psa2msa - reformat PSA file to Pearson/Fasta multiple sequence
alignment file
- psa2msa
- [ -dhlpu ] [ -M insert_len ] [ -W width
] [ psa_file | - ] [ parameters ]
psa2msa reformats a psa(5) formatted
profile-sequence alignment file into a Pearson/Fasta-formatted multiple
sequence alignment file. The result is written to the standard output.
'psa_file' contains alignments of several sequence segments to the
same profile in psa(5) format. Such a file is typically generated by
the programs pfsearch(1) or pfscan(1) using option -x.
The output can be converted into other formats (e.g. MSF) with the
aid of the public domain program readseq (available from
ftp://ftp.bio.indiana.edu/molbio/readseq) or used directly with
pfmake(1) or pfw(1). If '-' is specified instead of a
filename, the psa(5) alignment is read from the standard input.
- psa_file
- Input multiple sequence alignment.
The content of the file must be in psa(5) format. If the filename is
replaced by a '-', psa2msa will read the input alignment
from stdin.
- -d
- Replace periods '.' by dashes '-' on output.
- -h
- Display usage help text.
- -l
- Replace upper case letters by lower case letters on output.
- -p
- Replace dashes '-' by periods '.' on output.
- -u
- Replace lower case letters by upper case letters on output.
- -M insert_len
- Maximal length of an insertion.
If the real length of an insertion exceeds this value, the excess number of
residues will be deleted from the center of the insertion. A negative
value of 'insert_len' means no upper limit for the length of an
insertion (i.e. no residues will be deleted from an insertion). If
'insert_len' is zero, all insert positions will be removed. Setting
an insertion length limit helps to keep the resulting alignment at
manageable size.
Type: integer
Default: -1
- Note:
- The meaning of the value '0' for this parameter has been changed
compared to version 2.2 of the pftools package.
- -W width
- Set alignment output width.
The value of 'width' specifies how many residues will be output on
one line.
Type: integer
Default: 60
- Note:
- for backwards compatibility, release 2.3 of the pftools package
will parse the version 2.2 style parameters, but these are
deprecated and the corresponding option (refer to the
options section) should be used instead.
- M=#
- Maximal insertion length
Use option -M instead.
- W=#
- Output width.
Use option -W instead.
- (1)
- pfsearch -bx ecp.prf CVPBR322 | psa2msa -du | readseq
-p -fMSF > ecp.msf
- Generates a multiple sequence alignment of predicted E. coli
promoters on both strands of plasmid pBR322. The file 'ecp.prf'
contains a profile for E. coli promoters. The file
'CVPBR322' contains EMBL entry J01749|CVPBR322. The
result in 'ecp.msf' can further be processed by GCG
programs accepting MSF files as input.
On successful completion of its task, psa2msa will return
an exit code of 0. If an error occurs, a diagnostic message will be output
on standard error and the exit code will be different from 0. When
conflicting options where passed to the program but the task could
nevertheless be completed, warnings will be issued on standard error.
The pftools package was developed by Philipp Bucher.
Any comments or suggestions should be addressed to
<pftools@sib.swiss>.