AB Delete Records

--delete_records, -dr

Description

Strip out entire rows from an alignment. The tool takes one or more strings as input, which are searched for in the record IDs; matches are deleted. If removing a row results in columns with 100% gaps, then those columns are also deleted.

Arguments

Search pattern ( regex )

At least one simple string or regular expression can be used. If the search pattern exists in a record ID, that row will be deleted.

Path to file of search patterns ( path )

Optional. If many patterns must be removed from an alignment, it may be easier to store those patterns in a file. Separate patterns with line breaks (see example 4)

Columns ( int )

Optional. Lists of deleted records are printed to stderr so you know what has been removed. By default these lists are ordered in a single column, but you can pass in an integer to flatten the list out into more columns. Note that this MUST be the final argument passed in, otherwise it will be treated as a search pattern.

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 -dr "PanxβC"

Output

# ####################### Deleted records ######################## #
# Alignment 2
Ael_PanxβC
# ################################################################ #
 3 100
Mle-Panxα9  ---atgttagacatactttcaaagtttaaaggagttactccttttaaaggtataacgatagatgacgggtgggatcaactcaatcggagttttatgttcg
Mle-Panxα4  atggttattgagctgctagctggatacaaaggtctgtccccgtttaaagacgcgactgttgacgactcatgggaccaaataaaccgatgttacgtgttca
Mle-Panxα6  atgttattggagatattagcgaacttcaaaggagcgacacctttcaaagaaatagttctagatgacaagtgggaccagattaaccgatgttacatgttcc

 2 13
Ael_PanxβA  ATGGTAGTCATTC
Ael_PanxβB  ATGGTTGTCATAC

Usage example 2

Regular expressions are understood and multiple search terms can be included

$: alb temp.del -dr α[46] βA

Output

# ####################### Deleted records ######################## #
# Alignment 1
Mle-Panxα4
Mle-Panxα6

# Alignment 2
Ael_PanxβA
# ################################################################ #
 1 97
Mle-Panxα9  atgttagacatactttcaaagtttaaaggagttactccttttaaaggtataacgatagatgacgggtgggatcaactcaatcggagttttatgttcg

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

Usage example 3

Include an integer to specify how many columns deleted record IDs should be organized in

$: alb Panx_C-terms.physr -dr α 2

Output

# ####################### Deleted records ######################## #
# Alignment 1
Mle-Panxα9	Mle-Panxα4
Mle-Panxα6
# ################################################################ #
 3 100
Ael_PanxβA  ---------------------------------------------------------------------------------------ATGGTAGTCATTC
Ael_PanxβB  ---------------------------------------------------------------------------------------ATGGTTGTCATAC
Ael_PanxβC  ATGCCCAACAACATATACCCAAACAGACTATTCGTGAAGACTAATGATATCCCGGAAAAATTAAACACTCCGTGGTCATACGAAAAAATGGTTGTAGTGC

Usage example 4

Feed in a file with list of regular expressions

List file: regexes.txt

^Mle-Panxα9$
^Ael_PanxβA$
^Ael_PanxβB$

$: alb Panx_C-terms.physr -dr regexes.txt

Output

# ####################### Deleted records ######################## #
# Alignment 1
Mle-Panxα9

# Alignment 2
Ael_PanxβA
Ael_PanxβB
# ################################################################ #
 2 100
Mle-Panxα4  atggttattgagctgctagctggatacaaaggtctgtccccgtttaaagacgcgactgttgacgactcatgggaccaaataaaccgatgttacgtgttca
Mle-Panxα6  atgttattggagatattagcgaacttcaaaggagcgacacctttcaaagaaatagttctagatgacaagtgggaccagattaaccgatgttacatgttcc

 1 100
Ael_PanxβC  ATGCCCAACAACATATACCCAAACAGACTATTCGTGAAGACTAATGATATCCCGGAAAAATTAAACACTCCGTGGTCATACGAAAAAATGGTTGTAGTGC