YamlDotNet- packet to yaml - yaml

Hello I wanted to create program that will help me with converting packet data from game to yaml it should look like this
monsters:
- map_monster_id: 1678
vnum: 333
map_x: 30
map_y: 165
- map_monster_id: 1679
vnum: 333
map_x: 24
map_y: 157
i have code that is supposed to write those things in database and I want rework so it can write to yaml anyone who should tell me where to start thank you :)

Related

How to load data using sqlldr

My raw file like below, Here Transaction Branch is different and Home branch is different
I need data like below, can any one help me to archive this (using sqlldr concept)
Tr_Bra Acc Name Bal Home_Bra
100 1000 bbbb 100 100
100 1001 bbbb 200 100
101 1003 bbbb 400 200
101 1004 bbbb 500 200
102 1005 bbbb 400 500
102 1006 bbbb 500 500

Assuming you want to upload the filename (ie: 100.csv) as a value for SQL Loader to load into the table, there no way for the program to identify the file name as a parameter.
I suggest concatenating the files with another script (Python would we great for the job) and then loading the final file with SQL Loader.

Consumed messages from Kafak is printed as numbers in spring-xd

I am trying to make a simple spring-xd experiment.
Spring-xd is downloaded and running in the single node mode. We already have a Kafka cluster and we have a spark streaming job that read tweets from twitter API and push it into Kafka.
I am trying to read from Kafka using spring-xd and write to file so I created the following stream
xd:>stream create tweet --definition "kafka --zkconnect=zkserver:2181 --topic=tweets | file" --deploy
The result in the output file will be something like what appears below
123,34,105,100,34,58,34,116,97,103,58,115,101,97,114,99,104,46,116,119,105,116,116,101,114,46,99,111,109,44,50,48,48,53,58,55,54,54,48,55,55,56,57,52,50,51,55,57,55,48,52,51,50,34,44,34,111,98,106,101,99,116,84,121,112,101,34,58,34,97,99,116,105,118,105,116,121,34,44,34,97,99,116,111,114,34,58,123,34,111,98,106,101,99,116,84,121,112,101,34,58,34,112,101,114,115,111,110,34,44,34,105,100,34,58,34,105,100,58,116,119,105,116,116,101,114,46,99,111,109,58,50,56,49,54,51,54,52,57,52,55,34,44,34,108,105,110,107,34,58,34,104,116,116,112,58,47,47,119,119,119,46,116,119,105,116,116,101,114,46,99,111,109,47,67,82,82,111,103,101,114,115,53,34,44,34,100,105,115,112,108,97,121,78,97,109,101,34,58,34,71,50,32,67,104,97,114,108,105,101,34,44,34,112,111,115,116,101,100,84,105,109,101,34,58,34,50,48,49,52,45,49,48,45,48,56,84,50,49,58,52,54,58,50,56,46,48,48,48,90,34,44,34,105,109,97,103,101,34,58,34,104,116,116,112,115,58,47,47,112,98,115,46,116,119,105,109,103,46,99,111,109,47,112,114,111,102,105,108,101,95,105,109,97,103,101,115,47,55,51,49,50,55,53,53,55,50,56,49,53,53,51,50,48,51,50,47,89,84,66,109,89,113