---
title: "10-comprehensive-annotation"
output: html_document
---

Run on raven
```{r}
Sys.info()
```


The C gigas protein sequence we are annotating 

```{bash}
head ../data/GCF_902806645.1_cgigas_uk_roslin_v1_translated_cds.faa
```

Creating tab delim file where seq name is separated from sequence

```{bash}
perl -e '$count=0; $len=0; while(<>) {s/\r?\n//; s/\t/ /g; if (s/^>//) { if ($. != 1) {print "\n"} s/ |$/\t/; $count++; $_ .= "\t";} else {s/ //g; $len += length($_)} print $_;} print "\n"; warn "\nConverted $count FASTA records in $. lines to tabular format\nTotal sequence length: $len\n\n";' data/GCF_902806645.1_cgigas_uk_roslin_v1_translated_cds.faa > output/GCF_902806645.1_cgigas_uk_roslin_v1_translated_cds.tab
```


Connecting gene ID (LOC#######) wiht NCBI Accession (query for blast)

```{bash}
cat ../output/GCF_902806645.1_cgigas_uk_roslin_v1_translated_cds.tab | awk '{print $2, $1}' | sed 's/\[gene=//g' | sed 's/\]//g' > ../output/LOC_Acc.tab
```

Drosophila Blast


```{bash}
/home/shared/ncbi-blast-2.11.0+/bin/tblastn \
-query ../data/GCF_902806645.1_cgigas_uk_roslin_v1_translated_cds.faa \
-db ../blastdb/dmel-all-CDS-r6.37 \
-out ../output/CgR-blastp-dmel.tab \
-num_threads 20 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt "6 qaccver saccver evalue"
```



```{bash}
/home/shared/ncbi-blast-2.11.0+/bin/blastp \
-query ../data/GCF_902806645.1_cgigas_uk_roslin_v1_translated_cds.faa \
-db /home/shared/blast_dbs/20210613_ncbi_sp_v5/swissprot \
-out ../output/CgR-blastp-sp.tab \
-num_threads 20 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt "6 qaccver saccver evalue"
```

```{bash}
cd ../blastdb
curl -O https://gannet.fish.washington.edu/seashell/bu-mox/blastdb/Caenorhabditis_elegans.WBcel235.pep.all.fa
```


```{bash}
/home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \
-in ../../blastdb/dmel-all-CDS-r6.37.fasta \
-dbtype nucl \
-out ../../blastdb/dmel-all-CDS-r6.37
```




```{bash}
/home/shared/ncbi-blast-2.11.0+/bin/blastp \
-query ../data/GCF_902806645.1_cgigas_uk_roslin_v1_translated_cds.faa \
-db ../blastdb/Caenorhabditis_elegans.WBcel235.pep \
-out ../output/CgR-blastp-cel.tab \
-num_threads 20 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt "6 qaccver saccver evalue"
```