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Jason Stajich hyphaltip

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hyphaltip / GC_compute_Nematocida.sh
Last active December 10, 2015 17:02
#module load emboss (need emboss tools - install on mac with homebrew or other methods)
#download
curl -C - -O http://microsporidiadb.org/common/downloads/Current_Release/NparisiiERTm1/fasta/data/MicrosporidiaDB-26_NparisiiERTm1_AnnotatedCDSs.fasta
curl -C - -O http://microsporidiadb.org/common/downloads/Current_Release/NematocidaSp1ERTm2/fasta/data/MicrosporidiaDB-26_NematocidaSp1ERTm2_AnnotatedCDSs.fasta
curl -C - -O http://microsporidiadb.org/common/downloads/Current_Release/NparisiiERTm3/fasta/data/MicrosporidiaDB-26_NparisiiERTm3_AnnotatedCDSs.fasta
geecee MicrosporidiaDB-26_NematocidaSp1ERTm2_AnnotatedCDSs.fasta Nsp1ERT2.geecee
geecee MicrosporidiaDB-26_NparisiiERTm1_AnnotatedCDSs.fasta NparERT1.geecee
geecee MicrosporidiaDB-26_NparisiiERTm3_AnnotatedCDSs.fasta NparERT3.geecee
@hyphaltip
hyphaltip / genome_size_gene_stat.pdf
Last active November 18, 2015 18:24
genome size, coding genes in fungi
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@hyphaltip
hyphaltip / Hordeum_vulgare.030312v2.16.cdna.all.test.fa
Last active August 29, 2015 14:17
qsub commands
This file has been truncated, but you can view the full file.
>MLOC_42952.1 cdna:novel contig:220312v1:morex_contig_2669042:2:251:-1 gene:MLOC_42952 transcript:MLOC_42952.1
GAGCTACTCGGGACTCCGCCGCCGCAGTCTTTCTCGATGGCCTTCTGTTTTTTCATACCC
TTGACCTTGAATATCATGATTGCATAGCTGCGGTGGACACCAAGGGAGAGACNNGCCTGA
TATTCAGGGTCCCTGGTGGTCAGGTTTATGATTTTGGCCAGGCTGATGACTTTGTTCAAC
ACGTCTTATTCAAGGTTCCTGGTGGTCGGTTTCATTATTTTGGTGTGGCTCATGGTTAAG
GTAAAGGAAG
>MLOC_42947.1 cdna:novel contig:220312v1:morex_contig_2668822:118:275:1 gene:MLOC_42947 transcript:MLOC_42947.1
CCCTTGGGCTCGCCGGGTTTCAGCACCGACCGGGTGCCTCCCAACACCACCACCAGCCGC
GGCGCCACCGACCCATCCTCCTACTCGGACGACGATGGCGAGGCGGAGGTCGACCCCAAT
GTGCACCCCGAGGACGACGGCACCACCGTTATCCTCGA
@hyphaltip
hyphaltip / Nc20H.expr.tab
Last active August 29, 2015 14:17
UNIX simple commands and sorting
gene_id bundle_id chr left right FPKM FPKM_conf_lo FPKM_conf_hi status
NCU10129 18585 supercont10.1 1166 2603 50.9314 36.6581 65.2046 OK
NCU09901 18586 supercont10.1 3197 4838 15.5736 7.68094 23.4663 OK
NCU11134 18588 supercont10.1 15929 16647 0 0 0 OK
NCU09904 18589 supercont10.1 17889 19368 67.7417 51.2807 84.2028 OK
NCU09903 18587 supercont10.1 9603 13334 31.5378 20.3061 42.7695 OK
NCU09908 18592 supercont10.1 43708 44551 0 0 0 OK
NCU09907 18591 supercont10.1 40949 42632 0 0 0 OK
NCU09906 18590 supercont10.1 35915 39245 139.627 115.994 163.26 OK
