#!/usr/bin/python

import arvados
import re
import hashlib

api = arvados.api('v1')

piece = 0
manifest_text = ""

# Look for paired reads

inp = arvados.CollectionReader(arvados.getjobparam('reads'))

prog = re.compile("(.*?)_1.fastq(.gz)?$")

manifest_text = ""

for s in inp.all_streams():
    if s.name() == ".":
        for f in s.all_files():
            result = prog.match(f.name())
            if result != None:
                p = [{}, {}]
                p[0]["reader"] = s.files()[result.group(0)]
                p[1]["reader"] = s.files()[result.group(1) + "_2.fastq" + result.group(2)]
                m0 = p[0]["reader"].as_manifest()[1:]
                m1 = p[1]["reader"].as_manifest()[1:]
                manifest_text += "./_" + str(piece) + m0
                manifest_text += "./_" + str(piece) + m1
                piece += 1

# No pairs found so just put each fastq file into a separate directory
if manifest_text == "":
    for s in inp.all_streams():
        prog = re.compile("(.*?).fastq(.gz)?$")
        if s.name() == ".":
            for f in s.all_files():
                result = prog.match(f.name())
                if result != None:
                    p = [{}]
                    p[0]["reader"] = s.files()[result.group(0)]
                    m0 = p[0]["reader"].as_manifest()[1:]
                    manifest_text += "./_" + str(piece) + m0
                    piece += 1

arvados.current_task().set_output(manifest_text)