I have this text file that is supposed to be tab delimited, except that in a couple of fields, there are tabs instead of spaces, making it hard to extract the data I need. It's too large to manually fix it, so I need any solution.
The columns SHOULD look something like this:
A\tB\tC\tsome info\tGO:123\t
But occassionally i get this:
A\tB\tC\tsome\tinfo\tGO:123\t
And the "some info" column can be any number of things, so i can't just sed replace. What should be column 5 always starts with "GO:" and columns 1, 2, and 3 are always correct. It's just this 4th column that's making things hard.
Any ideas?
Regular expression:
(A)\\t(B)\\t(C)\\t(.*)?\\t(GO:123)\\t
Get groups 1,2,3,4. You have your some data with and without tab in group 4.
Related
When viewed, any .csv file committed to a GitHub repository automatically renders as an interactive table, complete with headers and row numbering. By default, the first row is your header row. The tables were supposed to look nice as below:
However, there's an error happening in my tabular data, and despite indicating the error, I can't fix it:
I'm using a .csv file with a semicolon separator. Does anyone have an idea of what's happening?
According to the docs, Github can only do its lay-out thing with .csv (comma-separated) and .tsv (tab-separated) files.
Using a semicolon as a separator isn't supported, at least not officially, and a spurious comma in a semicolon-separated file could well throw the algorithm off.
You could try replacing all semicolons with tabs and see how you fare.
If that doesn't work, try using commas as separators and enclose all text table cell data with quotes, like:
"Liver fibrosis, sclerosis, and cirrhosis","c370800","102922","Cystic fibrosis related cirrhosis","Diagnosis of liver fibrosis, sclerosis, and cirrhosis"
Note: no spaces after the commas. Also, if you have quotes in the text fields, you will have to escape those to "" (two quotes), or the algorithm will get confused.
You may get away with using quotes only for the offending text data, but that could well be more difficult to generate than just putting the quotes around all fields.
I have an issue where extracting data from database it sometimes (quite often) adds spaces in between strings of texts that should not be there.
What I'm trying to do is create a small script that will look at these strings and remove the spaces.
The problem is that the spaces can be in any position in the string, and the string is a variable that changes.
Example:
"StaffID": "0000 25" <- The space in the number should not be there.
Is there a way to have the script look at this particular line, and if it finds spaces, to remove them.
Or:"DateOfBirth": "23-10-199 0" <-It would also need to look at these spaces and remove them.
The problem is that the same data also has lines such as:
"Address": " 91 Broad street" <- The spaces should be here obviously.
I've tried using TRIM, but that only removes spaces from start/end.
Worth mentioning that the data extracted is in json format and is then imported using API into the new system.
You should think about the logic of what you want to do, and whether or not it's programmatically possible to determine if you can teach your script where it is or is not appropriate to put spaces. As it is, this is one of the biggest problems facing AI research right now, so unfortunately you're probably going to have to do this by hand.
If it were me, I'd specify the kind of data format that I expect from each column, and try my best to attempt to parse those strings. For example, if you know that StaffID doesn't contain spaces, you can have a rule that just deletes them:
$staffid = $staffid.replace("\s+",'')
There are some more complicated things that you can do with forced formatting (.replace) that have already been covered in this answer, but again, that requires some expectation of exactly what data is going to come out of what column.
You might want to look more closely at where those spaces are coming from, rather than process the output like this. Is the retrieval script doing it? Maybe you can optimize the database that you're drawing from?
I am using Scala to parse CSV files. Some of these files have fields which are non-textual data like images or octet-streams. I would like to use Apache Spark's textFile() method to split up the CSV into rows, and
split(",[ ]*(?=([^\"]*\"[^\"]*\")*[^\"]*$)")
to split the row into fields. Unfortunatly this does not work with files that have these mentioned binary fields. There are two problems: 1) The octet-streams can contain newlines which make textFile() split rows which should be one, and 2) The octet-streams contain commas and/or double quotes which are not escaped and mess up my schema.
The files are usually big, couple of MBs up to couple of 100MBs. I have to take the CSV's as they are, although I could preprocess them.
All I want to achieve is a working split function so I can ignore the field with the octet-stream. Nevertheless, a great bonus would be to extract the textual information in the octet-stream.
So how would I go forward to solve my problems?
