09-05-2018
Thanks vgersh99. Code worked perfectly
10 More Discussions You Might Find Interesting
1. UNIX for Dummies Questions & Answers
Hello All - I am looking for help on how to solve a re-occuring problem. I have a file with certain sequences in it that need to be removed. The sequences are always different but the fix is always the same remove those sequences and leave the rest. Another team ID's the bad sequences and then I... (3 Replies)
Discussion started by: candyluv030
3 Replies
2. 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
3. Shell Programming and Scripting
Hi,
I am having a file of dna sequences in fasta format which look like this:
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat
with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
Discussion started by: margarita
5 Replies
4. Shell Programming and Scripting
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Discussion started by: nelsonfrans
7 Replies
5. Shell Programming and Scripting
Hello,
I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)
Discussion started by: empyrean
5 Replies
6. Shell Programming and Scripting
I have a fasta file as follows
>sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3
MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN
TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM
KGVTSTRVYERA
>sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Discussion started by: alexypaul
3 Replies
7. UNIX for Dummies Questions & Answers
Hi
How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this:
>H8V34IS02I59VP
SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG
YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
Discussion started by: Marion MPI
6 Replies
8. UNIX for Beginners Questions & Answers
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
14 Replies
9. Shell Programming and Scripting
I have a fasta file as follows
>sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3
MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM
ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC
NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
Discussion started by: jerrild
3 Replies
10. UNIX for Beginners Questions & Answers
Hi,
I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below
test.fasta
>TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
LEARN ABOUT DEBIAN
marc::charset::code
MARC::Charset::Code(3pm) User Contributed Perl Documentation MARC::Charset::Code(3pm)
NAME
MARC::Charset::Code - represents a MARC-8/UTF-8 mapping
SYNOPSIS
DESCRIPTION
Each mapping from a MARC-8 value to a UTF-8 value is represented by a MARC::Charset::Code object in a MARC::Charset::Table.
METHODS
new()
The constructor.
name()
A descriptive name for the code point.
marc()
A string representing the MARC-8 bytes codes.
ucs()
A string representing the UCS code point in hex.
charset_code()
The MARC-8 character set code.
is_combining()
Returns true/false to tell if the character is a combining character.
to_string()
A stringified version of the object suitable for pretty printing.
char_value()
Returns the unicode character. Essentially just a helper around ucs().
marc_value()
The string representing the MARC-8 encoding.
charset_name()
Returns the name of the character set, instead of the code.
to_string()
Returns a stringified version of the object.
marc8_hash_code()
Returns a hash code for this Code object for looking up the object using MARC8. First portion is the character set code and the second is
the MARC-8 value.
utf8_hash_code()
Returns a hash code for uniquely identifying a Code by it's UCS value.
default_charset_group
Returns 'G0' or 'G1' indicating where the character is typicalling used in the MARC-8 environment.
get_marc8_escape
Returns an escape sequence to move to the Code from another marc-8 character set.
charset_value
Returns the charset value, not the hex sequence.
perl v5.12.4 2010-03-29 MARC::Charset::Code(3pm)