Implement tool for SAI filtered sequence export

[westram]

Specification:

1. load ARB database
2. filter sequences by existing SAI(s)
3. export remaining columns of all sequences to FASTA file
   • skip sequences with < --min-bases base positions
   • logged skipped species to stderr (using field 'name')

CLI :

Switches…………………………….	Description
--db "database.arb"	name of ARB input database
--ali "aliname"	name of alignment in ARB
--fasta "flat.file"	name of FASTA output file
--id "ACI"	ACI defining FASTA header line (default: "readdb(name)") (see ​ACI manual)
--min-bases NUM	do not export sequences with < NUM bases left after applying filter
--count-bases "ACGTU"	list of base-characters to count for --min-bases (default: "A..Z")
(the following arguments may be specified multiple times)
--filterby "SAIname"	name of SAI used to filter sequence data
--pass [allbut] "chars"	characters that will forward column to output if found in SAI
--block [allbut] "chars"	characters that will block column from output if found in SAI

• --pass and --block may only occur after and always apply to the last preceding --filterby.
• the optional parameter [allbut] inverts the character set, i.e. if only one filter is specified the following are equivalent:
  • --pass "ABC" ⇔ --block allbut "ABC"
  • --block "XYZ" ⇔ --pass allbut "XYZ"

Filter combination:

OR	--filterby "PV1" --pass allbut ".-=0123" --filterby "PV2" --pass allbut ".-=012345"
AND	--filterby "PV1" --block ".-=0123" --filterby "PV2" --block ".-=012345"

Assuming the SAIs contain positional variability:

• OR: will export all columns where PV1 is ≥ 4 or PV2 is ≥ 6
• AND: will export all columns where PV1 is ≥ 4 and PV2 is ≥ 6

[westram]

• proposes add. switch --count-bases

[westram]

by [16119]

[westram]

• add sequence post-processing

[westram]

by [16234]