User: shoujun.gu

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shoujun.gu310
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Rockville/MD
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1 week, 3 days ago
Joined:
10 months, 2 weeks ago
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Posts by shoujun.gu

<prev • 58 results • page 1 of 6 • next >
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Answer: A: Comparing 2 Columns at once
... here is the python code, replace the real file name in the first two lines: input_file='your_input_file' output_file='your_output_file' import pandas as pd df=pd.read_csv(input_file, index_col=0) col=df.columns col_t=col[:-1] new_col=[col_t[i]+str(i+2) for ...
written 19 days ago by shoujun.gu310
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Answer: A: How to remove duplicate sequences in fasta file using python?
... This python code will combine all the input fasta files (any number of files), and output 1 file with duplicated sequences removed. Note: if your input fasta files are too big to load into memory, this code will fail. input_files=[list of input file names] output_file='output_file_name' ...
written 24 days ago by shoujun.gu310
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Answer: A: Technical question about python "to find the strings"
... I believe all your input file are actually csv file thus, the most efficient way is: 1) read these file into dataframe 2) inner join the column you want ...
written 24 days ago by shoujun.gu310
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Answer: A: How to extract all promoter regions in multi-fasta format from genome using GFF?
... 1. extract the gene id from GFF file 2. fetch the promoter sequence from BioMart by using the gene id you extracted ...
written 24 days ago by shoujun.gu310
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Answer: A: Fastest way to subset dataframe in python
... I think what you need is some code like this: import pandas as pd df=pd.read_csv('your blast file') labels=df['qseqid'].unique() for label in labels: df_temp=df.loc[df['qseqid']==label,:] # do whatever you want to do ...
written 26 days ago by shoujun.gu310
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Comment: C: Any easy was to run a differential expression analysis?
... You should follow DESeq/ DESeq2/edgeR vignette. If you cannot understand these documents, then it means it's beyond your ability to do the DE analysis. Go ahead and find some bioinformatician to help you. ...
written 6 weeks ago by shoujun.gu310
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Answer: A: Which is more useful - Seaborn or Matplotlib?
... please read seaborn introduction: https://seaborn.pydata.org/introduction.html#introduction ...
written 8 weeks ago by shoujun.gu310
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Comment: C: Transform duplicate rows into columns.
... I just don't understand why you want to convert file into that format. working on duplicated rows is way much easier than this conversion ...
written 10 weeks ago by shoujun.gu310
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Comment: C: about python module aln
... looks like its a customized module you should ask the author where to download this module ...
written 11 weeks ago by shoujun.gu310
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Comment: C: Removing gap using array
... Because this code : 'for word in file' treat file as a list of lines. Thus, you are counting lines. Maybe you could try this way: 1. remove all the '\n' in the fasta sequence 2. code a regex of more than 20 '-', such as --------------------[-]* 3. find the all matches and delete them. ...
written 11 weeks ago by shoujun.gu310

Latest awards to shoujun.gu

Scholar 26 days ago, created an answer that has been accepted. For A: Kallisto run error
Scholar 5 months ago, created an answer that has been accepted. For A: Kallisto run error
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Remove gap from files
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Remove gap from files
Scholar 5 months ago, created an answer that has been accepted. For A: Kallisto run error
Scholar 5 months ago, created an answer that has been accepted. For A: Kallisto run error
Scholar 5 months ago, created an answer that has been accepted. For A: Kallisto run error
Scholar 6 months ago, created an answer that has been accepted. For A: Kallisto run error

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