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"""
%prog some.fasta wanted-list.txt
"""
from Bio import SeqIO
import sys

wanted = [line.strip() for line in open(sys.argv[2])]
seqiter = SeqIO.parse(open(sys.argv[1]), 'fasta')
SeqIO.write((seq for seq in seqiter if seq.id in wanted), sys.stdout, "fasta")

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awk '
	BEGIN{print"in.var\tin.ancest\tout.var\tout.ancest\tninmissing\tnoutmissing"}
	NR <= 1 { next } 
	{ for(i=1;i<=n=split($4,a,"");i++)  if((a[i]=="1"))   b++;
	   for(i=1;i<=n=split($4,a,"");i++)  if((a[i]=="0"))  c++;
	   for(i=1;i<=n=split($4,a,"");i++)  if((a[i]=="."))  x++;
	   for(i=1;i<=n=split($3,a,"");i++)  if((a[i]=="1"))  d++;
	   for(i=1;i<=n=split($3,a,"");i++)  if((a[i]=="0"))  e++;
	   for(i=1;i<=n=split($3,a,"");i++)  if((a[i]=="."))  y++;
	   printf "%s\n",$2"\t"FS"\t"b"\t"c"\t"d"\t"e"\t"x"\t"y; 

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#WORKFLOW FOR GENOME RESEQUENCING:

#CONCATENATE CASAVA OUTPUT
# Annoying first step, Casava 1.8 splits files into groups of 4,000,000 reads, requiring you to stitch it back together...

cat *P1_GA1_*R1* > Limenitis_Pool_P1_GA1_R1.fastq.gz
cat *P1_GA1_*R2* > Limenitis_Pool_P1_GA1_R2.fastq.gz

#repeat for each group of files per each individual pool/sample

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import os
import sys
import glob
import shutil
import argparse
import subprocess
import multiprocessing
import itertools

class FullPaths(argparse.Action):

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#!/usr/bin/env python
import sys

inputfile = sys.argv[1]

with open(inputfile) as fd:
	next(fd)
    	for line in fd:
        	columns=line.split()
        	#print columns

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perl /projectnb/mullenl/programs/CORTEX_release_v1.0.5.15/scripts/calling/run_calls.pl \
--first_kmer 31 \
--last_kmer 61 \
--kmer_step 30 \
--fastaq_index index_file \
--auto_cleaning yes \
--bc yes \
--pd no \
--outdir ./cortexresults \
--outvcf cortextrial \

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find  /path/to/dest -type d -empty
# find all empty files in /tmp directory
find  /tmp -type d -empty

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Import existing Git repository into another

Folder structure before (2 separate repositories):

XXX
 |- .git
 |- (project files)
YYY
 |- .git

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Steps to submit to TSA

If you have a transcriptome that has been assembled from shotgun reads the TSA (Transcriptome Shotgun Assembly) database is a good place to put it so that it can be widely accessed.

This guide assumes that you simply want to submit the assembled sequences from your transcriptome without annotations. NCBI sets a high bar for inclusion of annotations so for most non-model organisms they are probably not going to meet the criteria.

To create a TSA submission take a look at the ncbi guidelines. This gist is based on those guidelines.

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