AB Pull Records

--pull_records, -pr

Description

Extract and return entire rows from an alignment. The tool takes one or more strings as input, which are searched for in the record IDs; matches are retained. Columns with 100% gaps in the new alignment are deleted.

Arguments

Search pattern ( regex )

At least one simple string or regular expression is required. If the search pattern exists in a record ID, that row will be retained.

'full' ( exact string )

Optional. By default, only the record IDs are searched. If the records have a description field, then you can pass in the word 'full' to expand the search to this metadata. In the rare case that you must search for the word 'full' in your IDs, turn it into an explicit regular expression by enclosing it in parentheses --> '(full)'

Examples

Input file: Panx_C-terms.physr

 3 100
Mle-Panxα9  ---atgttagacatactttcaaagtttaaaggagttactccttttaaaggtataacgatagatgacgggtgggatcaactcaatcggagttttatgttcg
Mle-Panxα4  atggttattgagctgctagctggatacaaaggtctgtccccgtttaaagacgcgactgttgacgactcatgggaccaaataaaccgatgttacgtgttca
Mle-Panxα6  atgttattggagatattagcgaacttcaaaggagcgacacctttcaaagaaatagttctagatgacaagtgggaccagattaaccgatgttacatgttcc

 3 100
Ael_PanxβA  ---------------------------------------------------------------------------------------ATGGTAGTCATTC
Ael_PanxβB  ---------------------------------------------------------------------------------------ATGGTTGTCATAC
Ael_PanxβC  ATGCCCAACAACATATACCCAAACAGACTATTCGTGAAGACTAATGATATCCCGGAAAAATTAAACACTCCGTGGTCATACGAAAAAATGGTTGTAGTGC

Usage example 1

$: alb Panx_C-terms.physr -pr "PanxβB" "PanxβC"

Output

 2 100
Ael_PanxβB  ---------------------------------------------------------------------------------------ATGGTTGTCATAC
Ael_PanxβC  ATGCCCAACAACATATACCCAAACAGACTATTCGTGAAGACTAATGATATCCCGGAAAAATTAAACACTCCGTGGTCATACGAAAAAATGGTTGTAGTGC

Usage example 2

Regular expressions are understood

$: alb temp.del -pr α[46] βA

Output

 2 100
Mle-Panxα4  atggttattgagctgctagctggatacaaaggtctgtccccgtttaaagacgcgactgttgacgactcatgggaccaaataaaccgatgttacgtgttca
Mle-Panxα6  atgttattggagatattagcgaacttcaaaggagcgacacctttcaaagaaatagttctagatgacaagtgggaccagattaaccgatgttacatgttcc

 1 13
Ael_PanxβA  ATGGTAGTCATTC