#!/usr/bin/python

from Bio import SeqIO

import os

import re

import glob

import sys

import numpy

digits = re.compile(r'(\d+)')

def tokenize(filename):

for fragment in digits.split(filename)))

#get details on all seqs in a folder (with specified extension_

folder = sys.argv[1] #working folder

fmt = sys.argv[2]

if fmt=="fa" or fmt=="fna":

fmt="fasta"

if fmt=="fq":

fmt="fastq"

if fmt=="gbk":

fmt="genbank"

print 'format:', fmt

filelist=glob.glob(folder)

filelist.sort(key=tokenize)

print filelist

print ""

ml=max(len(w.split("/")[-1]) for w in filelist)

print "File"+(" "*(ml-4))+"\tCount"+"\tTotal_bp"+"\tMax"+"\tMin"+"\tN50"+"\tMean"

for f in filelist:

seqs = SeqIO.index(f,fmt)

if len(seqs)<>0:

#get lengths and names

data={}

total=0

t=0

for i in seqs:

t=t+1

l1=len(seqs[i])

total=total+l1

data[i]=l1

keylist=sorted(data,key=data.__getitem__)

sizes=[]

for p in keylist:

sizes.append(data[p])

l2=0

min1= int(min(sizes))

max1= int(max(sizes))

ave=int(numpy.mean(sizes))

for k in reversed(keylist):

#print data[k]

l2=l2+int(data[k])

if l2>=int(total)/2:

n50=int(data[k])

break

else:

t=0

total=0

max1=0

min1=0

n50=0

ave=0

print f.split("/")[-1]+"\t"+str(t)+"\t"+str(total)+"\t\t"+str(max1)+"\t"+str(min1)+"\t"+str(n50)+"\t"+str(ave)