---------- Post updated at 04:21 AM ---------- Previous update was at 04:07 AM ----------
Hi Skrynesaver,
I am having a problem with the output. For every alternate record, the information is mising. An example of my output is given below. I do not have information for AC Q8IZP0. but it goes to the next record. This happens every alternate record.
Hi,
I want to calculate the number of pipe delimiters in a file for all lines seperately.
For eg:i have a file Project.txt
Mohit|chawla|123|678
File1|File2|345|767|678
And my file contains many lines like this
it shd give me the output as
4
5
or give me the output for all the... (0 Replies)
Hello guys
I want to retrieve two data from a file, like this:
bash-2.03$ cat numtest
123456
123457
bash-2.03$ more ./test_num
#!/bin/bash
num1=
num2=
cnt=1
while read x
do
num${cnt}=$x
cnt=$(($cnt+1))
done <$1
echo $num1 "\n" $num2
But when i executed this script, error... (2 Replies)
Hi Everyone,
I will try to explain my question please forgive my english here.
I am looking for shell script or command that can compare data in the files.
I have 50 files in one directory test1 test2 test3 ....so on.
I want to compare data in each files with each other and output each... (4 Replies)
hi all,
In an mp3 file , data is arranged in sequence of header and data ,how to retrieve data between two headers. Is the data between two headers fixed? because as per theory it says 1152 samples will be there , but dont knw how many bits one sample correspond to?
it would help if any c... (2 Replies)
How to write a shell script to retrieve datas from database after that this database are redirect to a excell sheet and then i got a mail that gives details about the database with the column name and data..
I m using oracle 9i...
Thanks,
Anup Das (2 Replies)
Hi Guys,
Please help me with my problem here:
I have a source file:
1212 23232 343434 ASAS1 4
3212 23232 343434 ASAS2 4
3234 23232 343434 QWQW1 4
1134 23232 343434 QWQW2 4
3212 23232 343434 QWQW3 4
and a mapping... (4 Replies)
Hi,
I need to compare a file with its contents matching to that of another file(filename , received date and record count).
Lets say has File A original data
Ex -
1,abc,1234
2,bcd,4567
3,cde,8901
and File B has details of File A
Ex-
FILEA.TXT|06/17|2010|3
(filename)|(received... (18 Replies)
I am having trouble matching *two* strings from one file anywhere in a line of a second file, and could use some help getting this figured out. My preference would be to use grep for this because I would like to take advantage of its -A option. The latter is due to the fact that I would like both... (2 Replies)
Discussion started by: jvoot
2 Replies
LEARN ABOUT DEBIAN
swiss::des
SWISS::DEs(3pm) User Contributed Perl Documentation SWISS::DEs(3pm)Name
SWISS::DEs.pm
Description
SWISS::DEs represents the DE lines of a UniProt Knowledgebase (Swiss-Prot + TrEMBL) entry as specified in the user manual
http://www.expasy.org/sprot/userman.html.
The DEs object basically holds lists of DE objects, each of them representing a protein name element. The "elements", "hasFragment",
"Includes" and "Contains" attributes/methods work as follows :
DE RecName: Full=CAD protein;
DE Short=CAD;
DE AltName: Full=Protein rudimentary;
DE Includes:
DE RecName: Full=Glutamine-dependent carbamoyl-phosphate synthase;
DE EC=6.3.5.5;
DE Includes:
DE RecName: Full=Aspartate carbamoyltransferase;
DE EC=2.1.3.2;
DE Flags: Fragment;
-= Entry::DEs =-
elements (for each DE object, see SWISS::DE.pm documentation) :
toText: "CAD protein", "CAD", "Protein rudimentary"
category: "RecName", "RecName", "AltName"
type: "Full", "Short" "Full"
hasFragment : "Fragment"
Includes : ListBase of DEs (child1, child2)
Contains : empty ListBase
-= child1 =-
elements (for each DE object) :
toText: "Glutamine-dependent carbamoyl-
phosphate synthase", "6.3.5.5"
category: "RecName", "RecName",
type: "Full", "EC"
hasFragment : undef
-= child2 =-
elements (for each DE object) :
toText: "Aspartate carbamoyltransferase", "2.1.3.2"
category: "RecName", "RecName",
type: "Full", "EC"
hasFragment : undef
Note: the old unstructured DE format can still be used, and will be parsed the same way into DE objects (but without setting their
attributes 'category' and 'type'.
DE CAD protein (Protein rudimentary) [Includes: Glutamine-dependent
DE carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate
DE carbamoyltransferase (EC 2.1.3.2)] (Fragment).
Inherits from
SWISS::ListBase.pm
Attributes
"text"
The (raw) text of the DE line (without the 'DE ' line type prefixes)
"list"
Array reference to the SWISS::DE objects containing the different names for the entry. The first element of the list is the recommended
name. Note: use "elements" method (inherited from ListBase) to get (and loop through) the array of DE objetcs.
"Includes"
"Contains"
Each of these is a SWISS::ListBase object whose list contains a SWISS::DEs object for each 'child' of the protein (i.e. peptide or
functional domain). See the UniProtKB user manual for an explanation. It is possible to have both Includes and Contains in a single
entry:
DE RecName: Full=Arginine biosynthesis bifunctional protein argJ;
DE Includes:
DE RecName: Full=Glutamate N-acetyltransferase;
DE EC=2.3.1.35;
DE AltName: Full=Ornithine acetyltransferase;
DE Short=OATase;
DE AltName: Full=Ornithine transacetylase;
DE Includes:
DE RecName: Full=Amino-acid acetyltransferase;
DE EC=2.3.1.1;
DE AltName: Full=N-acetylglutamate synthase;
DE Short=AGS;
DE RecName: Full=Arginine biosynthesis bifunctional protein argJ alpha chain;
DE Contains:
DE RecName: Full=Arginine biosynthesis bifunctional protein argJ beta chain;
"hasFragment"
Contains 'Fragment' or 'Fragments' (evaluates to true) if the DE lines contain the 'Fragment(s)' indication (in 'Flags:' line with the
new DE line format), otherwise evaluates to false. Compare to the more robust Entry::isFragment which also checks the FT lines for a
NON_CONS or NON_TER.
"isPrecursor"
Returns 1 if the flag 'Precursor' is present (undef if not). Note: only with new DE line format.
Methods
Standard methods
new
fromText
toText
Evidence Tags
With the new DE line format, each DE element can have distinct evidence tags, which are stored in the DE object themself (see SWISS::DE.pm
documentation). The evidence tags for the 'Flags' line are stored in the parent DEs object itself. With the old DE line format, since the
DE line did not have a fixed syntax in TrEMBL, it is impossible to reliably assign evidence tags separately to the different elements of
the DE lines. Therefore, the DE line can only be evidence tagged as a whole, and the following methods have their prototype defined in
SWISS::BaseClass instead of the direct parent of SWISS::DEs, SWISS::ListBase :
addEvidenceTag
deleteEvidenceTags
getEvidenceTags
getEvidenceTagsString
hasEvidenceTag
setEvidenceTags
example :
$evidenceTag = $entry->Stars->EV->addEvidence('P', 'DEfix', '-', 'v1.3');
# add global DE evtag if old DE line format, 'Flags' evtag if new format
$entry -> DEs -> addEvidenceTag($evidenceTag);
perl v5.10.1 2008-07-17 SWISS::DEs(3pm)