Edit: A typical record obtained with cat, the newlines are from the file, not for cosmetic purposes (shortened):
7,url,user,02/24/2015 02:29:00 AM,03/22/2015 03:12:36 PM,octet-stream,27156,"MSCF^#^#^#^#�,^#^#^#^#^#^#D^#^#^#^#^#^#^#^C^A^A^#^C^#^D^#^#^#^#^#^T^#^#^#^#^#^P^#�,^#^#^X=^#^#^#^#^#^#^#^#^#^#�^#^#^#^E^#^A^#��^A^#^#^#^#^#^#^#WF6�!^#Info.txt^#=^B^#^#��^A^#^#^#WF7�^#^#List.xml^#^�^#^#��^A^#^#^#WF:�^#^#Filename.txt^#��>��
^#�CK�]�r��^Q��T�^O�^#�-�j�]��FI�Ky��Ei�Je^K""!�^Qx #�*^U^?�^_�;��ħ�^LI^#$(�^Q���b��\N����t�����+������ȷgvM�^L̽�LǴL�^L��^ER��w^Ui^M��^X�Kޓ�^QJȧ��^N~��&�x�bB��D]1�^B|^G���g^SyG�����:����^_P�^T�^_�����U�|B�gH=��%Z^NY���,^U�^VI{��^S�^U�!�^Lpw�T���+�a�z�l������b����w^K��or��pH� ��ܞ�l��z�^\i=�z�:^C�^S!_ESCW��ESC""��g^NY2��s�� u���X^?�^R^R+��b^]^Ro�r���^AR�h�^D��^X^M�^]ޫ���ܰ�^]���0^?��^]�92^GhCx�DN^?
mY<{��L^Zk�^\���M�^V^HE���-Ե�$f�f����^D�e�^R:�u����� ^E^A�Ȑ�^B�^E�sZ���Yo��8Eސ�}��&JY���^A9^P������^P����~Jʭy��`�^9«�""�U� �:�}3���6�Hߧ�v���A7^Xi^L^]�sA�^Q�7�5d�^Xo˛�tY
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�Z�^c�6N�ESCG����^_��>��t^L^R�^:�x���^]v�{^#+KM��qԎ�.^S�%&��=^W-�=�^S�����^CI���&^]_�s�˞�y�z�Jc^W�kڠ�^\��^]j�����^O��;�oY^^�^V59;�c��^B��T�nb����^C��^N��s�x�<{�9-�F�T�^N�5�^Se-���^T�Y[���`^ZsL��v�բ<C�+�~�^ۚ��""�Yκ2^_�^VxT�>��/ݳ^U�m�^#���3^Ge�n^Vc�V�^#�NVn�,�q��^^^]gy�R�S��Ȃ$���>A�d����xg�^GB3�M�J�^QJ^]�^\�{.�D��碎�^W�8a����qޠl?,'^R�^X�Cgy�P[����mڞ��H�Z�s�SD&蠤�s�E��nu�O#O<��3wj`C-%w�W�J�^WP^T�^]r^NT�TC�Lq�Z�f�!�;�l�Y��Gb��>�ud�hx�Ԭ^N)9�^N!k�҉s�35v������.�""^]��~4������۴�Z^]u�^Ti^^�i:�)K��P᳕!�#�^?�>��EE^VE-u�^SgV^L��<��^D�O<�+�J.�c�Z#>�.l����^S�
ESC��(��E�j�π쬖���2{^U&b\��P^S�`^O^XdL�^ 6bu��FD��^#^#^#^#","field_x, data",field_y,field_z
Expected output would be an array
("7","url","user","02/24/2015 02:29:00 AM","03/22/2015 03:12:36 PM","octet-stream","27156","field_x, data",field_y",field_z")
Or, but this is probably another question, such an array (like running strings on the octet-stream field):
("7","url","user","02/24/2015 02:29:00 AM","03/22/2015 03:12:36 PM","octet-stream","27156","Info.txt List.xml Filename.txt","field_x, data",field_y",field_z")
Edit 2: Every file that has a binary field also contains a length field for it. So instead of splitting directly I can walk left to right through my record and extract the fields. This is certainly a great improvement of my current situation but problem 1) still persists. How can I split those files reliably?
