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https://github.com/adamtaranto/reconcile
Take clustered element fragment coordinates from RECON and write sequences to fasta for alignment and consensus calling.
https://github.com/adamtaranto/reconcile
Last synced: 3 days ago
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Take clustered element fragment coordinates from RECON and write sequences to fasta for alignment and consensus calling.
- Host: GitHub
- URL: https://github.com/adamtaranto/reconcile
- Owner: Adamtaranto
- License: mit
- Created: 2017-03-11T22:23:57.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2017-09-19T02:48:51.000Z (over 7 years ago)
- Last Synced: 2024-11-21T02:33:38.639Z (2 months ago)
- Language: Python
- Size: 5.86 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# RECONcile
# Table of contents
* [About RECONcile](#about-reconcile)
* [Options and usage](#options-and-usage)
* [Installing RECONcile](#installing-reconcile)
* [Example Workflow](#example-workflow)
* [Standard options](#standard-options)
* [License](#license)
# About RECONcile
Take clustered element fragment coordinates from RECON and write sequences to FASTA for alignment and consensus calling.
# Options and usage
## Installing RECONcile
Install from this repository.
```bash
git clone https://github.com/Adamtaranto/RECONcile.git && cd RECONcile
```
## Example Workflow
**Get total count and names of candidate TEs for RECON**
```bash
awk '/^>/ {print $1;} ' Unclustered_candidate_TEs.fa | wc -l | sed 's/^ *//g' > denovo_names.txt
awk '/^>/ {print $1;} ' Unclustered_candidate_TEs.fa | sed 's/>//g' | sed 's/^ *//g' >> temp_names.txt
```
**Sort in lexical order**
```bash
cat temp_names.txt | sort >> denovo_names.txt
rm temp_names.txt
```
**Run All vs All BLAST**
```bash
blastn -subject Unclustered_candidate_TEs.fa -query Unclustered_candidate_TEs.fa \
-out denovo_all_v_all.tab -evalue 0.001 -outfmt 6 -task blastn -max_target_seqs 1000
```
**Keep all non-self hits with bitscore > 100**
```bash
awk '{if ($1 != $2 && $12 >= 100) print;}' denovo_all_v_all.tab > filtered_hits.tab
```
**MSPCollect fails, use [blast2MSP.pl](https://gist.github.com/sestaton/ea770a26032983e49189#file-blast2msp-pl) to convert to blast result to MSP format instead:**
```bash
./blast2MSP.pl filtered_hits.tab > MSP_denovo.out
```
**Run RECON**
```bash
./RECON-1.08/scripts/recon.pl denovo_names.txt MSP_denovo.out 1
```
**Clean up eles output file from RECON**
```bash
awk '!/^#/ {print;}' eles | sed 's/\( \)*/\1/g' | cut -d' ' -f 2- > Clean_Eles.txt
```
**Fetch fragments for each family**
```bash
./RECON_cluster.py -i Unclustered_candidate_TEs.fa -e Clean_Eles.txt -d output_clusters
```
**Align clustered fragments with MAFFT**
```bash
mkdir mafftaligns
for i in $(find output_clusters -name '*.fa' | sort);do
base=$(basename $i)
name="${base%.*}"
mafft $i > 'mafftaligns/'$name'.aln'
done
```
**Build concensus sequences from alignments with [cons](http://www.bioinformatics.nl/cgi-bin/emboss/help/cons)**
```bash
mkdir consensus_fasta
for i in $(find mafftaligns -name '*.aln' | sort);do
base=$(basename $i)
name="${base%.*}"
cons -sequence $i -identity 0 -snucleotide1 -supper1 -name $name'_consensus' \
-outseq 'consensus_fasta2/'$name'_consensus.fa' -auto
done
```
**Concatenate all consensus sequences and convert to uppercase**
```bash
rm RECON_consensus.fa
touch RECON_consensus.fa
for x in $(find consensus_fasta -name '*.fa' | sort);do
tr [:lower:] [:upper:] < $x >> RECON_consensus.fa
done
```
## Standard options
```bash
Usage: RECONcile [-h] -i INFASTA [-e ELES] [-d OUTDIR]
Extracts and orients TE frags belonging to RECON clusters.
Optional arguments:
-h, --help Show this help message and exit
-i, --inFasta Multi fasta containing all TE sequences.
-e, --eles Space delimited 'ele' file from RECON.
-d, --outDir Directory for new cluster files to be written to.
```
# License
Software provided under MIT license.