,78,111,95,110,111,114,109,97,108,46,106,112,103,34,44,34,115,117,109,109,97,114,121,34,58,110,117,108,108,44,34,108,105,110,107,115,34,58,91,123,34,104,114,101,102,34,58,110,117,108,108,44,34,114,101,108,34,58,34,109,101,34,125,93,44,34,102,114,105,101,110,100,115,67,111,117,110,116,34,58,55,49,50,44,34,102,111,108,108,111,119,101,114,115,67,111,117,110,116,34,58,52,57,52,44,34,108,105,115,116,101,100,67,111,117,110,116,34,58,54,48,44,34,115,116,97,116,117,115,101,115,67,111,117,110,116,34,58,51,57,53,50,53,44,34,116,119,105,116,116,101,114,84,105,109,101,90,111,110,101,34,58,34,69,97,115,116,101,114,110,32,84,105,109,101,32,40,85,83,32,38,32,67,97,110,97,100,97,41,34,44,34,118,101,114,105,102,105,101,100,34,58,102,97,108,115,101,44,34,117,116,99,79,102,102,115,101,116,34,58,34,45,49,52,52,48,48,34,44,34,112,114,101,102,101,114,114,101,100,85,115,101,114,110,97,109,101,34,58,34,67,82,82,111,103,101,114,115,53,34,44,34,108,97,110,103,117,97,103,101,115,34,58,91,34,101,110,34,93,44,34,108,111,99,97,116,105,111,110,34,58,123,34,111,98,106,101,99,116,84,121,112,101,34,58,34,112,108,97,99,101,34,44,34,100,105,115,112,108,97,121,78,97,109,101,34,58,34,67,84,34,125,44,34,102,97,118,111,114,105,116,101,115,67,111,117,110,116,34,58,51,53,57,125,44,34,118,101,114,98,34,58,34,115,104,97,114,101,34,44,34,112,111,115,116,101,100,84,105,109,101,34,58,34,50,48,49,54,45,48,56,45,49,56,84,48,52,58,48,50,58,53,55,46,48,48,48,90,34,44,34,103,101,110,101,114,97,116,111,114,34,58,123,34,100,105,115,112,108,97,121,78,97,109,101,34,58,34,84,119,105,116,116,101,114,32,102,111,114,32,105,80,104,111,110,101,34,44,34,108,105,110,107,34,58,34,104,116,116,112,58,47,47,116,119,105,116,116,101,114,46,99,111,109,47,100,111,119,110,108,111,97,100,47,105,112,104,111,110,101,34,125,44,34,112,114,111,118,105,100,101,114,34,58,123,34,111,98,106,101,99,116,84,121,112,101,34,58,34,115,101,114,118,105,99,101,34,44,34,100,105,115,112,108,97,121,78,97,109,101,34,58,34,84,119,105,116,116,101,114,34,44,34,108,105,110,107,34,58,34,104,116,116,112,58,47,47,119,119,119,46,116,119,105,116,116,101,114,46,99,111,109,34,125,44,34,108,105,110,107,34,58,34,104,116,116,112,58,47,47,116,119,105,116,116,101,114,46,99,111,109,47,67,82,82,111,103,101,114,115,53,47,115,116,97,116,117,115,101,115,47,55,54,54,48,55,55,56,57,52,50,51,55,57,55,48,52,51,50,34,44,34,98,111,100,121,34,58,34,82,84,32,64,115,116,101,112,104,57,51,48,54,53,58,32,78,101,119,116,58,32,84,114,117,109,112,32,73,83,73,83,32,83,112,101,101,99,104,32,39,72,105,115,116,111,114,105,99,39,32,45,32,39,77,111,115,116,32,73,109,112,111,114,116,97,110,116,32,70,111,114,101,105,103,110,32,80,111,108,105,99,121,32,83,112,101,101,99,104,32,83,105,110,99,101,32,82,111,110,97,108,100,32,82,101,97,103,97,110,39,32,45,32,66,114,101,105,116,98,97,114,116,32,104,116