03-10-2014
Post example input and example output of what you want.
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1. Shell Programming and Scripting
Please advice how can we search for a string say (abc) in multiple files and to get total occurrence of that searched string. (Need number of records that exits in period of time).
File look like this (read as filename.yyyymmdd)
a.20100101
b.20100108
c.20100115
d.20100122
e.20100129... (2 Replies)
Discussion started by: zooby
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2. Shell Programming and Scripting
Hi.. I have a seperate chromosome sequences and i wanted to parse some regions of chromosome based on start site and end site.. how can i achieve this?
For Example Chr 1 is in following format
I need regions from 2 - 10 should give me AATTCCAAA
and in a similar way 15- 25 should give... (8 Replies)
Discussion started by: empyrean
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3. UNIX for Dummies Questions & Answers
Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
for i in *.rtf.out
do
awk '/^>/{f=++d".fasta"} {print > $i.out}' $i
done (1 Reply)
Discussion started by: Ann Mc Cartney
1 Replies
4. UNIX for Dummies Questions & Answers
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
Discussion started by: baika
2 Replies
5. UNIX for Dummies Questions & Answers
I have fasta files with multiple sequences in each. I need to change the sequence name headers from:
>accD:_59176-60699
ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA
>atpA_(reverse_strand):_showing_revcomp_of_10525-12048
ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC... (2 Replies)
Discussion started by: tyrianthinae
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6. Shell Programming and Scripting
Hi,
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
input
> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
> fefrwefrwef X937... (2 Replies)
Discussion started by: ritakadm
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7. Shell Programming and Scripting
Hi,
I want to search only duplicate sequence number in file e.g
4757610
4757610
should display only duplicate sequence number in file.
file contain is:
4757610 6zE:EXPNL ORDER_PRIORITY='30600022004757610' ORDER_IDENTIFIER='4257771056' MM_ASK_VOLUME='273' MM_ASK_PRICE='1033.0000' m='GBX'... (5 Replies)
Discussion started by: ashfaque
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8. Shell Programming and Scripting
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 Replies)
Discussion started by: Ibk
3 Replies
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I could calculate the length of entire fasta sequences by following command,
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta
But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be... (14 Replies)
Discussion started by: dineshkumarsrk
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10. UNIX for Beginners Questions & Answers
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
AAGCZ-N16-AAGCZ
Z represents A, C or G (Except T)
N16 represents any of the four... (3 Replies)
Discussion started by: dineshkumarsrk
3 Replies
LEARN ABOUT DEBIAN
font::ttf::post
Font::TTF::Post(3pm) User Contributed Perl Documentation Font::TTF::Post(3pm)
NAME
Font::TTF::Post - Holds the Postscript names for each glyph
DESCRIPTION
Holds the postscript names for glyphs. Note that they are not held as an array, but as indexes into two lists. The first list is the
standard Postscript name list defined by the TrueType standard. The second comes from the font directly.
Looking up a glyph from a Postscript name or a name from a glyph number is achieved through methods rather than variable lookup.
This class handles PostScript table types of 1, 2, 2.5 & 3, but not version 4. Support for version 2.5 is as per Apple spec rather than
MS.
The way to look up Postscript names or glyphs is:
$pname = $f->{'post'}{'VAL'}[$gnum];
$gnum = $f->{'post'}{'STRINGS'}{$pname};
INSTANCE VARIABLES
Due to different systems having different limitations, there are various class variables available to control what post table types can be
written.
$Font::TTF::Post::no25
If set tells Font::TTF::Post::out to use table type 2 instead of 2.5 in case apps can't handle version 2.5.
VAL Contains an array indexed by glyph number of Postscript names. This is used when writing out a font.
STRINGS
An associative array of Postscript names mapping to the highest glyph with that name. These may not be in sync with VAL.
In addition there are the standard introductory variables defined in the standard:
FormatType
italicAngle
underlinePosition
underlineThickness
isFixedPitch
minMemType42
maxMemType42
minMemType1
maxMemType1
METHODS
$t->read
Reads the Postscript table into memory from disk
$t->out($fh)
Writes out a new Postscript name table from memory or copies from disk
$t->XML_element($context, $depth, $key, $val)
Outputs the names as one block of XML
BUGS
o No support for type 4 tables
AUTHOR
Martin Hosken Martin_Hosken@sil.org. See Font::TTF::Font for copyright and licensing.
perl v5.10.1 2009-01-21 Font::TTF::Post(3pm)