Aljamia - Revision history

Mtrevisan at 12:39, 14 March 2018

2018-03-14T12:39:55Z

Mtrevisan: Aljamia v1.12, including options for curly brackets and word logical operators useful when the default options generate conflicts

2018-03-14T12:39:46Z

Aljamia v1.12, including options for curly brackets and word logical operators useful when the default options generate conflicts

Mtrevisan at 14:18, 19 February 2018

2018-02-19T14:18:53Z

Mtrevisan: version

2017-11-02T13:12:56Z

version

Mtrevisan: adding argument -F, --filter-using-numbers

2017-11-02T13:12:19Z

adding argument -F, --filter-using-numbers

Mtrevisan: Created page with "Aljamia v1.10 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to convert data in xml tables i..."

2017-10-03T14:43:09Z

Created page with "Aljamia v1.10 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used to convert data in xml tables i..."

New page

Aljamia v1.10 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.
-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.
In forthcoming versions filters will be available for
numerical operations, but currently the filter doesn't
work with conditionals such as [Mass] > 565.2, only for
(in)equalities such as [Mass] == 565.2

-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).
-x, --input=filename, --filename=filename
Input xml or txt (tsv) file.

← Older revision		Revision as of 12:39, 14 March 2018
Line 1:		Line 1:
−	Aljamia v1.11 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 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:		Aljamia needs an XML input file, and:

← Older revision		Revision as of 14:18, 19 February 2018
Line 106:		Line 106:
	-x, --input=filename, --filename=filename		-x, --input=filename, --filename=filename
	Input xml or txt (tsv) file.		Input xml or txt (tsv) file.
		+
		+	[[Category:SanXoT software package]]

← Older revision		Revision as of 13:12, 2 November 2017
Line 1:		Line 1:
−	Aljamia v1.10 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 v1.11 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:		Aljamia needs an XML input file, and:

@@ Line 36: / Line 36: @@
                         Will return "887" and "900-3" i- and j-fields,
                         respectively. By default, no operations are allowed.
     -d, --allow-duplicates
                         To avoid removal of duplicated relations.
@@ Line 60: / Line 64: @@
                         Note that the filter is case sensitive.
                         Warning: using this argument, the filter is seen as
                         text-only, which means that [Mass] > 3 will not include
@@ Line 104: / Line 115: @@
     -t, --table=number  To select fields from a table different than QuiXML's
                         peptide_match (which corresponds to the default, 3).
     -x, --input=filename, --filename=filename
                         Input xml or txt (tsv) file.
 [[Category:SanXoT software package]]

@@ Line 60: / Line 60: @@
                         Note that the filter is case sensitive.
-                        In forthcoming versions filters will be available for
+                        Warning: using this argument, the filter is seen as
-                        numerical operations, but currently the filter doesn't
+                       text-only, which means that [Mass] > 3 will not include
-                        work with conditionals such as [Mass] > 565.2, only for
+                       Mass = 10, as in ASCII order "3" comes after "1". For
-                        (in)equalities such as [Mass] == 565.2
+                        numerical operations use -F.
     -i, --id1=string    Identifier for the first column. XML tags must be in