NCU09910 18594 supercont10.1 49271 51866 22.6875 13.1612 32.2138 OK
@hyphaltip
hyphaltip / vividMutant
Created December 17, 2014 06:26
vividMutant
>vividMutant
ATGAGCCATACCGTGAACTCGAGCACCATGAACCCATGGGAGGTTGAGGC
GTAACAGCAATACCACTATGACCCTCGAACCGCGCCCACGGCCAACCCTC
TCTTCTTCCATACGCTCTACGCTCCCGGCGGTTATGACATTATGGGCTAT
CTGATTCAGATTATGAACAGGCCAAACCCCCAAGTAGAACTGGGACCTGT
TGACACGTCATGCGCTCTGATTCTGTGCGACCTGAAGCAAAAAGACACGC
CAATTGTGTACGCCTCGGAAGCTTTTCTCTATATGACAGGATACAGCAAT
GCGGAGGTCTTGGGGAGAAACTGCCGTTTTCTTCAGTCACCCGACGGAAT
GGTCAAGCCGAAATCGACAAGGAAGTACGTCGACTCCAACACGATCAATA
CGATGAGGAAAGCGATTGATAGGAACGCCGAGGTGCAGGTTGAGGTGGTC
@hyphaltip
hyphaltip / cegma_format.pl
Last active August 29, 2015 14:07
process some sequences for CEGMA processing
#!env perl
use strict;
use warnings;
my $dir = shift || "marker_files";
my $odir = shift || "marker_hmm";
mkdir($odir) unless -d $odir;
opendir(DIR,$dir)|| die "cannot open $dir: $!";
my $locusct =1;
for my $file ( readdir(DIR) ) {
@hyphaltip
hyphaltip / get_isolate_info.pl
Last active August 29, 2015 14:06
Extract isolate metadata from accession names
#!env perl
use strict;
use warnings;
use Bio::DB::GenBank;
use Bio::SeqIO;
use Getopt::Long;
# remote retrieval of sequences from GenBank
my $db = Bio::DB::GenBank->new;
@hyphaltip
hyphaltip / get_nearest_tree_neighbor.pl
Last active August 29, 2015 14:01
Get Nearest neighbor on tree
#!/usr/bin/perl
use strict;
use warnings;
use Bio::TreeIO;
my ($treefile,$taxon_name) = @ARGV;
my $in = Bio::TreeIO->new(-format => 'newick', -file => $treefile);
my $tree = $in->next_tree;
if( ! $tree ) {
die "cannot parse treefile $treefile and find a valid tree";
@hyphaltip
hyphaltip / parser_hmmer3_domtbl.pl
Created April 8, 2014 05:04
HMMER3 simple parsing
#Here is code for parsing
use strict;
use warnings;
my $hmmertable = shift @ARGV;
open(HMMERTABLE, $hmmertable) || die "$hmmertable: $!";
while(<HMMERTABLE>){
chomp;
next if /^\#/ || /^\s+$/;
my ($domain,$domacc,$tlen,$qname,$qacc,$qlen, $fullevalue,$fullscore,$fullbias,
@hyphaltip
hyphaltip / gist:5843924
Created June 23, 2013 05:39
gh61-family alignment
CLUSTAL FORMAT for T-COFFEE Version_8.97_101117 [http://www.tcoffee.org] [MODE: ], CPU=0.01 sec, SCORE=88, Nseq=4, Len=381
NCU05969 MPSFTSKSLLAVLAGAASVAAHGHVSNIVINGEYYRGFDS-SLNYMANPP
NCU07898 MKTF-----ATLLASIGLVAAHGFVDNATIGGQFYQPYQ---DPYMGSPP
NCU07760 MARM---SILTALAGASLVAAHGHVSKVIVNGVEYQNYDPTSFPYNSNPP
TRIREDRAFT_73643 MIQKLSNLLVTALAVATGVVGHGHINDIVINGVWYQAYDPTTFPYESNPP
* : ** *..**.:.. :.* *: :: * ..**
NCU05969 AVVGWKANNQDNGFVGPDAFSSPDIICHKDATNAKGHAVVKAGDKISIQW
NCU07898 DRISRKIP--GNGPV--EDVTSLAIQCNADSAPAKLHASAAAGSTVTLRW