Notebook

Tools¶

In developing qdod there are several handy tools for aggretating data. Here we will try to list them.

Downloading data¶

Section on how to get data automatically down from different resources including

NCBI
Ensembl
Sigenae

Sqlshare !python {spd}fetchdata.py -s "SELECT ProbeName,GB_ACC,Column2 as sequence,Description FROM [sr320@washington.edu].[GPL11353_array]ar left join [sr320@washington.edu].[Cgigas_EST__Nuc_NCBI_040414_cl]est on ar.GB_ACC=est.Column5" -f tsv -o /Volumes/web/cnidarian/GPL11353_fasta2.tab

Uploading data¶

#uploading to SQLSHARE spd="/Users/sr320/sqlshare-pythonclient/tools/" !python {spd}singleupload.py -d Cgigas_EST_NCBI_040414_cl /Volumes/web/cnidarian/Cgigas_EST_NCBI_040414_cl.tab

Manipulating¶

Fasta to tab

!perl -e '$count=0; $len=0; while(<>) {s/\r?\n//; s/\t/ /g; if (s/^>//) { if ($. != 1) {print "\n"} s/ |$/\t/; $count++; $_ .= "\t";} else {s/ //g; $len += length($_)} print $_;} print "\n"; warn "\nConverted $count FASTA records in $. lines to tabular format\nTotal sequence length: $len\n\n";' /Volumes/web/cnidarian/oyster.v9.fa > /Volumes/web/cnidarian/cgigas_v9_genome01.tab

Tab to fasta !awk -F "," '{print ">"$1"\n"$2}' /Volumes/web/cnidarian/GPL11353_v6fasta.csv > /Volumes/web/cnidarian/GPL11353_v6fasta.fa

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