User: SMK
SMK • 350
- Reputation:
- 350
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- Gentopia, Belgium
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- 15 minutes ago
- Joined:
- 2 years, 7 months ago
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Posts by SMK
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... Hi [sw.knudsen][1],
`specimen_voucher` will be `record["GBSeq_feature-table"][0]["GBFeature_quals"][3]["GBQualifier_value"]`:
```
$ cat test.py
from Bio import Entrez
Entrez.email = "email@any_email.com"
organisms=["Diaphus anderseni"]
genes = ["H3"]
specs = {}
acclist = {}
for org in organisms:
...
written 1 hour ago by
SMK • 350
1
vote
1
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36
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1
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Comment:
C: Biopython problem again
... You're welcome, good luck! ...
written 3 hours ago by
SMK • 350
2
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1
answer
36
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1
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Answer:
A: Biopython problem again
... Hi [psschlogl][1],
How many sequences are there in your `alpha.faa` and `beta.faa`?
If both contain one, it works for me:
```
$ cat data/alpha.faa
>seq1
MLLPLRRVLLKAVRQHNFFSESHATSINTRKGLVLGVYEKQSDDEGILLTEAAASFDSSISGKLSEML
PTEFANTIEQKLSPFAHKVTVHKRPQSWIESEQMGAFLSVSKGSEEPPVFLELHYKGSLDSAQP
$ cat da ...
written 3 hours ago by
SMK • 350
0
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3
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79
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3
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... Nice tips! 👍 Thanks, zx8754. ...
written 7 hours ago by
SMK • 350
2
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3
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79
views
3
answers
... Hi [saamar.rajput][1],
See the answer from [benformatics][2] (credits goes to him), the key is to make sure your "Gene" is in character type instead of factor.
```
> results <- read.delim("example.txt", header = TRUE, stringsAsFactors = FALSE)
> head(results)
Gene Fold pva ...
written 9 hours ago by
SMK • 350
0
votes
1
answer
45
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1
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... You're welcome. Try this:
```
(for i in *.tsv; do echo -ne "${i}\t" && awk '$3>=40{print $2}' ${i} | sort -u | wc -l; done) > output.txt
``` ...
written 10 hours ago by
SMK • 350
2
votes
1
answer
45
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1
answers
... Hi [fex2][1],
Try:
```
for i in *.tsv; do echo -ne "${i}\t" && awk '$3>=40{print $2}' ${i} | sort -u | wc -l; done
```
It should returns something like:
```
blast_out1.tsv 217
blast_out2.tsv 172
blast_out3.tsv 215
```
[1]: https://www.biostars.org/u/48471/ ...
written 10 hours ago by
SMK • 350
0
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0
answers
57
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... Hi felipead66,
Please check out the "Effect prediction details" section on [Input & output files][1] from snpEff document.
Starting from version 4.0 VCF output uses SO terms by default, so the classic "NON_SYNONYMOUS_CODING" is now "missense_variant", "initiator_codon_variant", and "stop_retain ...
written 10 hours ago by
SMK • 350
0
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0
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57
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... You can add `-csvStats` when running snpEff: `java -jar snpEff.jar eff -csvStats snpEffoutput.csv snpEff_database snpEffinput.vcf > snpEffoutput.vcf`.
There will be a section counting each effect in the csv:
```
$ grep -A24 "# Count by effects" snpEffoutput.csv
# Count by effects
Type , Count , ...
written 12 hours ago by
SMK • 350
2
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0
answers
64
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0
answers
... If the GFF format is correct, try [gffread][1] with `-y`:
(`-y write a protein fasta file with the translation of CDS for each record`)
```
$ gffread -y proteins.fa -g Homo_sapiens.GRCh38.dna.chromosome.1.fa Homo_sapiens.GRCh38.96.chromosome.1.gff3
$ head proteins.fa
>transcript:ENST00000641515 ...
written 12 hours ago by
SMK • 350
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For A: Uploading data files to Webin upload area under Linux
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