Moderator: Philipp Bayer
Philipp Bayer ♦ 4.2k
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Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org
Posts by Philipp Bayer
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... Good to see it works for you :) ...
written 2 days ago by
Philipp Bayer ♦ 4.2k
1
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... I just tried it with some made-up test data and it works fine for me, I get the output that I expected - what is the error you're seeing? ...
written 3 days ago by
Philipp Bayer ♦ 4.2k
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Answer:
A: How to convert .gff3 to .gff
... Normally a gff3 file and a gff file should be indistinguishable to most parsers (in fact often a gff file is a gff3 file, but not always), do you get an error in Gff2GeneTable when you load your gff file?
Have a look at what a gff3 validator tool such as [this one][1] tells you about your gff file, ...
written 3 days ago by
Philipp Bayer ♦ 4.2k
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Answer:
A: error in cuffmerge
... I haven't encountered this before, but it looks like it doesn't like the () in the file name for '/home/mra/Desktop/ensan/Homo-sapiens(hg19).fa'? Have you tried just renaming that file, removing those brackets? ...
written 4 days ago by
Philipp Bayer ♦ 4.2k
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Answer:
A: RepeatMasker in Maker
... I assume that option is the '-nolow' flag in RepeatMasker ([ref][1]).
By default it's not too easy to get non-standard flags into RepeatMasker, in the past I think there was a way to get no_low into RepeatMasker directly, looking at the code in the maker folder in `lib/GI.pm`:
runRepeatMask ...
written 6 days ago by
Philipp Bayer ♦ 4.2k
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... I see! I slightly changed the code - I now use a defaultdict, which by default stores an empty list for any possible key, so I can just append to that.
I run it like this:
python3 compare.py KOG.2 FASTA.fasta
Code is:
from Bio import SeqIO
import sys
from collections import defa ...
written 7 days ago by
Philipp Bayer ♦ 4.2k
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Comment:
C: Excel Files corrupted in R.
... That's about it!
An xlsx file is a compressed archive of your data, while read.table() assumes that your input data is uncompressed, flat text. The garbled text you're seeing is compressed binary. The xlsx package can read that. ...
written 7 days ago by
Philipp Bayer ♦ 4.2k
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... Hmm I'd do this using Biopython because it's easier.
The following assumes that the kog file fits into memory, is tab-delimited, and has the gene name in column 1.
It's also got bad argumentparsing, argparse would be the way to go. It's untested.
from Bio import SeqIO
import sys
...
written 10 days ago by
Philipp Bayer ♦ 4.2k
1
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70
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... This is the code that is triggered:
#walk out edges to force completion
if($CTL_OPT->{always_complete} && (!$has_start || !$has_stop)){
$f = PhatHit_utils::adjust_start_stop($f, $seq);
$transcript_seq = get_transcript_seq($f, $seq);
($translation_seq, $ ...
written 15 days ago by
Philipp Bayer ♦ 4.2k
1
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118
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... Your table looks non-standard to me so I don't think there's a publicly available parser, but I might be wrong.
Here are some rules to get you going with your own parser, you'll have to transpose that table and add a few columns like you have them there.
- Only the combination of family and indivi ...
written 23 days ago by
Philipp Bayer ♦ 4.2k
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