Timeline for What is the full script to extract sequences from fasta file by using Ids in text file in python 3 and pycharm?
Current License: CC BY-SA 4.0
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| Jan 18, 2021 at 1:00 | history | bumped | CommunityBot | This question has answers that may be good or bad; the system has marked it active so that they can be reviewed. | |
| Jun 3, 2020 at 20:30 | answer | added | StupidWolf | timeline score: 1 | |
| Jun 3, 2020 at 19:22 | comment | added | Samer Habash | Hi @StupidWolf, that would be great thank you. All my target sequences IDs are like (HSC_gene_996) in a text file which are missing the (.t1 and .t2 in some cases). in the fasta file they are all ending with ( .t1 or some cases .t2- like this one : >Hsc_gene_9627.t1 ) | |
| Jun 3, 2020 at 19:05 | comment | added | StupidWolf | Hi @SamerHabash, i can write it in python. Can you give an example where it is supposed to hit (i suppose Hsc_gene_9627.t1 and Hsc_gene_9627) and instances where it doesn't? | |
| Jun 3, 2020 at 18:07 | history | edited | terdon♦ | CC BY-SA 4.0 |
added 33 characters in body
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| Jun 3, 2020 at 15:24 | comment | added | Ram RS | OP's problem seems to be their platform. Python excels in being a cross-platform solution, hence OP looking for Python based solutions makes sense. | |
| Jun 3, 2020 at 15:08 | comment | added | Joe Healey |
To second @RamRS, that script should work indeed - provided your IDs are exact full or substring matches (excluding the >). It's been a while since I used it, so if it could be tweaked to be more useful, I'm happy to take suggestions. Whilst I love bash etc., I'd probably disagree with NatWH that it is easier than using something like biopython which is purpose built for this.
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| Jun 3, 2020 at 14:07 | comment | added | Ram RS | You may want to try Joe Healey's bioinfo-tools repository. This script looks like the one to use. | |
| Jun 3, 2020 at 12:37 | comment | added | Samer Habash | I just have python in my computer, if there is please help me, I tried to find some online tools but it didn't work | |
| Jun 3, 2020 at 11:47 | comment | added | NatWH | Does it have to be python? There are far easier ways using only bash, etc. | |
| Jun 3, 2020 at 11:15 | review | First posts | |||
| Jun 4, 2020 at 11:08 | |||||
| Jun 3, 2020 at 11:13 | history | asked | Samer Habash | CC BY-SA 4.0 |