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https://github.com/htruong/grep.fas

FASTA grep
https://github.com/htruong/grep.fas

Last synced: about 1 month ago
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FASTA grep

Host: GitHub
URL: https://github.com/htruong/grep.fas
Owner: htruong
Created: 2013-06-27T22:21:46.000Z (over 11 years ago)
Default Branch: master
Last Pushed: 2013-10-22T22:26:40.000Z (about 11 years ago)
Last Synced: 2024-10-12T16:58:42.376Z (2 months ago)
Language: Go
Size: 125 KB
Stars: 0
Watchers: 2
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md

Awesome Lists containing this project

README

grep.fas
====

This one is like grep, but it works for fasta files.

Install
---
$ go get -u github.com/htruong/grep.fas

Usage
---
Usage of grep.fas:
-1=false: Match the first sequence only
-d=true: Prints description lines
-n=false: Match the numbered sequences instead of matching strings, separated by commas (,)
-s=true: Prints sequences lines

Examples
---

$ cat myfile.fas
>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY
>gi|157367481|gb|ABV45613.1| cytochrome b [Mammuthus primigenius]
MTHIRKSHPLLKIINKSFIDLPTPSNISTWWNFGSLLGACLITQILTGLFLAMHYTPDTMTAFSSMSHIC
RDVNYGWIIRQLHSNGASIFFLCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSF
WGATVITNLFSAIPYIGTDLVEWIWGGFSVDKATLNRFFALHFILPFTMIALAGVHLTFLHETGSNNPLG
LTSDSDKIPFHPYYTIKDFLGLLILISLLLLLALLSPDMLGDPDNYMPADPLNTPLHIKPEWYFLFAYAI
LRSVPNKLGGVLALLLSILILGMMPLLHTSKHRSMMLRPLSQVLFWTLATDLLMLTWIGSQPVEHPYIII
GQMASILYFSIILAFLPIAGMIENYLIK
>junk
GQMASILYFSIILAFLPIAGMIENYLIK

$ cat myfile.fas | grep.fas "Mammuthus"
>gi|157367481|gb|ABV45613.1| cytochrome b [Mammuthus primigenius]
MTHIRKSHPLLKIINKSFIDLPTPSNISTWWNFGSLLGACLITQILTGLFLAMHYTPDTMTAFSSMSHIC
RDVNYGWIIRQLHSNGASIFFLCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSF
WGATVITNLFSAIPYIGTDLVEWIWGGFSVDKATLNRFFALHFILPFTMIALAGVHLTFLHETGSNNPLG
LTSDSDKIPFHPYYTIKDFLGLLILISLLLLLALLSPDMLGDPDNYMPADPLNTPLHIKPEWYFLFAYAI
LRSVPNKLGGVLALLLSILILGMMPLLHTSKHRSMMLRPLSQVLFWTLATDLLMLTWIGSQPVEHPYIII
GQMASILYFSIILAFLPIAGMIENYLIK

$ cat myfile.fas | grep.fas -d=false "Mammuthus"
MTHIRKSHPLLKIINKSFIDLPTPSNISTWWNFGSLLGACLITQILTGLFLAMHYTPDTMTAFSSMSHIC
RDVNYGWIIRQLHSNGASIFFLCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSF
WGATVITNLFSAIPYIGTDLVEWIWGGFSVDKATLNRFFALHFILPFTMIALAGVHLTFLHETGSNNPLG
LTSDSDKIPFHPYYTIKDFLGLLILISLLLLLALLSPDMLGDPDNYMPADPLNTPLHIKPEWYFLFAYAI
LRSVPNKLGGVLALLLSILILGMMPLLHTSKHRSMMLRPLSQVLFWTLATDLLMLTWIGSQPVEHPYIII
GQMASILYFSIILAFLPIAGMIENYLIK

$ cat myfile.fas | grep.fas -n 1,3
>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY
>junk
GQMASILYFSIILAFLPIAGMIENYLIK