Timeline for What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?
Current License: CC BY-SA 3.0
9 events
| when toggle format | what | by | license | comment | |
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| S Jun 2, 2017 at 13:41 | history | suggested | terdon♦ | CC BY-SA 3.0 |
There's nothing bash-specific or even bash-related there.
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| Jun 2, 2017 at 12:34 | review | Suggested edits | |||
| S Jun 2, 2017 at 13:41 | |||||
| Jun 1, 2017 at 18:11 | comment | added | Iakov Davydov | @KonradRudolph, I updated the answer to indicate that this works only in the simple case | |
| Jun 1, 2017 at 18:08 | history | edited | Iakov Davydov | CC BY-SA 3.0 |
Mention that this is a simple case
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| Jun 1, 2017 at 17:14 | comment | added | Konrad Rudolph |
FASTQ is tricky because @ can also start the quality string line; see chat.stackexchange.com/transcript/message/37809200#37809200 and following lines. For reference, here’s a Perl script that parses FASTQ and trims the mate information off of the identifier. It can probably serve as a starting point; I think this is very close to the minimal code: gist.github.com/klmr/81a2b86cd93c706d28611f40bdfe2702
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| Jun 1, 2017 at 17:07 | comment | added | Iakov Davydov | @KonradRudolph with -o grep outputs individual symbols, I will think how to correct fastq code | |
| Jun 1, 2017 at 17:04 | history | edited | Iakov Davydov | CC BY-SA 3.0 |
small/capital
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| Jun 1, 2017 at 17:03 | comment | added | Konrad Rudolph | Now you’re counting lines containing Ns, not Ns. Also, FASTQ records can span more than four lines. :-( | |
| Jun 1, 2017 at 17:00 | history | answered | Iakov Davydov | CC BY-SA 3.0 |