos-prompt>type find_acronyms.py
import re
try:
set
except NameError:
try:
from sets import Set as set # Python 2.3
except ImportError:
class set: # Python 2.2 and earlier
# VERY minimal implementation
def __init__(self):
self.d = {}
def add(self, element):
self.d[element] = None
def __str__(self):
return 'set(%s)' % self.d.keys()
word_regex = re.compile(r"\w{2,}", re.LOCALE)
# min length is 2 characters
def accumulate_acronyms(a_set, an_iterable):
# updates a_set in situ
for line in an_iterable:
for word in word_regex.findall(line):
if word.isupper() and "_" not in word:
a_set.add(word)
test_data = """
A BB CCC _DD EE_ a bb ccc k9 K9 A1
It's a CHARLIE FOXTROT, said MAJ Major Major USAAF RETD.
FBI CIA MI5 MI6 SDECE OGPU NKVD KGB FSB
BB CCC # duplicates
_ABC_DEF_GHI_ 123 666 # no acronyms here
"""
result = set()
accumulate_acronyms(result, test_data.splitlines())
print(result)
dos-prompt>\python26\python find_acronyms.py
set(['CIA', 'OGPU', 'BB', 'RETD', 'CHARLIE', 'FSB',
'NKVD', 'A1', 'SDECE', 'KGB', 'MI6', 'USAAF', 'K9', 'MAJ',
'MI5', 'FBI', 'CCC', 'FOXTROT'])
# Above output has had newlines inserted for ease of reading.
# Output from 3.0 & 3.1 differs slightly in presentation.
# Output from 2.1 differs in item order.
Related
I've been working on creating a YAML re-formatter based on ruamel.yaml (which you can see here).
I'm currently using version 0.17.20.
Cleaning up comments and whitespace has been difficult. I want to:
ensure there is only one space before the # for EOL comments
align full line comments with the key or item immediately following
remove duplicate blank lines so there is at most one blank line
To get closer to achieving that, I have a custom Emitter class where I extend write_comment to adjust the comments just before writing with super().write_comment(...). However, the Emitter does not know about which key or item comes next because comments are generally attached as post comments.
As I've studied the ruamel.yaml code to figure out how to do this, I found the rtsc mode (Round Trip Split Comments) which looks fantastic because it separates EOLComment, BlankLineComment and FullLineComment instead of lumping them together.
From what I can tell, the Parser and Scanner have been adjusted to capture the comments. So, loading is (mostly?) implemented with this "NEWCMNT" implementation. But Emitter.write_comment expects CommentToken instead of comment line numbers, so dumping does not work yet.
If I update my Emitter.write_comment method, is that enough to finish dumping? Or what else might be necessary? In one of my tries, I ran into a sys.exit in ScannedComments.assign_eol() - what else is needed to finish that?
PS: I wouldn't normally ask how to collaborate on StackOverflow, but this is not a bug report or a feature request, and I'm trying/failing to use a new (undocumented) feature, so I'm filing this here instead of sourceforge.
rtsc is work in progress cq work started but unfinished. It's internals will almost certainly change.
Two of the three points you indicate can relatively easy be implemented:
set the column of each comment to 0 ( by recursively going over a loaded data structure similar to here ) if the column is before the position of the end of the value on a line, you'll get one space between the value and the column
at the same time doing the recursion in the previous point. Take each comment value and do something like:
value = '\n'.join(line.strip() for line in value.splitlines()
while '\n\n\n' in value:
value = value.replace('\n\n\n', '\n\n')
The indentation to the following element is difficult, depends on the
data structure etc. Given that these are full line comments, I suggest
you do some postprocessing of the YAML document you generate:
find a full line comment, gather full line comments until next line is
not full line comment (i.e. some "real" YAML). Since full line comments
are in column[0] if the previous stuff is applied, you don't have to
track if you are in a (multi-line) literal or folded scalar string where
one of the lines happens to start with #
determine number of spaces
before real YAML and apply these to the full line comments.