,116,112,115,58,47,47,116,46,99,111,47,50,105,-30,-128,-90,34,44,34,111,98,106,101,99,116,34,58,123,34,105,100,34,58,34,116,97,103,58,115,101,97,114,99,104,46,116,119,105,116,116,101,114,46,99,111,109,44,50,48,48,53,58,55,54,53,53,53,50,56,57,54,51,56,53,52,56,50,55,53,50,34,44,34,111,98,106,101,99,116,84,121,112,101,34,58,34,97,99,116,105,118,105,116,121,34,44,34,97,99,116,111,114,34,58,123,34,111,98,106,101,99,116,84,121,112,101,34,58,34,112,101,114,115,111,110,34,44,34,105,100,34,58,34,105,100,58,116,119,105,116,116,101,114,46,99,111,109,58,50,54,49,55,52,57,55,51,53,34,44,34,108,105,110,107,34,58,34,104,116,116,112,58,47,47,119,119,119,46,116,119,105,116,116,101,114,46,99,111,109,47,115,116,101,112,104,57,51,48,54,53,34,44,34,100,105,115,112,108,97,121,78,97,109,101,34,58,34,83,116,101,112,104,34,44,34,112,111,115,116,101,100,84,105,109,101,34,58,34,50,48,49,49,45,48,51,45,48,54,84,49,57,58,51,54,58,52,52,46,48,48,48,90,34,44,34,105,109,97,103,101,34,58,34,104,116,116,112,115,58,47,47,112,98,115,46,116,119,105,109,103,46,99,111,109,47,112,114,111,102,105,108,101,95,105,109,97,103,101,115,47,55,53,49,53,55,49,50,54,49,50,55,55,52,49,51,51,55,54,47,86,110,114,119,50,75,55,109,95,110,111,114,109,97,108,46,106,112,103,34,44,34,115,117,109,109,97,114,121,34,58,34,65,109,101,114,105,99,97,32,70,105,114,115,116,32,35,84,114,117,109,112,50,48,49,54,32,35,87,111,109,101,110,102,111,114,84,114,117,109,112,32,35,67,65,102,111,114,84,114,117,109,112,34,44,34,108,105,110,107,115,34,58,91,123,34,104,114,101,102,34,58,34,104,116,116,112,115,58,47,47,119,119,119,46,108,121,105,110,103,99,114,111,111,107,101,100,104,105,108,108,97,114,121,46,99,111,109,47,34,44,34,114,101,108,34,58,34,109,101,34,125,93,44,34,102,114,105,101,110,100,115,67,111,117,110,116,34,58,57,54,51,48,53,44,34,102,111,108,108,111,119,101,114,115,67,111,117,110,116,34,58,49,50,55,57,52,55,44,34,108,105,115,116,101,100,67,111,117,110,116,34,58,49,48,53,49,44,34,115,116,97,116,117,115,101,115,67,111,117,110,116,34,58,50,51,51,54,48,51,44,34,116,119,105,116,116,101,114,84,105,109,101,90,111,110,101,34,58,34,65,114,105,122,111,110,97,34,44,34,118,101,114,105,102,105,101,100,34,58,102,97,108,115,101,44,34,117,116,99,79,102,102,115,101,116,34,58,34,45,50,53,50,48,48,34,44,34,112,114,101,102,101,114,114,101,100,85,115,101,114,110,97,109,101,34,58,34,115,116,101,112,104,57,51,48,54,53,34,44,34,108,97,110,103,117,97,103,101,115,34,58,91,34,101,110,34,93,44,34,108,111,99,97,116,105,111,110,34,58,123,34,111,98,106,101,99,116,84,121,112,101,34,58,34,112,108,97,99,101,34,44,34,100,105,115,112,108,97,121,78,97,109,101,34,58,34,67,97,108,105,102,111,114,110,105,97,44,32,85,83,65,34,125,44,34,102,97,118,111,114,105,116,101,115,67,111,117,110,116,34,58,49,55,51,55,52,56,125,44,34,118,101,114,98,34,58,34,112,111,115,