User: st.ph.n

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st.ph.n1.6k
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Posts by st.ph.n

<prev • 457 results • page 1 of 46 • next >
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Comment: C: Split the multiple sequences file into a separate files
... Can you show an example? ...
written 1 day ago by st.ph.n1.6k
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Comment: C: Remove gap from files
... If you want to remove all gaps from the file: sed -i 's/-//g' input.fasta Otherwise, you need to know the positions, for specific gaps if you're not removing all of them. The OP is vague on how you intend to identify gaps to be removed. ...
written 1 day ago by st.ph.n1.6k
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Comment: C: Suggesstion for annotating transcript asembly of a gymnosperm
... If you assembled your transriptome with Trinity, use [Trinotate][1]. [1]: https://trinotate.github.io/ ...
written 4 days ago by st.ph.n1.6k
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Comment: C: Remove gap from files
... provide examples of the positions in which to remove gaps ...
written 4 days ago by st.ph.n1.6k
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Comment: C: Transform a GTF file into a data frame in R
... > I am quite able with R Have you tried anything? If so, show it. Or, find a tutorial, try some code and come back with any errors and edit the OP with code and said errors. ...
written 4 days ago by st.ph.n1.6k
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Comment: C: Remove gap from files
... > I want remove the long unaligned gap from the files with position wise Do you know the positions of the gaps to remove? Are they based on the blast result? ...
written 4 days ago by st.ph.n1.6k
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Answer: A: How to split columns into rows based on gene ids in R?
... Python solution. #!/usr/bin/env python import sys # Open input file with open(sys.argv[1], 'r') as f: # Empty dictionary go = {} # grab header header = next(f).split('\t') # for each line in file for line in f: # Dictionary {key: value}, ...
written 4 days ago by st.ph.n1.6k
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Comment: C: Combining two columns in a tab-delimited file where there is a zero in one
... This is messy, and you're naming your list as the same as what you're opening your file as. with open(sourcefile, "r") as germ: germ = [item.lower().replace("\n", "") for item in germ.readlines()] Try this: with open('gene_name.txt', 'r') as source: germ = [line.strip() ...
written 6 days ago by st.ph.n1.6k
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Comment: C: Question: Converting Blast Results/Output to FASTA format
... Ok so it looks like you piped the output of both commands into the same file, or copied/paste right from the terminal. Good practice for a log, bad practice for parsing. If the blast result was a separate file, you would have a much easier time. Use `-out blast.out.txt` in your blast command to name ...
written 6 days ago by st.ph.n1.6k
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Comment: C: Combining two columns in a tab-delimited file where there is a zero in one
... > The ultimate reason for this is so that I can make a list of > identifiers for downstream purposes. Can you show an example of the annotations, to see delimiters and possible ids? ...
written 6 days ago by st.ph.n1.6k

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Teacher 4 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 8 days ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
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Scholar 9 weeks ago, created an answer that has been accepted. For A: Using Trinity with case/control data
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