Aljamia
Aljamia v1.12 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to convert data in xml tables into a tab-separated values archive.
Aljamia needs an XML input file, and:
- up to four strings to combine information from the xml field.
- Commands:
-i, -j, -k and -l.
- Usage:
-i[FirstScan] -j[Sequence]
- It is possible to combine fields:
-i[RAWFileName]-[FirstScan]_[Charge]
(which would deliver something like "sampleA.raw-1029-3"). Everything outside brackets will be copied unchanged. Note that the fields are case sensitive.
- the name of the table where these fields are (command -t). Default is "peptide_match".
And delivers:
- an output data file with three columns (id, x, v) suitable to work as input for SanXoT.
Usage:
aljamia.py -x[xml file] -i[fold field] [-j[weight field] -k[id string], ...] [OPTIONS]
Arguments:
-h, --help Display this help and exit.
-a, --analysis=string
Use a prefix for the output files. If this is not
provided, then the prefix will be garnered from the data
file.
-A, --allow-operations
Allow python-style operations for the indicated fields.
Example: having Scan = 900, Charge = 3, and using
-i"[Scan]-[Charge]" -j"[Scan]-[Charge]" -A"i"
Will return "887" and "900-3" i- and j-fields,
respectively. By default, no operations are allowed.
-c, --curly-brackets
To use curly brackets, {}, instead of the default
parentheses, (), when using the filters (see options -f
and -F).
-d, --allow-duplicates
To avoid removal of duplicated relations.
-f, --filter=string To filter data to import. Use as in these examples:
-f"[Charge]==2"
-f"[st_excluded]!=excluded", which means
st_excluded must NOT be equal to "excluded"
-f"[Charge]=2&&[st_excluded]!=excluded", which
means charge must be 2, and st_excluded must
not be equal to "excluded"
-f"[FirstScan]>=1000"
-f"[FASTAProteinDescription]~~clathrin", which means
FASTAProteinDescription must include "clathrin"
-f"[Sequence]!~C", which means
Sequence must NOT include "C"
-f"[Sequence]!=ABABABABK", which means
Sequence must be different than "ABABABABK"
-f"!([Sequence]~~C || [Sequence]~~M)", which means
Sequence must not (via "!") contain "C" or
(via "||") "M". Note you can use parentheses
-f"[Sequence]~~C && [Sequence]~~M", wchich means
Sequence must contain "C" and (via "&&") "M"
Note that the filter is case sensitive.
Warning: when using parentheses () generate conflicts
in the commandline, the option -c can be used to switch
to curly-brackets {} mode.
Warning: when using && or || as logical operators
generate conflicts in the commandline, the option -w can
be used to switch to word operators such as *and* or
*or*.
Warning: using this argument, the filter is seen as
text-only, which means that [Mass] > 3 will not include
Mass = 10, as in ASCII order "3" comes after "1". For
numerical operations use -F.
-F, --filter-using-numbers
Same as -f, but considering a number everything that
looks like a number. Note that this doesn't currently
make operations with those numbers, it can only be used
for conditionals, such as [Mass] > 565.2
Note that whenever an error occurs (for example when
text cannot be converted to a number, or when the
text-only conditions ~~ or !~ are used), the concerning
operation will be treated as text in all cases.
-i, --id1=string Identifier for the first column. XML tags must be in
square brackets, while the rest of the text will be kept
unaltered. Here are some examples using tags such as
"FirstScan", "Charge", "Mass" or "Sequence" or "PTM":
"ABCD" -> "ABCD" (no tags -> unchanged, to all rows)
"FS[FirstScan]_q=[Charge]" -> "FS2991_q=2"
"ABCD-[Charge]" -> "ABCD-3"
"ABCD_[Charge]_[Mass]" -> "ABCD_3_578.1684"
"[Sequence]_[PTM]" -> "SAPEREAVDEK_15.994915"
Note that tags are case-sensitive.
-j, --id2=string Identifier for the second column (see -i).
-k, --id3=string Identifier for the third column (see -i).
-l, --id4=string Identifier for the fourth column (see -i).
-L, --logfile=filename
To use a non-default name for the log file.
-o, --output=filename
To use a non-default name for the output file.
-p, --place, --folder=foldername
To use a different common folder for the output files.
If this is not provided, the the folder used will be the
same as the input folder.
-R, --initialrow=integer
To set the position of row with headers (default is 1).
-t, --table=number To select fields from a table different than QuiXML's
peptide_match (which corresponds to the default, 3).
-w, --word-operators
To use *and* and *or* (including asterisks) as logical
operators instead of the default && and || in filters
(see options -f and -F).
-x, --input=filename, --filename=filename
Input xml or txt (tsv) file.