116,34,44,34,112,111,115,116,101,100,84,105,109,101,34,58,34,50,48,49,54,45,48,56,45,49,54,84,49,55,58,49,54,58,52,56,46,48,48,48,90,34,44,34,103,101,110,101,114,97,116,111,114,34,58,123,34,100,105,115,112,108,97,121,78,97,109,101,34,58,34,77,111,98,105,108,101,32,87,101,98,34,44,34,108,105,110,107,34,58,34,104,116,116,112,58,47,47,109,111,98,105,108,101,46,116,119,105,116,116,101,114,46,99,111,109,34,125,44,34,112,114,111,118,105,100,101,114,34,58,123,34,111,98,106,101,99,116,84,121,112,101,34,58,34,115,101,114,118,105,99,101,34,44,34,100,105,115,112,108,97,121,78,97,109,101,34,58,34,84,119,105,116,116,101,114,34,44,34,108,105,110,107,34,58,34,104,116,116,112,58,47,47,119,119,119,46,116,119,105,116,116,101,114,46,99,111,109,34,125,44,34,108,105,110,107,34,58,34,104,116,116,112,58,47,47,116,119,105,116,116,101,114,46,99,111,109,47,115,116,101,112,104,57,51,48,54,53,47,115,116,97,116,117,115,101,115,47,55,54,53,53,53,50,56,57,54,51,56,53,52,56,50,55,53,50,34,44,34,98,111,100,121,34,58,34,78,101,119,116,58,32,84,114,117,109,112,32,73,83,73,83,32,83,112,101,101,99,104,32,39,72,105,115,116,111,114,105,99,39,32,45,32,39,77,111,115,116,32,73,109,112,111,114,116,97,110,116,32,70,111,114,101,105,103,110,32,80,111,108,105,99,121,32,83,112,101,101,99,104,32,83,105,110,99,101,32,82,111,110,97,108,100,32,82,101,97,103,97,110,39,32,45,32,66,114,101,105,116,98,97,114,116,32,104,116,116,112,115,58,47,47,116,46,99,111,47,50,105,119,54,56,79,119,56,73,118,34,44,34,111,98,106,101,99,116,34,58,123,34,111,98,106,101,99,116,84,121,112,101,34,58,34,110,111,116,101,34,44,34,105,100,34,58,34,111,98,106,101,99,116,58,115,101,97,114,99,104,46,116,119,105,116,116,101,114,46,99,111,109,44,50,48,48,53,58,55,54,53,53,53,50,56,57,54,51,56,53,52,56,50,55,53,50,34,44,34,115,117,109,109,97,114,121,34,58,34,78,101,119,116,58,32,84,114,117,109,112,32,73,83,73,83,32,83,112,101,101,99,104,32,39,72,105,115,116,111,114,105,99,39,32,45,32,39,77,111,115,116,32,73,109,112,111,114,116,97,110,116,32,70,111,114,101,105,103,110,32,80,111,108,105,99,121,32,83,112,101,101,99,104,32,83,105,110,99,101,32,82,111,110,97,108,100,32,82,101,97,103,97,110,39,32,45,32,66,114,101,105,116,98,97,114,116,32,104,116,116,112,115,58,47,47,116,46,99,111,47,50,105,119,54,56,79,119,56,73,118,34,44,34,108,105,110,107,34,58,34,104,116,116,112,58,47,47,116,119,105,116,116,101,114,46,99,111,109,47,115,116,101,112,104,57,51,48,54,53,47,115,116,97,116,117,115,101,115,47,55,54,53,53,53,50,56,57,54,51,56,53,52,56,50,55,53,50,34,44,34,112,111,115,116,101,100,84,105,109,101,34,58,34,50,48,49,54,45,48,56,45,49,54,84,49,55,58,49,54,58,52,56,46,48,48,48,90,34,125,44,34,102,97,118,111,114,105,116,101,115,67,111,117,110,116,34,58,48,44,34,116,119,105,116,116,101,114,95,101,110,116,105,116,105,101,115,34,58,123,34,104,97,115,104,116,97,103,