I took a closer look at the files and a header looks like this:
RecordId, Field_A, Content_Type, Content_Length, Content, Field_B
(Where Content_Type can be "octet-stream", Content_Length the number of bytes in the Content field, and Content obviously the data). And good for me, the value of Field_B is predictable, let's assume for a certain file it's always "Hello World".
So instead of using Spark's default behaviour splitting on newlines, how can I achieve that Spark is only splitting on newlines following "Hello World"? (I also edited the question title since the focus of the question changed)
As answered in Spark: Reading files using different delimiter than new line, I used textinputformat.record.delimiter to split on "Hello World\n" because I am a bit lucky that the last column always contains the same value. After that I simply walk left to right through the record and when I reach the length field I skip the next n bytes. Everything works now. Thanks for pointing me in the right direction.
There are two problems: 1) The octet-streams can contain newlines
which make textFile() split rows which should be one, and 2) The
octet-streams contain commas and/or double quotes which are not
escaped and mess up my schema.
Well, actually that csv file is properly escaped:
the multiline field is enclosed in double quotes: "MSCF^# .. ^#^#" (which also handles possible separators inside the field)
double quotes inside the field are escaped with another double quote as it should be: Je^K""!
Of course a simple split will not work in this case (and should never be used on csv data), but any csv reader able to handle multiline fields should parse that data correctly.
Also keep in mind that the double quotes inside the octet-stream have to be unescaped, or that data won't be valid (another reason not to use split, but a csv reader that handles this).
I have a file that looks like this in notepad++
I can easily see the spaces (being the orange dots), and tabs (being the orange arrows). I can also right click this in MATLAB and import it in a variety of ways. The problem is firstly the delimiters are not consistent. It seems to go TAB then some spaces to make sure the total field equals 6 characters...
The only way I understand reading a file in is if you already know how it is delimited. But in this case I would like to parse each line so MATLAB has some 'token' of what goes where eg:
Line1: Text Space Text Space Text Tab Space Space Text NEWLINE
(Notepad++ seems to know just fine so surely MATLAB can get this info too?).
Is this possible? Then it would be nice to use this information to save the imported data back out to a file with exactly the same formatting.
The data is below. For some reason copying this into notepad++ does not preserve its delimiting, you will need to add the tabs in yourself so it looks like the file in the screenshot.
Average Counts : 56.2
Time : 120
Thanks
If you use textscan, the default behaviour should probably suit your needs:
Within each row of data, the default field delimiter is white space. White space can be any combination of space (' '), backspace ('\b'), or tab ('\t') characters. If you do not specify a delimiter, textscan interprets repeated white-space characters as a single delimiter.
The output is a cell array, where each column is saved as a cell. So C{1} would contain the strings, C{2} the colons, and C{2} the values.
I've prepared a macro in Notepad++ to transform a ldif file in a csv file with a few fields. Everything is OK but I have a final problem: I have to have 2 fields with a specific length and in this moment I cannot ensure that length because in the source file they are not coming so
For instance, I generate this line:
12345,namenamename,123456
And I have to ensure that the 2nd and 3rd fields have 30 (filling with spaces at right side) and 9 (filling with zeros at left) characters, so in this case I should generate:
12345,namenamename ,000123456
I haven't found how Notepad++ could match a pattern in order to add spaces/zeros, so I have though in to add 1 space/zero to the proper field and repeat this step so many times as needed to ensure the lengths (this is, 29 and 8, because they cannot come empty) and search with the length in the regex (for instance: \d{1,8} for the third field)
My question is: can I repeat only one step of the macro several times (and the rest of the macro only 1 repetition)?
I've read the wiki related to this point (http://sourceforge.net/apps/mediawiki/notepad-plus/index.php?title=Editing_Configuration_Files#.3CMacros.3E) and I don't found anything neither
If not possible, how could be a good solution? Create another 2 different macros and after execute the main one, execute this new 2 macros several times?
Thanks in advance!
A two pass solution with Notepad++ is possible. Find a pair of characters or two short sequence of characters that never occurs in your data file. I will use =#<= and =>#= here.
First pass, generate or convert the input text into the form 12345,=#<=namenamename______________________________,000000000123456=>#=. Ie add 30 spaces after the name and nine zeroes before the number (underscores used here just to make things clearer).
Second pass, do a regular expression search for =#<=(.{30})_*,0*(\d{9})=>#= and replace with \1,\2.
I have just suggested a similar solution in special timestamp format of csv