User: cristian
cristian • 80
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Posts by cristian
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... It's also marking the heterozygotes. I think table 2 is as you wish. ...
written 3 days ago by
cristian • 80
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... The code above is now exporting the 3 columns into a single file. ...
written 3 days ago by
cristian • 80
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... What does this mean: ' i want to check whether P1 and P2 match for M1 or not' ?
Do you only want to export columns where both parents are homozygous? ...
written 3 days ago by
cristian • 80
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... How do you define 'between them' when the parents are not homozygous or the data not available, M3 and M2 respectively. ...
written 3 days ago by
cristian • 80
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... Sorry, can you explain the problem more clearly? Do you want to output columns M2 and M3 in the first step? Also, I still haven't sorted out the heterozygote bit. I am on it. ...
written 3 days ago by
cristian • 80
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... Maybe you can consolidate your comments into an answer and I can accept it? ...
written 3 days ago by
cristian • 80
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... Correct guess, thanks. It worked now. So you made use of the fact that the GTF file just had 'CHROMOSOME_' prepended to all my FASTA chromosome names, right? Do you mind explaining this: 's/CHROMOSOME_//g' ? ...
written 3 days ago by
cristian • 80
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... I edited my answer in my first comment. Check it out and tell me where you got. There were mistakes in my first code. For example, when you fetch a column:
df[['column name']]
the i-th value of that column:
df[['column name']][i]
There are brackets missing in your blue code. ...
written 3 days ago by
cristian • 80
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... Hi,
sed -e 's/CHROMOSOME_//g' celegans.gtf
works but the command with the '-i' option gives the following error:
sed: 1: "output/genome/celegans/ ...": invalid command code o
Does the '-i' mean 'in-place' so changes the file directly? I am going to try to redirect the output of the '-e' ...
written 3 days ago by
cristian • 80
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... Hi,
I have a GTF file with the following head:
head celegans.gtf
CHROMOSOME_I Coding_transcript exon 4119 4358 . - transcript_id "Transcript:Y74C9A.3.1"; gene_id "Gene:Y74C9A.3";
CHROMOSOME_I Coding_transcript exon 5195 5296 . - transcript_id "Transcript:Y74C9A.3.1"; gene_id "Gene:Y74C ...
written 3 days ago by
cristian • 80
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