115,34,58,91,93,44,34,117,115,101,114,95,109,101,110,116,105,111,110,115,34,58,91,93,44,34,115,121,109,98,111,108,115,34,58,91,93,44,34,117,114,108,115,34,58,91,123,34,117,114,108,34,58,34,104,116,116,112,115,58,47,47,116,46,99,111,47,50,105,119,54,56,79,119,56,73,118,34,44,34,101,120,112,97,110,100,101,100,95,117,114,108,34,58,34,104,116,116,112,58,47,47,98,105,116,46,108,121,47,50,98,117,55,48,81,87,34,44,34,100,105,115,112,108,97,121,95,117,114,108,34,58,34,98,105,116,46,108,121,47,50,98,117,55,48,81,87,34,44,34,105,110,100,105,99,101,115,34,58,91,49,48,56,44,49,51,49,93,125,93,125,44,34,116,119,105,116,116,101,114,95,102,105,108,116,101,114,95,108,101,118,101,108,34,58,34,108,111,119,34,44,34,116,119,105,116,116,101,114,95,108,97,110,103,34,58,34,101,110,34,125,44,34,102,97,118,111,114,105,116,101,115,67,111,117,110,116,34,58,48,44,34,116,119,105,116,116,101,114,95,101,110,116,105,116,105,101,115,34,58,123,34,104,97,115,104,116,97,103,115,34,58,91,93,44,34,117,115,101,114,95,109,101,110,116,105,111,110,115,34,58,91,123,34,115,99,114,101,101,110,95,110,97,109,101,34,58,34,115,116,101,112,104,57,51,48,54,53,34,44,34,110,97,109,101,34,58,34,83,116,101,112,104,34,44,34,105,100,34,58,50,54,49,55,52,57,55,51,53,44,34,105,100,95,115,116,114,34,58,34,50,54,49,55,52,57,55,51,53,34,44,34,105,110,100,105,99,101,115,34,58,91,51,44,49,52,93,125,93,44,34,115,121,109,98,111,108,115,34,58,91,93,44,34,117,114,108,115,34,58,91,123,34,117,114,108,34,58,34,104,116,116,112,115,58,47,47,116,46,99,111,47,50,105,119,54,56,79,119,56,73,118,34,44,34,101,120,112,97,110,100,101,100,95,117,114,108,34,58,34,104,116,116,112,58,47,47,98,105,116,46,108,121,47,50,98,117,55,48,81,87,34,44,34,100,105,115,112,108,97,121,95,117,114,108,34,58,34,98,105,116,46,108,121,47,50,98,117,55,48,81,87,34,44,34,105,110,100,105,99,101,115,34,58,91,49,50,52,44,49,52,48,93,125,93,125,44,34,116,119,105,116,116,101,114,95,102,105,108,116,101,114,95,108,101,118,101,108,34,58,34,108,111,119,34,44,34,116,119,105,116,116,101,114,95,108,97,110,103,34,58,34,101,110,34,44,34,114,101,116,119,101,101,116,67,111,117,110,116,34,58,48,44,34,103,110,105,112,34,58,123,34,109,97,116,99,104,105,110,103,95,114,117,108,101,115,34,58,91,123,34,116,97,103,34,58,34,105,115,105,115,69,110,103,108,105,115,104,79,110,108,121,86,56,34,125,44,123,34,116,97,103,34,58,34,73,83,73,83,69,110,103,108,105,115,104,79,110,108,121,118,50,34,125,44,123,34,116,97,103,34,58,34,73,83,73,83,69,110,103,108,105,115,104,118,50,34,125,44,123,34,116,97,103,34,58,34,73,83,73,83,69,110,103,108,105,115,104,79,110,108,121,118,51,34,125,44,123,34,116,97,103,34,58,34,105,115,105,115,69,110,103,108,105,115,104,79,110,108,121,86,55,80,97,114,116,49,34,125,44,123,34,116,97,103,34,58,34,105,115,105,115,69,110,103,108,10
Is there any explanation to this result?

