User: st.ph.n
st.ph.n • 1.6k
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Posts by st.ph.n
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... Can you show an example? ...
written 1 day ago by
st.ph.n • 1.6k
0
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1
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230
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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.n • 1.6k
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85
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... If you assembled your transriptome with Trinity, use [Trinotate][1].
[1]: https://trinotate.github.io/ ...
written 4 days ago by
st.ph.n • 1.6k
0
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1
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230
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1
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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.n • 1.6k
2
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3
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160
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... > 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.n • 1.6k
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230
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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.n • 1.6k
2
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4
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213
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... 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.n • 1.6k
1
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1
answer
114
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1
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... 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.n • 1.6k
0
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124
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... 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.n • 1.6k
0
votes
1
answer
114
views
1
answers
... > 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.n • 1.6k
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