CODEWITHSUNDEEP
ruby
Sebastian Zeki
Sebastian Zeki

Reputation: 6874

count specific lines in specific files in a folder

I'm fairly new to ruby but this is testing me

I want to count all the lines in any file that ends in bowtie.txt in a folder

The lines have to start with a number of varying length followed by a '+' or a '-' (with or without whitespace inbetween. Sometimes the lines are wrapped but I don't know if this matters).

I want to then create a hash that stores the filename with the count associated with it.

I've got as far I think as looping through the directory to select the files out and then counting the number of lines in that file but how do I then create the hash and return it?

The file data looks like:

0   +   chr12   129402816   ACACAGGGAGGGGAATAACACACACTGGGACCTGTCAGGAGAGGGTAGGGCTGGGGGCATCAGGAGAGCATCAGGAAAAATAGCTAATGCATGCTGGGCT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    0   
2   -   chr5    93625939    TCAACCTGTCATCTACATTAGGTATTTCTCCTAATGCTATCCCTCCCCTAGCCCCCCACCACCCAACAGACCCTGGTGTGTGATGTTCCCCTCCCTGTGT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    0   5:T>C
5   +   chr3    155023119   ACACAGGGAGGGGAACATCACACACCGGGGCCTGTAGTGGGGGTGAGGGGCAAGAGGAGGAATAGCATTAGGAGAAATACCTAATGTAGATGACCGGTTG    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    0   
7   +   chr2    22818055    ACACAGGGAGGGGAAAAACACACACTGGGGCTTCTCAGGGGTGGTGGGGGGAGAGCATCAGGATAAATAGCTAATGCATGCAGGGCTTAATACCTAGGTG    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    0   
8   +   chr3    131206106   ACACAGGGAGGGGAACATCACACACCAGGCCCTGTCAGCGGTGAGGGGCTGGGGGAGGGATAGCATTAAGAGAAATACCTAATATAAATGACGAGTTGAT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    0   8:C>A
10  +   chrX    108455592   ACACAGGGAGGGGAACATCACACACCAGGGCCTGTCGGGCAGTGGGGGGGCAAAGGGAGGGATTAAGTCATACACCCAATGCATGTGGGGCTTAAAACCC    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    0   7:A>G
11  -   chr2    31936302    ACCCATTAACTCGTCATTTACATTAGGTATATCTCCTAATGCTATCCCTCCCCCCACCCCACAACAGGCCCCCCGGTGTGTGATGTTCCCCTCCCTGTGT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    0   7:T>C

This is what I am trying to get at the end

blablabla.bowtie.txt : 27998
blablafsfds.bowtie.txt : 25987
etc

This is my attempt at the code:

Dir[File.join('/Volumes/SeagateBackupPlusDriv/SequencingRawFiles/TumourOesophagealOCCAMS/SequencingScripts/3finalcounts', '*.bowtie.txt')].each |file| do
  puts File.open(file) { |f| f.grep(/^[0-9]*.\+|\-/).count }
end

Upvotes: 0

Views: 77

Answers (1)

Aleksei Matiushkin
Aleksei Matiushkin

Reputation: 121000

Untested, since I have no input files, but likely working:

# `Dir[]` expects it’s own format
#                                ⇓ will inject results into hash
Dir['/Volumes/.../*.bowtie.txt'].inject({}) do |memo, file|
  memo[file] = File.readlines(file).select do |line| 
                 line =~ /^[0-9]+\s*(\+|\-)/ # only those, matching
               end.count
  memo
end

Additional references: IO#readlines, Enumerable#select, Enumerable#inject.

Upvotes: 3

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