Your output looks like an array of characters. If you take the fist numbers and translate them, you can see this is an array of codes for a JSON String.
123 34 105 100 34 58 34 116 97 103 58 115 101 97 114 99 104 46...
Translates to:
{"id":"tag:search...
I believed this has been answered here:
Spring XD: "tcp" source outputs byte array instead of string? How to output regular text?

orthAgogue incorrectly processing BLAST files

Need to recruit the help of any budding bioinformaticians that are lurking in the shadows here.
I am currently in the process of formatting some .fasta files for use in a set of grouping programs but I cannot for the life of me get them to work. First things first, all the files have to have a 3 or 4 character name such as the following:
PP41.fasta
PP59.fasta
PPBD.fasta
...etc...
The files must have headers for each gene sequence that look like so: >xxxx|yyyyyyyyyy where xxxx is the same 3 or 4 letter 'taxon' identifier as the file names I put above and yyyyyyy is a numerical identifier for each of the proteins within each of the taxons (the pipe symbol can also be replaced with an _ as below). I then cat all of these in to one file which has a header that looks correct like so:
>PP49_00001
MIENFNENNDMSDMFWEVEKGTGEVINLVPNTSNTVQPVVLMRLGLFVPTLKSTKRGHQG
EMSSMDATAELRQLAIVKTEGYENIHITGARLDMDNDFKTWVGIIHSFAKHKVIGDAVTL
SFVDFIKLCGIPSSRSSKRLRERLGASLRRIATNTLSFSSQNKSYHTHLVQSAYYDMVKD
TVTIQADPKIFELYQFDRKVLLQLRAINELGRKESAQALYTYIESLPPSPAPISLARLRA
RLNLRSRVTTQNAIVRKAMEQLKGIGYLDYTEIKRGSSVYFIVHARRPKLKALKSSKSSF
KRKKETQEESILTELTREELELLEIIRAEKIIKVTRNHRRKKQTLLTFAEDESQ*
>PP49_00002
MQNDIILPINKLHGLKLLNSLELSDIELGELLSLEGDIKQVSTGNNGIVVHRIDMSEIGS
FLIIDSGESRFVIKAS*
Next step is to construct a blast database which I do as follows, using the formatdb tool of NCBI Blast:
formatdb -i allproteins.fasta -p T -o T
This produces a set of files for the database. Next I conduct an all-vs-all BLAST of the concatenated proteins against the database that I made of them like so, which outputs a tabular file which I suspect is where my issues are beginning to arise:
blastall -p blastp -d allproteins.fasta -i allproteins.fasta -a 6 -F '0 S' -v 100000 -b 100000 -e 1e-5 -m 8 -o plasmid_allvall_blastout
These files have 12 columns and look like the below. It appears correct to me, but my supervisor suspects the error is in the blast file - I don't know what I'm doing wrong however.
PP49_00001 PP51_00025 100.00 354 0 0 1 354 1 354 0.0 552
PP49_00001 PP49_00001 100.00 354 0 0 1 354 1 354 0.0 552
PP49_00001 PPTI_00026 90.28 288 28 0 1 288 1 288 3e-172 476
PP49_00001 PPNP_00026 90.28 288 28 0 1 288 1 288 3e-172 476
PP49_00001 PPKC_00016 89.93 288 29 0 1 288 1 288 2e-170 472
PP49_00001 PPBD_00021 89.93 288 29 0 1 288 1 288 2e-170 472
PP49_00001 PPJN_00003 91.14 79 7 0 145 223 2 80 8e-47 147
PP49_00002 PPTI_00024 100.00 76 0 0 1 76 1 76 3e-50 146
PP49_00002 PPNP_00024 100.00 76 0 0 1 76 1 76 3e-50 146
PP49_00002 PPKC_00018 100.00 76 0 0 1 76 1 76 3e-50 146
SO, this is where the problems really begin. I now pass the above file to a program called orthAgogue which analyses the paired sequences I have above using parameters laid out in the manual (still no idea if I'm doing anything wrong) - all I know is the several output files that are produced are all just nonsense/empty.
Command looks like so:
orthAgogue -i plasmid_allvsall_blastout -t 0 -p 1 -e 5 -O .
Any and all ideas welcome! (Hope I've covered everything - sorry about the long post!)
EDIT Never did manage to find a solution to this. Had to use an alternative piece of software. If admins wish to close this please do, unless it is worth having open for someone else (though I suspect its a pretty niche issue).

