File position and buffers

[Cee Joe]

Hi Jake,

I would still need the header intact, which should be away from the rest
of the entry:

gi|329295464|ref|NM_2005745.3Acc1| Def1 zgc:65895 (zgc:65895), mRNA

AGCTCGGGGGCTCTAGCGATTTAAGGAGCGATGCGATCGAGCTGACCGTCGCG

instead of:

">gi|329295464|ref|NM_2005745.3Acc1| Def1 zgc:65895 (zgc:65895),
mRNAAGCTCGGGGGCTCTAGCGATTTAAGGAGCGATGCGATCGAGCTGACCGTCGCG>"

Still need the header line so I can extract information from that and
the lines after that in each entry. Your delete() will delete all the
newlines, which would not be beneficial in this scenario. Thanks for the
input, appreciate it.

-Cee

 

[7stud --]

Cee Joe wrote in post #995830:

7stud -- wrote in post #995821:

I understand the logic, it makes sense. What if the file looked like
this, where there is one newline seperating the entries? :

What if you had presented that possibility from the very beginning?


require 'stringio'

str =<<ENDOFSTRING

gi|329295464|ref|NM_2005745.3Acc1| Def1 zgc:65895 (zgc:65895), mRNA AGCTCGGGGGCTCTAGCGATTTAAGGAGCGATGCGATCGAGCTGACCGTCGCG

gi|456299107|ref|NM_2342343.3Acc2| Def2 zgc:65895 (zgc:65895), mRNA GTCGCTGGGTCGAAAAGTGGTGCTATATCGCGGCTCGCGTCGATGTCGCGATG
CGTGCGCGCGAGAGCGCGCTATGATGAAAGGATGAGAGAG

gi|3542945647|ref|NM_7453343.5Acc3| Def3 zgc:65895 (zgc:65895), mRNA

CGTGCGGGGABCCGTACGTGCCGTGGGGGTTT
AATAGCGCGCCATCTGAGCAG
TTAGTCGCTGACGCATGCACG

ENDOFSTRING

input = StringIO.new(str)
buffer = ''

input.each do |line|
if line[0, 1] == '>'
if buffer != ''
puts buffer #or do something else to buffer
puts '-' * 20
end

buffer = ''
buffer << line
else
buffer << line.sub(/ \n+ \z /xms, '')
end

end

puts buffer #or do something else to buffer

--output:--

gi|329295464|ref|NM_2005745.3Acc1| Def1 zgc:65895 (zgc:65895), mRNA AGCTCGGGGGCTCTAGCGATTTAAGGAGCGATGCGATCGAGCTGACCGTCGCG

CGTGCGGGGABCCGTACGTGCCGTGGGGGTTTAATAGCGCGCCATCTGAGCAGTTAGTCGCTGACGCATGCACG