Timeline for using python to write bioinformatics pipelines tutorial
Current License: CC BY-SA 3.0
32 events
| when toggle format | what | by | license | comment | |
|---|---|---|---|---|---|
| Aug 18, 2017 at 2:58 | vote | accept | novicebioinforesearcher | ||
| Aug 18, 2017 at 2:57 | vote | accept | novicebioinforesearcher | ||
| Aug 18, 2017 at 2:58 | |||||
| Aug 18, 2017 at 2:57 | vote | accept | novicebioinforesearcher | ||
| Aug 18, 2017 at 2:57 | |||||
| Aug 18, 2017 at 2:57 | vote | accept | novicebioinforesearcher | ||
| Aug 18, 2017 at 2:57 | |||||
| Jul 6, 2017 at 20:56 | vote | accept | novicebioinforesearcher | ||
| Aug 18, 2017 at 2:57 | |||||
| Jul 6, 2017 at 20:56 | vote | accept | novicebioinforesearcher | ||
| Jul 6, 2017 at 20:56 | |||||
| Jul 6, 2017 at 20:56 | vote | accept | novicebioinforesearcher | ||
| Jul 6, 2017 at 20:56 | |||||
| Jul 6, 2017 at 20:56 | vote | accept | novicebioinforesearcher | ||
| Jul 6, 2017 at 20:56 | |||||
| Jul 6, 2017 at 18:44 | comment | added | novicebioinforesearcher | @quantik because I am learning to write codes in python and also because (i may be wrong here) in case you have a greater number of samples bash would not be a good way to work(foreg 40 samples to be processed) i can use os.walk etc in python to submit jobs correct me if i am wrong | |
| Jul 6, 2017 at 18:28 | comment | added | quantik | I'm curious as to why you are averse to writing your pipeline in bash? @novicebioinforesearcher | |
| Jul 6, 2017 at 16:41 | comment | added | bli | @novicebioinforesearcher These comments are not adapted to give examples. What I mean is that you will still need python3 for snakemake, but if there are things you can only do in python2, you can write whatever computation you want to do in python2 in the form of an independent program (presumably accepting command-line arguments). Then, you will call this program from within snakemake (or whatever workflow management tool you happen to use, or a python script using subprocess) exactly like you would do for samtools, hisat or any other program. | |
| Jul 6, 2017 at 15:31 | comment | added | novicebioinforesearcher | @bli how can I do that, sorry I am still learning stuff here could you share an example | |
| Jul 6, 2017 at 15:02 | comment | added | bli | @novicebioinforesearcher Note that if you need to program in python2, you can still do it in external scripts and call them from snakemake like you would do for any other program. | |
| Jul 6, 2017 at 12:57 | vote | accept | novicebioinforesearcher | ||
| Jul 6, 2017 at 20:56 | |||||
| Jul 6, 2017 at 12:29 | comment | added | Devon Ryan | @novicebioinforesearcher Yes, that's correct. | |
| Jul 6, 2017 at 12:28 | comment | added | novicebioinforesearcher | @DevonRyan I looked snakemake it is available only in python3 is that correct? | |
| Jul 6, 2017 at 12:25 | vote | accept | novicebioinforesearcher | ||
| Jul 6, 2017 at 12:57 | |||||
| Jul 6, 2017 at 12:24 | vote | accept | novicebioinforesearcher | ||
| Jul 6, 2017 at 12:25 | |||||
| Jul 6, 2017 at 12:22 | comment | added | novicebioinforesearcher | @bli this was useful | |
| Jul 6, 2017 at 11:58 | comment | added | bli | I agree that snakemake is worth learning. If you want to use subprocess, I found the following tutorial just yesterday, which looked quite clear: crashcourse.housegordon.org/python-subprocess.html | |
| S Jul 6, 2017 at 11:22 | history | suggested | Dan |
Added a tag.
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| Jul 6, 2017 at 9:53 | answer | added | Iakov Davydov | timeline score: 4 | |
| Jul 6, 2017 at 9:12 | answer | added | agapow | timeline score: 13 | |
| Jul 6, 2017 at 9:04 | review | Suggested edits | |||
| S Jul 6, 2017 at 11:22 | |||||
| Jul 6, 2017 at 9:00 | answer | added | Dan | timeline score: 0 | |
| Jul 6, 2017 at 6:53 | comment | added | Devon Ryan | If you ever need more elaborate pipelines in python, then I would strongly encourage you to look into snakemake, which is pretty commonly used for this purpose. | |
| Jul 6, 2017 at 3:45 | vote | accept | novicebioinforesearcher | ||
| Jul 6, 2017 at 12:24 | |||||
| Jul 6, 2017 at 3:45 | vote | accept | novicebioinforesearcher | ||
| Jul 6, 2017 at 3:45 | |||||
| Jul 6, 2017 at 1:35 | vote | accept | novicebioinforesearcher | ||
| Jul 6, 2017 at 3:45 | |||||
| Jul 6, 2017 at 0:25 | answer | added | gringer♦ | timeline score: 4 | |
| Jul 5, 2017 at 22:30 | answer | added | Bioathlete | timeline score: 5 | |
| Jul 5, 2017 at 22:18 | history | asked | novicebioinforesearcher | CC BY-SA 3.0 |