Discovered this issue (of orthAgogue) first today:
though my reply may be old, I hope it may help future users;
issue is due to a missing parameter: seems like you forgot to specify the separator: -s '_', ie, the following set of command-line parameters should do the trick*:
orthAgogue -i plasmid_allvsall_blastout -t 0 -p 1 -e 5 -O -s '_'
(* Under the assumption that your input-file is a tabular-seperated file of columns.)
A brief update after comment made by Joe:
In brief, the problem described in the intiail error report (by Joe) is (in most cases) not a bug. Instead it is one of the core properties of the Inparanoid algorithm which orthAgogue implements: if your ortholog-result-file is empty (though constructed), this (in most cases) implies that there are no reciprocal best match between a protein-pair from two different taxa/species.
One (of many) explanations for this could be that your blastp-scores are too similar, a case where I would suggest a combined tree-based/homology clustering as in TREEFAM.
Therefore, when I receive your data, I'll send it to one of the biologists I'm working with, with goal of identifying the tool proper for your data: hope my last comment makes your day ;)
Ole Kristian Ekseth, developer of orthAgogue

Reading a text file in Ruby gives wrong output

I am not an experienced ruby programmer, so bear with me. I have a problem with this specific text file containing two lines ( this issue shows up only on occasions) :
trim(0, 15447)
0, 15447
I am trying to read these two lines with the following code:
File.open(trim).each do |line|
puts line
end
I normally obtain the normal output, but here, I get only one line, with some characters missing:
0, 1544715447)
If I want to check the character codes, I get this:
irb(main):120:0> File.open(trim).each do |line|
irb(main):121:1* puts '========================'
irb(main):122:1> puts line
irb(main):123:1> puts '........................'
irb(main):124:1> puts line.each_byte {|c| print c, ' ' }
irb(main):125:1> end
========================
0, 1544715447)
........................
116 114 105 109 40 48 44 32 49 53 52 52 55 41 13 48 44 32 49 53 52 52 55 trim(0,0, 15447
=> #<File:E:\Public\Public_videos\Soccer\1995_0129_odp_es\950129-ODP_&m3_trim30.txt>
I frankly don't understand what is going on, as I don't see any hidden character, and this happen randomly, but consistently with some files.
Any suggestion to help me understand or avoid this issue would be greatly appreciated.

What happened is that your file had two "lines" separated by a carraige return character, and not a linefeed.
You showed the bytes in your file as
116 114 105 109 40 48 44 32 49 53 52 52 55 41 13 48 44 32 49 53 52 52 55
That 13 is a carriage return, which is sometimes "displayed" by the writer going back to the start of the line it is writing.
So first it wrote out
trim(0, 15447)
then it went back to the start of the same line and wrote
0, 15447
overlaying the initial line! What do you end up with?
0, 1544715447)
Your "problem" is probably best fixed by reencoding that text file of yours to use a better way to separate lines. On Unix systems, including OSX these days, the line terminator is character 10 - known as LINE FEED. Windows uses the two-character combination 13 10 (CR LF). Only old Mac systems to my knowledge used the 13.
Many text editors today will allow you to select a "line ending" option, so you might be able to just open that file, then save it using a different line ending option. FWIW my guess is that you are using Windows now, which is known for rendering CRs and LFs differently than *Nix systems.

Module#__temp__ in perftools.rb output

While profiling some of our Ruby code perftools.rb shows the following output:
Total: 291 samples
110 37.8% 37.8% 112 38.5% #<Module:0x007ff364e2bfd0>#__temp__
19 6.5% 44.3% 19 6.5% BigDecimal#div
18 6.2% 50.5% 171 58.8% BinSearch::Methods#_bin_search
15 5.2% 55.7% 15 5.2% BigDecimal#add
So, most of the time is spent in a method designated as #<Module:0x007ff364e2bfd0>#__temp__. How do I get more information on where this is exactly?

If you're using Rails, that's probably where it's coming from: http://api.rubyonrails.org/classes/ActiveRecord/AttributeMethods/Read/ClassMethods.html#method-i-define_method_attribute
I'm still not sure why it shows up, though. It looks like that method should exist for only a very short time.

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