suryasaha

The files in this directory represent functional annotations of the following dataset:
https://i5k.nal.usda.gov/data/Arthropoda/phopyr-%28Photinus_pyralis%29/Ppyr1.3/2.Official%20or%20Primary%20Gene%20Set/Photinus_pyralis_Annotation_Release_100/GCF_008802855.1_Ppyr1.3_cds_from_genomic.fna.gz

Information about the functional annotation process can be found here: https://agbase-docs.readthedocs.io/en/latest/


The file GCF_008802855.1_Ppyr1.3_cds_from_genomic.fna.gz was processed with agbase/goanna:2.2 (https://hub.docker.com/repository/docker/agbase/goanna/tags?page=1) docker container to generate GO functional annotation. GOanna was run with the following parameters: -a invertebrates -b yes -g 70 -x 7054 -k 9 -q 70 -r 1.2. Please see the documentation for details at https://agbase-docs.readthedocs.io/en/latest/goanna/intro.html#help-and-usage-statement

The resulting files are:
GCF_008802855_GOanna.asn

suryasaha

tomcat8 log

2020-11-27 12:10:16,879 [http-nio-8080-exec-4] WARN  apollo.TrackService  - Directory does not exist so trying to make
2020-11-27 12:10:18,082 [http-nio-8080-exec-7] INFO  apollo.UserController  - updateTrackListPreference
2020-11-27 12:10:18,083 [http-nio-8080-exec-7] INFO  apollo.UserController  - Added userOrganismPreference false
2020-11-27 12:10:19,842 [http-nio-8080-exec-7] WARN  apollo.TrackService  - File /opt/apollo/temporary_data/1659667-TmadTest does not exist
2020-11-27 12:10:19,842 [http-nio-8080-exec-7] WARN  apollo.TrackService  - File /opt/apollo/temporary_data/1659667-TmadTest can not be read
2020-11-27 12:10:19,842 [http-nio-8080-exec-7] WARN  apollo.TrackService  - File /opt/apollo/temporary_data/1659667-TmadTest can not be written to
2020-11-27 12:10:19,842 [http-nio-8080-exec-7] WARN  apollo.TrackService  - File /opt/apollo/temporary_data/1659667-TmadTest/extendedTrackList.json does not exist

suryasaha

surya@hlb orthomcl_plasmids (master *%)$ cat proteomes/*.faa > allproteins.faa
surya@hlb orthomcl_plasmids (master *%)$ cat proteomes/*.faa | grep '^>' > names.txt
surya@hlb orthomcl_plasmids (master *%)$ wc -l names.txt
15899 names.txt

surya@hlb orthomcl_plasmids (master *%)$ ./orthomcl.ValidateGroups.pl -s groups.txt.eval-5percent50 -c groups.txt.eval-5percent60 -r groups.txt.eval-5percent30 -m map.txt -n names.txt
4169 records read from groups.txt.eval-5percent50 ..
4159 records read from groups.txt.eval-5percent60 ..
4172 records read from groups.txt.eval-5percent30 ..
Runtime details

suryasaha

Github repo for Shell
https://github.com/suryasaha/shell-novice
Github repo web page
http://suryasaha.github.io/shell-novice/


Clone the repo
git clone https://github.com/suryasaha/shell-novice.git
OR

suryasaha

 fastq-stats 120613_I176_FCC0VM8ACXX_L8_SZAXPI009284-57_                      2.fq.gz
reads   180701702
len     100
len mean        100.0000
len stdev       0.0000
len min 100
phred   64
window-size     2000000
cycle-max       35
dups    6146153

suryasaha

# Publication list of suryasaha
 File generated using the impact_cv widget, created by Guillaume Lobet (Université de Liège) 

 Website: www.guillaumelobet.be/impact 

 Source code: https://github.com/guillaumelobet/impact_cv 

 Tue, 24 Jun 2014 01:51:33 +0000
 
## Overview 

suryasaha

#!/usr/bin/perl -w
# MGEL
# Surya Saha 05/28/04
# reading fasta file,writing out fasta file, names from given file
# seq not found to .notfound file

use strict;
use warnings;

unless (@ARGV == 3){

suryasaha

 feature_id |             name             |             uniquename             | type_id |   fmin   |   fmax   |  type_name  
------------+------------------------------+------------------------------------+---------+----------+----------+-------------
   17711944 | Solyc01g112000.2.1           | mRNA:Solyc01g112000.2.1            |   22157 | 89896493 | 89898383 | mRNA
   17711943 | Solyc01g112000.2             | gene:Solyc01g112000.2              |   22627 | 89896493 | 89898383 | gene
   17711945 | exon:Solyc01g112000.2.1.1    | exon:Solyc01g112000.2.1.1          |   22070 | 89896493 | 89896528 | exon
   17711946 | intron:Solyc01g112000.2.1.1  | intron:Solyc01g112000.2.1.1        |   22111 | 89896528 | 89896791 | intron
   17711947 | exon:Solyc01g112000.2.1.2    | exon:Solyc01g112000.2.1.2          |   22070 | 89896791 | 89896911 | exon
   18050281 | Solyc01g112000.2.1           | auto18050281                       |   22027 | 89896799 | 89898180 | polypeptide
   17711948 | intron:Solyc01g112000.2.1.2  | in

suryasaha

use strict;
use autodie qw/open close/;
use DBI;
use Getopt::Long;
use Bio::GFF3::LowLevel qw/gff3_parse_feature/;

my ( $dsn, $user, $pass );
GetOptions(
    'dsn=s'        => \$dsn,
    'u|user=s'     => \$user,

suryasaha

[core]
	repositoryformatversion = 0
	filemode = true
	bare = false
	logallrefupdates = true
[remote "origin"]
	fetch = +refs/heads/*:refs/remotes/origin/*
	url = git.sgn.cornell.edu:/git/private/cxgn/local-lib
[branch "master"]
	remote = origin