01-05-2014
Post sample input and expected output in code tags
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1. Shell Programming and Scripting
Hi ,
I have a typical situation. I have 4 files and with different headers (number of headers is varible ).
I need to make such a merged file which will have headers combined from all files (comman coluns should appear once only).
For example -
File 1
H1|H2|H3|H4
11|12|13|14
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Discussion started by: marut_ashu
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Hello,
A bioperl problem I thought could be done with awk: convert the fasta format (Note: the length of each row is not the same for each entry as they were combined from different files!) to tabular format.
input.fasta:
>YAL069W-1.334 Putative promoter sequence... (6 Replies)
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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
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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
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I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
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I have the following script:
awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }'
and the following file:
>P39PT-1224 Freq 900
cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg
>P39PT-784 Freq 2... (2 Replies)
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I would like to extract all entries containing the following patterns: ccccta & ccccccccc from the following infile:
>P39PT-1224_Freq_900
cccctacgacggcattggtaatggctcccgcaagccatctctcttcagccaagg
>P39PT-784_Freq_2
cccctacgacggcattggtaatggcacccgcaagccatctctcttccccccccc
>P39PT-678_Freq_5... (4 Replies)
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9. UNIX for Beginners Questions & Answers
I have two fasta files as shown below,
File:1
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>Contig_24:26615-28387... (11 Replies)
Discussion started by: dineshkumarsrk
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I have 5 sequences in a fasta file namely gene1.fasta as follows,
gene1.fasta
>1256
ATGTAGC
>GEP
TAGAG
>GTY578
ATGCATA
>67_iga
ATGCTGA
>90_ld
ATGCTG
I need to rename the gene1.fasta file based on the sequence position specified in list.txt as follows,
list.txt
position1=org5... (5 Replies)
Discussion started by: dineshkumarsrk
5 Replies
LEARN ABOUT DEBIAN
lintian-info
LINTIAN-INFO(1) User Contributed Perl Documentation LINTIAN-INFO(1)
NAME
lintian-info - give detailed information about Lintian's error tags
SYNOPSIS
lintian-info [log-file...]
lintian-info --tags tag ...
DESCRIPTION
The lintian-info command parses the output of the lintian command and gives verbose information about the listed Lintian error tags, parses
a Lintian override file and gives verbose information about the tags included, or (if given the -t or --tags option) explains a given tag
or tags.
If no log-file is specified on the command line, this command expects its input on stdin. Thus, the output of lintian can either be piped
through lintian-info or a log file produced by lintian can be processed with this command. (Note, though, that the lintian command has a
command line option -i to display the same results as lintian-info, so you will not normally need to pipe the output of lintian into this
command.)
OPTIONS
-a, --annotate
Read from standard input or any files specified on the command line and search the input for lines formatted like Lintian override
entries. For each one that was found, display verbose information about that tag.
-h, --help
Display usage information and exit.
--profile prof
Use the severities from the vendor profile prof when displaying tags. If the profile name does not contain a slash, the default
profile for than vendor is chosen.
If not specified, lintian-info loads the best profile for the current vendor.
Please Refer to the Lintian User Manual for the full documentation of profiles.
-t, --tags
Rather than treating them as log file names, treat any command-line options as tag names and display the descriptions of each tag.
EXIT STATUS
If -t or --tags was given and one or more of the tags specified were unknown, this command returns the exit code 1. Otherwise, it always
returns with exit code 0.
SEE ALSO
lintian(1)
AUTHORS
Niels Thykier <niels@thykier.net>
Richard Braakman <dark@xs4all.nl>
Christian Schwarz <schwarz@monet.m.isar.de>
perl v5.14.2 2013-02-16 LINTIAN-INFO(1)