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convert_project - convert assembly and sequencing file types


This program is part of the MIRA assembler package. It is used to convert project file
types into other types. Please check out the documentation below for more detailed
information about convert_project.


[-f <fromtype>] [-t <totype> [-t <totype> ...]] [-aChimMsuZ] [-AcflnNoqrtvxXyz
{...}] {infile} {outfile} [<totype> <totype> ...]


-f <fromtype>
load this type of project files, where fromtype is:

caf a complete assembly or single sequences from CAF

maf a complete assembly or single sequences from CAF

fasta sequences from a FASTA file

fastq sequences from a FASTQ file

gbf sequences from a GBF file

phd sequences from a PHD file

sequences in EXP files from file of filenames

-t <totype>
write the sequences/assembly to this type (multiple mentions of -t are allowed):

ace sequences or complete assembly to ACE

caf sequences or complete assembly to CAF

maf sequences or complete assembly to MAF

sam complete assembly to SAM

samnbb like above, but leaving out reference (backbones) in mapping assemblies

gbf sequences or consensus to GBF

gff3 consensus to GFF3

wig assembly coverage info to wiggle file

gcwig assembly gc content info to wiggle file

fasta sequences or consensus to FASTA file (qualities to


fastq sequences or consensus to FASTQ file

exp sequences or complete assembly to EXP files in

directories. Complete assemblies are suited for gap4 import as directed assembly.
Note: using caf2gap to import into gap4 is recommended though

text complete assembly to text alignment (only when -f is

caf, maf or gbf)

html complete assembly to HTML (only when -f is caf, maf or


tcs complete assembly to tcs

hsnp surrounding of SNP tags (SROc, SAOc, SIOc) to HTML (only when -f is caf, maf or

asnp analysis of SNP tags (only when -f is caf, maf or gbf)

cstats contig statistics file like from MIRA (only when source contains contigs)

crlist contig read list file like from MIRA (only when source contains contigs)

reads where sequencing vector is masked out (with X) to FASTA file (qualities to

scaf sequences or complete assembly to single sequences CAF

-a Append to target files instead of rewriting

-A <string>
String with MIRA parameters to be parsed Useful when setting parameters affecting
consensus calling like -CO:mrpg etc. E.g.: -a "454_SETTINGS -CO:mrpg=3"

-b Blind data Replaces all bases in reads/contigs with a 'c'

-C Perform hard clip to reads When reading formats which define clipping points, will

save only the unclipped part into the result file.

Applies only to files/formats which do not contain


-d Delete gap only columns When output is contigs: delete columns that are

entirely gaps (like after having deleted reads during editing in gap4 or similar)

When output is reads: delete gaps in reads

-F Filter to read groups Special use case, do not use yet.

-m Make contigs (only for -t = caf or maf) Encase single reads as contig singlets into
the CAF/MAF file.

-n <filename>
when given, selects only reads or contigs given by name in that file.

-i when -n is used, inverts the selection

-o fastq quality Offset (only for -f = 'fastq') Offset of quality values in FASTQ
file. Default of 0 tries to automatically recognise.

-Q <quality>
Set default quality for bases in file types without quality values Furthermore, do
not stop if expected quality files are missing (e.g. '.fasta')

-R <name>
Rename contigs/singlets/reads with given name string to which a counter is
appended. Known bug: will create duplicate names if input

contains contigs/singlets as well as free reads, i.e. reads not in contigs nor

-S <name>
(name)Scheme for renaming reads, important for paired-ends Only 'solexa' is
currently supported.

The following switches work only when input (CAF or MAF) contains contigs.
Beware: CAF and MAf can also contain just reads.

-M Do not extract contigs (or their consensus), but the sequence of the reads they are
composed of.

-N <filename>
like -n, but sorts output according to order given in file.

-r [cCqf]
Recalculate consensus and / or consensus quality values and / or SNP feature tags.
'c' recalc cons & cons qualities (with IUPAC) 'C' recalc cons & cons qualities
(forcing non-IUPAC) 'q' recalc consensus qualities only 'f' recalc SNP features
Note: only the last of cCq is relevant, f works as a

switch and can be combined with cQq (e.g. "-r C -r f")

Note: if the CAF/MAF contains multiple strains, recalculation of cons & cons
qualities is forced, you

can just influence whether IUPACs are used or not.

-s split output into multiple files instead of creating a single file

-u 'fillUp strain genomes' Fill holes in the genome of one strain (N or @) with
sequence from a consensus of other strains Takes effect only with -r and -t gbf or
fasta/q in FASTA/Q: bases filled up are in lower case in GBF: bases filled up are
in upper case

-q <integer>
Defines minimum quality a consensus base of a strain must have, consensus bases
below this will be 'N' Default: 0 Only used with -r, and -f is caf/maf and -t is

or gbf)

-v Print version number and exit

-x <integer>
Minimum contig or read length When loading, discard all contigs / reads with a
length less than this value. Default: 0 (=switched off) Note: not applied to reads
in contigs!

-X <integer>
Similar to -x but applies only to reads and then to the clipped length.

-y <integer>
Minimum average contig coverage When loading, discard all contigs with an average
coverage less than this value. Default: 1

-z <integer>
Minimum number of reads in contig When loading, discard all contigs with a number
of reads less than this value. Default: 0 (=switched off)

-l <integer>
when output as text or HTML: number of bases shown in one alignment line. Default:

-c <character>
when output as text or HTML: character used to pad endgaps. Default: ' ' (blank)

Aliases: caf2html, exp2fasta, ... etc. Any combination of "<validfromtype>2<validtotype>"
can be used as program name (also using links) so as that convert_project automatically
sets -f and -t accordingly.


convert_project source.maf dest.sam

convert_project source.caf dest.fasta wig ace

convert_project -x 2000 -y 10 source.caf dest.caf

caf2html -l 100 -c . source.caf dest

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