import sys
import ruamel.yaml
yaml_str = """\
# the following is a example YAML doc
a:
- b: 42
# collapse multiple empty lines
c: |
# this is not a comment
it is the first line of a block style literal scalar
processing this gobbles a newline which doesn't go into a comment
# that is unless you have a (dedented) comment directly following
d: 42 # and some non-full line comment
e: # another one
# and some more comments to align
f: glitter in the dark near the Tannhäuser gate
"""
def redo_comments(d):
def do_one(comment):
if not comment:
return
comment.column = 0
value = '\n'.join(line.strip() for line in comment.value.splitlines()) + '\n'
while '\n\n\n' in value:
value = value.replace('\n\n\n', '\n\n')
comment.value = value
def do_values(v):
for x in v:
for comment in x:
do_one(comment)
def do_loc(v):
if v is None:
return
do_one(v[0])
if not v[1]:
return
for comment in v[1]:
do_one(comment)
if isinstance(d, dict):
do_loc(d.ca.comment)
do_values(d.ca.items.values())
for val in d.values():
redo_comments(val)
elif isinstance(d, list):
do_values(d.ca.items.values())
for elem in d:
redo_comments(elem)
def realign_full_line_comments(s):
res = []
buf = []
for line in s.splitlines(True):
if not buf:
if line and line[0] == '#':
buf.append(line)
else:
res.append(line)
else:
if line[0] in '#\n':
buf.append(line)
else:
# YAML line, determine indent
count = 0
while line[count] == ' ':
count += 1
if count > len(line):
break # superfluous?
indent = ' ' * count
for cline in buf:
if cline[0] == '\n': # empty
res.append(cline)
else:
res.append(indent + cline)
buf = []
res.append(line)
return ''.join(res)
yaml = ruamel.yaml.YAML()
# yaml.indent(mapping=4, sequence=4, offset=2)
# yaml.preserve_quotes = True
data = yaml.load(yaml_str)
redo_comments(data)
yaml.dump(data, sys.stdout, transform=realign_full_line_comments)
which gives:
# the following is a example YAML doc
a:
- b: 42
# collapse multiple empty lines
c: |
# this is not a comment
it is the first line of a block style literal scalar
processing this gobbles a newline which doesn't go into a comment
# that is unless you have a (dedented) comment directly following
d: 42 # and some non-full line comment
e: # another one
# and some more comments to align
f: glitter in the dark near the Tannhäuser gate
In Ruby, I'm reading an .ifc file to get some information, but I can't decode it. For example, the file content:
"'S\X2\00E9\X0\jour/Cuisine'"
should be:
"'Séjour/Cuisine'"
I'm trying to encode it with:
puts ifcFileLine.encode("Windows-1252")
puts ifcFileLine.encode("ISO-8859-1")
puts ifcFileLine.encode("ISO-8859-5")
puts ifcFileLine.encode("iso-8859-1").force_encoding("utf-8")'
But nothing gives me what I need.
I don't know anything about IFC, but based solely on the page Denis linked to and your example input, this works:
ESCAPE_SEQUENCE_EXPR = /\\X2\\(.*?)\\X0\\/
def decode_ifc(str)
str.gsub(ESCAPE_SEQUENCE_EXPR) do
$1.gsub(/..../) { $&.to_i(16).chr(Encoding::UTF_8) }
end
end
str = 'S\X2\00E9\X0\jour/Cuisine'
puts "Input:", str
puts "Output:", decode_ifc(str)
All this code does is replace every sequence of four characters (/..../) between the delimiters, which will each be a Unicode code point in hexadecimal, with the corresponding Unicode character.
Note that this code handles only this specific encoding. A quick glance at the implementation guide shows other encodings, including an \X4 directive for Unicode characters outside the Basic Multilingual Plane. This ought to get you started, though.
See it on eval.in: https://eval.in/776980
If someone is interested, I wrote here a Python Code that decode 3 of the IFC encodings : \X, \X2\ and \S\
import re
def decodeIfc(txt):
# In regex "\" is hard to manage in Python... I use this workaround
txt = txt.replace('\\', 'µµµ')
txt = re.sub('µµµX2µµµ([0-9A-F]{4,})+µµµX0µµµ', decodeIfcX2, txt)
txt = re.sub('µµµSµµµ(.)', decodeIfcS, txt)
txt = re.sub('µµµXµµµ([0-9A-F]{2})', decodeIfcX, txt)
txt = txt.replace('µµµ','\\')
return txt
def decodeIfcX2(match):
# X2 encodes characters with multiple of 4 hexadecimal numbers.
return ''.join(list(map(lambda x : chr(int(x,16)), re.findall('([0-9A-F]{4})',match.group(1)))))
def decodeIfcS(match):
return chr(ord(match.group(1))+128)
def decodeIfcX(match):
# Sometimes, IFC files were made with old Mac... wich use MacRoman encoding.
num = int(match.group(1), 16)
if (num <= 127) | (num >= 160):
return chr(num)
else:
return bytes.fromhex(match.group(1)).decode("macroman")
I am working with Graphchi's pagerank example: https://github.com/GraphChi/graphchi-cpp/wiki/Example-Apps#pagerank-easy
The example app writes a binary file with vertex information that I would like to read/convert to a plan text file (to later call into R or some other language).
