out.write("".join(seqs))
out.write("//\n//\n")
//\n//\n
comes after the seqs
//
's are before the seqs?
--------------------------------------------------
ipyrad [v.0.1.73]
Interactive assembly and analysis of RADseq data
--------------------------------------------------
New Assembly: cli
ipyparallel setup: Local connection to 4 Engines
Step1: Demultiplexing fastq data to Samples
Saving Assembly.
Step2: Filtering reads
Saving Assembly.
Step3: Clustering/Mapping reads
Reference sequence index exists
[Engine Exception]
---------------------------------------------------------------------------IndexError Traceback (most recent call last)<string> in <module>()
/home/deren/Documents/ipyrad/ipyrad/assemble/cluster_within.pyc in muscle_align(args)
149 if len(names) <= 1:
150 if names:
--> 151 stack = [names[0]+"\n"+seqs[0]]
152 else:
153 ## split seqs if paired end seqs
IndexError: list index out of range
None
Saving Assembly.
Step4: Joint estimation of error rate and heterozygosity
Saving Assembly.
ipyrad error -
No Samples ready for joint estimation. First run step3().
//
//
>1A_0_2813_r1;size=19;*
TGCAGACTGTGACCGGATATGTTGGGGATTTAAAGAGATACGCGCCAAGACGGTGAGGAGGCGAACACCGTTGTACGTCTGGACATTGTTCGGG
>1A_0_2816_r1;size=1;+
TGCAGACTGTGACCGGATATGTTGGGGATTTAAAGAGATACGCGCCAAGTCGGTGAGGAGGCGAACACCGTTGTACGTCTGGACATTGTTCGGG
//
//
>1A_0_6303_r1;size=20;*
TGCAGAAAAAGCGCGGAGAACTATGGTCACACCTAATTCAAACCTCAGCCAAGCATGCGGTTCGGGATCAGTCAAATACTGTGTTCCTAGAATT
>1A_0_6320_r1;size=1;+
TGCAGAAAAAGCGCGGAGAACTATGGTCAGACCTAATTCAAACCTCAGCCAAGCATGCGGTTCGGGATCAGTCAAATACTGTGTTCCTAGAATT
//
//
>1A_0_2197_r1;size=18;*
TGCAGTCTGCGCCCGGGATGGATAACTTCCCTCAGTGCCGTAGACCAATAAAATGTTCACCGTCTGTGCGACAAATGATCGCCAGGCTCACAGC
>1A_0_4543_r1;size=12;+
TGCAGTCCTACCATGAATGGAGTTTCTTCCTAGTTCAACATCCCCGTAATGTAATTGTAGGTGTCGAGCTTCACATGCGACCAGTAAGGAACAT
>1A_0_4547_r1;size=1;+
TGCAGTCCTACCATGAATGGAGTTTCTTCCCAGTTCAACATCCCCGTAATGTAATTGTAGGTGTCGAGCTTCACATGCGACCAGTAAGGAACAT
//
//