Timeline for open and read Fasta file (raw data)
Current License: CC BY-SA 4.0
25 events
| when toggle format | what | by | license | comment | |
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| Feb 19, 2023 at 21:32 | comment | added | Supertech | Just read every third line in the file and do sth with it. | |
| Feb 19, 2023 at 21:28 | comment | added | Supertech |
Based on your description, your file is not a FASTA file. I suggest you modify your question. Here is the description of FASTA file> https://www.ncbi.nlm.nih.gov/genbank/fastaformat/. Perhaps that is why it's not working.
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| Feb 19, 2023 at 20:50 | history | edited | M__♦ |
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| S Feb 19, 2023 at 20:21 | vote | accept | Amal | ||
| Feb 19, 2023 at 20:21 | vote | accept | Amal | ||
| S Feb 19, 2023 at 20:21 | |||||
| Feb 8, 2023 at 9:15 | comment | added | Amal |
This awk 'NR%5==3{ print length ($0);}' file name works and gives me the len of characters in the sequences line 3. Now how can I plot a histogram for it? Also calculate the frequency of the same line?
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| Feb 7, 2023 at 17:05 | comment | added | M__♦ | Sorry before we continue we need to establish why it's not working. Is it the file size is too big and it just freezes or is it throwing a bug? There are bugs in the code, but passing this via Biopython will likely hit a RAM bottleneck | |
| Feb 7, 2023 at 17:00 | answer | added | terdon♦ | timeline score: 4 | |
| Feb 7, 2023 at 16:46 | comment | added | terdon♦ |
no, that will print every line in the file whose line number modulo 4 is equal to 3, so it will print the 2nd, 6th, 10th, 14th and so on. But are you now saying you want some string along with the length? Should the solutions print The length for the Nth seq is and then the length?
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| Feb 7, 2023 at 16:39 | comment | added | Amal | awk 'NR%4==3' file is calculated just the first sequence while I have half a million of sequences in the same dataset | |
| Feb 7, 2023 at 16:38 | history | edited | Amal | CC BY-SA 4.0 |
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| Feb 7, 2023 at 16:11 | comment | added | terdon♦ |
And what output do you want from this? Just the number 247? I ask you again, for the third time, please show us the output you are expecting. And does it have to be in python? I mean, all you want here is awk 'NR%4==2' file, is that enough or do you absolutely need a whole python script?
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| Feb 7, 2023 at 16:03 | history | edited | terdon♦ | CC BY-SA 4.0 |
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| Feb 7, 2023 at 15:28 | history | edited | Amal | CC BY-SA 4.0 |
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| Feb 7, 2023 at 15:23 | history | edited | Amal | CC BY-SA 4.0 |
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| Feb 7, 2023 at 15:18 | history | edited | Amal | CC BY-SA 4.0 |
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| Feb 7, 2023 at 15:09 | comment | added | terdon♦ | Thanks for the edit, but please don't post images of text: we can't use those to test our solutions. We need a few lines of your actual file and the output you want to see from those lines. Both as text so we can copy/paste them. | |
| Feb 7, 2023 at 15:08 | history | edited | terdon♦ | CC BY-SA 4.0 |
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| Feb 7, 2023 at 14:34 | answer | added | M__♦ | timeline score: 0 | |
| Feb 7, 2023 at 14:15 | history | edited | Amal | CC BY-SA 4.0 |
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| Feb 7, 2023 at 14:01 | comment | added | terdon♦ |
Oh, and please use the formatting tools to format your input and output examples and the code you show as code (the {} button).
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| Feb 7, 2023 at 13:57 | comment | added | terdon♦ |
Hi and welcome to the site! We need more detail to be able to help you, so please edit your question and i) add a few lines of your fasta.dataset file; maybe 3-4 protein entries so we can see what we are working with since what you describe is not fasta; ii) show us the exact output you would want to see from that example input; iii) show us the code you wrote so we don't need to start from 0; iv) explain exactly how it "did not work"; v) tell us what operating system you are working with. Note that since this is not fasta, I doubt there is any reason to use biopython.
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| Feb 7, 2023 at 13:54 | history | edited | terdon♦ | CC BY-SA 4.0 |
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| S Feb 7, 2023 at 12:53 | review | First questions | |||
| Feb 7, 2023 at 14:25 | |||||
| S Feb 7, 2023 at 12:53 | history | asked | Amal | CC BY-SA 4.0 |