The documentation states that:
"GraphChi will write the values of the edges in a binary file, which is easy to handle in other programs. Name of the file containing vertex values is GRAPH-NAME.4B.vout. Here "4B" refers to the vertex-value being a 4-byte type (float)."
The 'easy to handle' part is what I'm struggling with - I have experience with high level languages but not C++ or dealing with binary files. I have found a few things through searching stackoverflow but no luck yet in reading this file. Ideally this would be done through bash or python.
thanks very much for your help on this.
Update: hexdump graph-name.4B.vout | head -5 gives:
0000000 999a 3e19 7468 3e7f 7d2a 3e93 d8e0 3ec4
0000010 cec6 3fe4 d551 3f08 eff2 3e54 999a 3e19
0000020 999a 3e19 3690 3e8c 0080 3f38 9ea3 3ef5
0000030 b7d6 3f66 999a 3e19 10e3 3ee1 400c 400d
0000040 a3df 3e7c 999a 3e19 979c 3e91 5230 3f18
Here is example code how you can use GraphCHi to write the output out as a string:
https://github.com/GraphChi/graphchi-cpp/wiki/Vertex-Aggregators
But the array is simple byte array. Here is example how to read it in python:
import struct
from array import array as binarray
import sys
inputfile = sys.argv[1]
data = open(inputfile).read()
a = binarray('c')
a.fromstring(data)
s = struct.Struct("f")
l = len(a)
print "%d bytes" %l
n = l / 4
for i in xrange(0, n):
x = s.unpack_from(a, i * 4)[0]
print ("%d %f" % (i, x))
I was having the same trouble. Luckily I work with a bunch of network engineers who helped me out! On Mac Linux, the following command works to print the 4B.vout data one line per node, with the integer values the same as is given in the summary file. If your file is called eg, filename.4B.vout, then some command line perl gets you:
cat filename.4B.vout | LANG= perl -0777 -e '$,=\"\n\"; print unpack(\"L*\",<>),\"\";'
Edited to add: this is for the assignments of connected component ID and community ID, written implicitly the 1st line is the ID of the node labeled 0, the 2nd line is the node labeled 1 etc. But I am copypasting here so I'm not sure how it would need to change for floats. It works great for the integer values per node.
I'm moving my bookmarks from kippt.com to pinboard.in.
I exported my bookmarks from Kippt and for some reason, they were storing tags (preceded by #) and description within the same field. Pinboard keeps tags and description separated.
This is what a Kippt bookmark looks like after export:
<DT>This is a title
<DD>#tag1 #tag2 This is a description
This is what it should look like before importing into Pinboard:
<DT>This is a title
<DD>This is a description
So basically, I need to replace #tag1 #tag2 by TAGS="tag1,tag2" and move it on the first line within <A>.
I've been reading about moving chunks of data here: sed or awk to move one chunk of text betwen first pattern pair into second pair?
I haven't been to come up with a good recipe so far. Any insight?
Edit:
Here's an actual example of what the input file looks like (3 entries out of 3500):
<DT>Phabricator
<DD>#bug #tracking
<DT>The hidden commands for diagnosing and improving your Netflix streaming quality – Quartz
<DT>Icelandic Farm Holidays | Local experts in Iceland vacations
<DD>#iceland #tour #car #drive #self Self-driving tour of Iceland
This might not be the most beautiful solution, but since it seems to be a one-time-thing it should be sufficient.
import re
dt = re.compile('^<DT>')
dd = re.compile('^<DD>')
with open('bookmarks.xml', 'r') as f:
for line in f:
if re.match(dt, line):
current_dt = line.strip()
elif re.match(dd, line):
current_dd = line
tags = [w for w in line[4:].split(' ') if w.startswith('#')]
current_dt = re.sub('(<A[^>]+)>', '\\1 TAGS="' + ','.join([t[1:] for t in tags]) + '">', current_dt)
for t in tags:
current_dd = current_dd.replace(t + ' ', '')
if current_dd.strip() == '<DD>':
current_dd = ""
else:
print current_dt
print current_dd
current_dt = ""
current_dd = ""
print current_dt
print current_dd
If some parts of the code are not clear, just tell me. You can of course use python to write the lines to a file instead of printing them, or even modify the original file.
Edit: Added if-clause so that empty <DD> lines won't show up in the result.
script.awk
BEGIN{FS="#"}
/^<DT>/{
if(d==1) print "<DT>"s # for printing lines with no tags
s=substr($0,5);tags="" # Copying the line after "<DT>". You'll know why
d=1
}
/^<DD>/{
d=0
m=match(s,/>/) # Find the end of the HREF descritor first match of ">"
for(i=2;i<=NF;i++){sub(/ $/,"",$i);tags=tags","$i} # Concatenate tags
td=match(tags,/ /) # Parse for tag description (marked by a preceding space).
if(td==0){ # No description exists
tags=substr(tags,2)
tagdes=""
}
else{ # Description exists
tagdes=substr(tags,td)
tags=substr(tags,2,td-2)
}
print "<DT>" substr(s,1,m-1) ", TAGS=\"" tags "\"" substr(s,m)
print "<DD>" tagdes
}
awk -f script.awk kippt > pinboard
INPUT
<DT>Phabricator
<DD>#bug #tracking
<DT>The hidden commands for diagnosing and improving your Netflix streaming quality – Quartz
<DT>Icelandic Farm Holidays | Local experts in Iceland vacations
<DD>#iceland #tour #car #drive #self Self-driving tour of Iceland
OUTPUT:
<DT>Phabricator
<DD>
<DT>The hidden commands for diagnosing and improving your Netflix streaming quality – Quartz
<DT>Icelandic Farm Holidays | Local experts in Iceland vacations
<DD> Self-driving tour of Iceland
I have written a python script that calls unix sort using subprocess module. I am trying to sort a table based on two columns(2 and 6). Here is what I have done
sort_bt=open("sort_blast.txt",'w+')
sort_file_cmd="sort -k2,2 -k6,6n {0}".format(tab.name)
subprocess.call(sort_file_cmd,stdout=sort_bt,shell=True)
The output file however contains an incomplete line which produces an error when I parse the table but when I checked the entry in the input file given to sort the line looks perfect. I guess there is some problem when sort tries to write the result to the file specified but I am not sure how to solve it though.
The line looks like this in the input file
gi|191252805|ref|NM_001128633.1| Homo sapiens RIMS binding protein 3C (RIMBP3C), mRNA gnl|BL_ORD_ID|4614 gi|124487059|ref|NP_001074857.1| RIMS-binding protein 2 [Mus musculus] 103 2877 3176 846 941 1.0102e-07 138.0
In output file however only gi|19125 is printed. How do I solve this?
Any help will be appreciated.
Ram
Using subprocess to call an external sorting tool seems quite silly considering that python has a built in method for sorting items.
Looking at your sample data, it appears to be structured data, with a | delimiter. Here's how you could open that file, and iterate over the results in python in a sorted manner:
def custom_sorter(first, second):
""" A Custom Sort function which compares items
based on the value in the 2nd and 6th columns. """
# First, we break the line into a list
first_items, second_items = first.split(u'|'), second.split(u'|') # Split on the pipe character.
if len(first_items) >= 6 and len(second_items) >= 6:
# We have enough items to compare
if (first_items[1], first_items[5]) > (second_items[1], second_items[5]):
return 1
elif (first_items[1], first_items[5]) < (second_items[1], second_items[5]):
return -1
else: # They are the same
return 0 # Order doesn't matter then
else:
return 0
with open(src_file_path, 'r') as src_file:
data = src_file.read() # Read in the src file all at once. Hope the file isn't too big!
with open(dst_sorted_file_path, 'w+') as dst_sorted_file:
for line in sorted(data.splitlines(), cmp = custom_sorter): # Sort the data on the fly
dst_sorted_file.write(line) # Write the line to the dst_file.
FYI, this code may need some jiggling. I didn't test it too well.
What you see is probably the result of trying to write to the file from multiple processes simultaneously.
To emulate: sort -k2,2 -k6,6n ${tabname} > sort_blast.txt command in Python:
from subprocess import check_call
with open("sort_blast.txt",'wb') as output_file:
check_call("sort -k2,2 -k6,6n".split() + [tab.name], stdout=output_file)
You can write it in pure Python e.g., for a small input file:
def custom_key(line):
fields = line.split() # split line on any whitespace
return fields[1], float(fields[5]) # Python uses zero-based indexing
with open(tab.name) as input_file, open("sort_blast.txt", 'w') as output_file:
L = input_file.read().splitlines() # read from the input file
L.sort(key=custom_key) # sort it
output_file.write("\n".join(L)) # write to the output file
If you need to sort a file that does not fit in memory; see Sorting text file by using Python