wdecoster/nanostat

Wrong stats

Closed this issue · 6 comments

haowenz commented

Hi,

I tested NanoStat on my toy example and got wrong number of reads. It seems that other statistics are also wrong.

Read files:

ERR764952.1 channel_100_read_97/1
CCAGTCTGCTTACTGTTATACTGAGTCGCCTTCGGGTAGTAGGCATGCCACTAACACATTGTTCACCTGCGATTAAGAACCAGGGCTCGAACGTGCAGCTGCCTGGCCAGCTAAGCCCCGCTTGCAGACCGCGCCCGGCCTTCGCTTCAACCGCTTCAAAGATACCCCCGTTCTCGTTTGGTCAAATCAACAATTTCTACCTGCTCGTAAAACTAACACAGGAGTAAGTACCCAGCGGCGGTGACTCTACACCAATGACTAATAACCAGGTAGGTTACACCAGCTGGCTGTTGCTTTCAGTTCCGCAACAGGTGTTGGATGAATGATATCCAGCGTACCTCCCCGAAACGTTTTGTTTTTGTCACTCCCGGCTTTTCAGCACTTCAGCAGCGTGAATAGTGGTGTTAACCGGGTAGTGATAATGAATGCACATTTCGGGCAGGTTTACGAAATTGGTACCGAGGTTTTCGCCGATGCCGTGAATTTTAACGTTAAACAGGTCGGAACACCGTAGCATACGCAGTTTACCGACTACGCTGCAGAGAGGCCGCAGAACGACATCTGCGCCTTCCATAGAATCGCATCTTTCACAAAACCTTTATCTTTACAGCAGTAGAAATGGCTCAGGTCAAAAGGCTAGGGACGGGAATCCTCCAACGATATCATGAGAGTTGTCTAAACCTGAAGGCAGTTGGGTTTTTAACAACAGTAGTGCGGGCGAACCGAAGGGACAAATGGCCAATACCACAGCAGCACGAGGACTGCATATTTCAAGGTACATATCTCCTCTTATTATTAAACTAGATATGTTGCTCCTGCCCATATTAATCCGCTGCTTGCTAGGCGTTTATAAACCCATCTCGAATGTGATCGCAAAGTTCTACCGGCCGTTTATTGAAGTCGGATTAATGATCAGGAACAACTTATAGTAATGCTCGGTCGCTTATGCATTATCAAGAAGCGTGTCACGGCTATCTTATAAATATGACCTACCGTTCAGCCGACCCTCGTAATTTACTGGGACAATTAATTTATTTTAAGCAGTTGCATTAATCGCAGGCATGTTCTCAACGAATTTGATAAAATCCGCTCTTTCACTCATTATTTCAACCTTCTTCGACAAACTTTCCCATAAATTCAATGGTATGCGAGTAATGTTGTATCTGCCGGCTAGCGGCCCATATCAATATGCGAAGCTCGGCTAAGCGGAGGACCACAGTCCCTACCAGCTTTAGGCATTACTTAGAAGAGAATTCTCTATGATCCCAGAAATCGTCGCCGCATTTTGCAAGGAGCGGATTGACATATTAATCAGTCTAATCTCACAATGTTATCGCCAAGTTGGTTAGCTGTGTAATCCCACATGTCGCACTGAAACGTTACTGCCTGCCACATAACTCGCTCTTACCAACCACCTCCGGTTCATTGAAGAATCTGGTGCTCATCATCTAATGAATGCAGTTGATTCATACCAGCCTGGCGCGCGGCGCAGTTAATCCCCTGCTCTGACCACTGGGCAGGGCGAGGTATTCTGGGCACAACCGCTTATCATCCCCATCTTTACCGGCCTCCGTTTCAGTCGGACCTGTATTAGGCGGCGTATTTAGAGCTGTCAGCGCATTCAAATCTCTGATCCCCGTCGTTTCTGACGGCGGGAGGAGAAGGAGAAGGAGGGATGTTGCTTATCCTGACCCCCTGCTTTCCCTGCAATTTAATTTAACGATAATCCGTTTTTACTGCATGTCGACTTCACAATGAATACATAGGTAAGGCGGCCGATCAAGGTCCGCTTATCTAGTGCAAAAGCCGATTAACGATAGTAACCGTATTCCTCGTTATTTTTGTTGGTCTAGGTCCCCTTTTAGCCTTAGTAACCCAAACAGTCTCCCGGTATTAGTCACTCATAGATCCTGTATTATTTTGTATGACGTACCGAAACAGCCCAGCTAAAGATTATGTCGAGCCTGCTGAAAATCAAAACCACTGTTGCTATGCATGCCGTACTTTCTGTTCTCTTTCACCTGCATTCACGCTGCCAAACGATCATGCTGCACGAGCACGGTAGTTAGCAGCATGAGGCTCGTGGTATCCGTAAAATCTTGGCGTGTGCCCAATGAAACTGCGTGAATTAGGCTCCAAAGGTAGAAGAGAAAGAGAAACTGATAATAGTAAGGGCGTGAGAAACTGATAAGTAGCGTAAAGTAATAGCAACGGGATGGATATCCGGATACATCCCTCATCGTCTTGTCCCTACAATGCCCCCGGTTCACATTTTGCTAATGACAGAACACTTAAACGCAAATTAGGTTTCGCTACTCTTCCTCTGCCTCATCGACCCGATTAGTACCCACGGCCATATGAAGGCGTTCTCCCAAATGAACAAGTTAAATCCCTAGTATGACGGGGACATCGTCCTTGCTCCCATCCCGACTTATCCGTGGAGGTCGATCCTTATTTCGCCAACAAAATTTGGCTAGCACATTACGATAAAGTTATACATGGTAAGTACATCAAATCAATAGTATTCATCTGTTGCCCGTCACGTTCGCGGCGCGGTGTTATGCGTCCATCTAAGTAGCCATGAAAAACCGACATTTTGGCGTCGGTTTTTGATCAACTATCATTCAACGCATGTTGATACTTATGGAGCATCCCCACAGCCGATTACCGTCGTCACTGCGGTGAGTTACAGATGCATGATTTCAACTTAATTCCAGTTCTTCCGATAACCACAATACCCCGACGTTTATCATCGGGCAGATGACAGGTATTGCTGTGCATGGAGTTGTCGGGCATGGACAAGAACGGACTACCGTTTTAACTCTCGGATCGGTGCATCACGGAGAAGGCATGGTTGGCAATAGTATCATCGTCATAGCGCCGAGCAGTGGTTTAGGCAAATCTACGGCTGGAGTATTCATCAGCATACATAGTGAGTAAATCCGGGAGACCTTCTCTTTGGAGGTTGCCACATTGGGTCATCGCGGAATAGGACACCGGCGAATAAACTGATTAAGCATCCGTCCGTCTTCTTACCGCGATTTGCACCAGAGAGCTCATCCGGCAGCGCAGCTACGATTTGCCTAATCCATGTCAGAAACTGAAATGGAGATCATCGTATCCAGCACAAGCCTGGTCTTATTGATATGAGAGAAGTCCCAACCCAACGCGATCGCCGTTCTGTATATTCAACCAGGAGAATCCCAGCACATGCACCAATCCAAGGGGCTCATCCTGTTGGGTTAGAAGCTGTAGAACCCAGCAGCCATACTGAAGGGAGACACGTCTCCAGTAAACTCCATTAGGGTCGCCACCATTAATTAATTCGCAAACGATTGCGAGTGACCTTCGACGAAATCATGACAGGTCAACCGCCTGCCAGAAGTTACAGCCCGTCCCAGCCGAGAGACGATTGCCCGAGAATGCAGGAAAATGGTTGGACACCGAAGTTACCAATGCATGATGTGACGTTCAGTATGATAATTTATTCGCATTTCGCCTTGCGATCTCTTCGTGCTTGGCGTTGTGATTTTGTTGTGTGTGTACTGAGCCCCATCCAGAAGCTGATAGCGTTGCGCCGCAGCTCGAGACATAATGGTAAGGCGGAGTTTCCGCGTTCTTCCCGCATTCCCGGCGAGCTCTCCGCAGGCGTTTAGCTGCGTAGCTTCCTGCGGGATTTCACCAGCGTACGTTAGGGGGTGGTGACAGTGGGCCAATTCCAGTGAGTTTTACCGGAACAAGGCAAGTTTCGCAGGATTACTATCAGGACAGTCGAGATAGAGTATTGGGCCTTTTTAGACGTCAAACCCGCGCCCAGCGGGAAGCGTTACAATTCAATTGCTGCGCATGCCTTACCACGTGATGCGTCGCGCAGGTCGAAGCATTTATCACCTATATTCACCATCACATGCTTGATCTCGAGATCCATTAATTAGTGTCGCAACAGCGGACTTTCCAGCTCAAGTCGACATTCTTTGATCGATCTAGAGAGAGGATCCGCCATAATCGCACACAATACCAACTCGATCTCCCTACAACGTTCGACGCGACGATATTATGTGAAGCGTAGGCAATCGTTTGGCTTTCTCGGCTCTGAGTGGTGGTGCGAGTGATCAGCGCATGACCGTGCGAGCCAGCCCCGCAACCGAGTTCTATTCGTACCAGCAAAGGAGTATCCGAACTCAAAACCAACCCAATACAAGCACACCGAATCATCAATAATGGTTAGGGATCGTCTAGAAATACTGATCGCGGTTGCGCCGGACGAACAATACAGCCAGCCTGTGCTCCTTATGCGCGGGGCCCTAATAGCGAACGATGGATTTCTACCTCCCGCAGCAGCCAGTACGGCGCAGCCGGGCCGGGTCAATCTCGCCCGGTGAGCGTTCGCACTGGAAGTGAAGCCAACAAGCACACACGATCAACAATGGCGGTCGGCGTCTCGCCCAGCCGAATATGTTGGTTATGCGAGTGAGAGAGATACCCATCGTGATTAACCAAACGCAGAATGGGCCGGTTTGGAAACGAATCTGCTCCTTTCGTCGCAGTGAGTCTGTTGCTAGTACTAAAGTGGCAGTGATTAGAGAAACAGATGTTCTCTTGCTGATGTCCGGCGTATAGCGAACCACAGCCGTTGCGCCAGCACCGCATTTCAAGGTCAGTCTATTACCATCCTTTGGTCACCCGTGCTGCTGGCGTTGGTACATGCAGGCAACACTGACGGCTTTATTTCGCTATTTGTTACTGCCGGGGGCGTATTCTCTGGGCGCGCCATCTCCCCGACTAAGCCATTCCACTTAGTTTTATCTTCCAACTAACGATCACAGGATTTCTGTTACCCGGCGCAACCACGTTGGTGTCTGGAATAAACTCACCGGTATAAACGTTTGCAAATTGGTCGAAGCCATCTTATTAGTGGATTCTGGACGGTCCGTTCGGGACCTTCACAGGTTTTTACGTACCTGTGTCTATTCCTGATTTTCACTGGTAATGCAAATCGTTTGTAATCGCTTTGTTGGCCTCTGGTCACGTGGTCTCTTCACATCACGGGCACACCAAGCTTTACACCTTCCGGCTCCAGTTTCTCCTGTTGCGGTACCTGATAGCCCAACATCGCTTGCACTTCGGCGCCCCTTTCTTTTCACCAGTAATTGTCGCCGCTGGCTCCTTATCTTATTCCTTTTCACAATATTGCTGAACACTTCACTATACTATCAGTTAGAATCGTCCGGCGCAGTCACGAAACGACGTCGGGACGGGGCCGGAGTCACCGTTTCCAGGGAATTCAATAGTTGTAATAGACCCAGGCAACGTAATTGGCAATGAAGCCACCACCGCCAGTGACAATGAACGTGATGGGTCCTCCTACGGGAGTTTCTTATTAGTGTTTCATTCACTGATACAGCTGAAACAGTCGCGATACGGCCACTCCGGCGCAGCAACAGGCGGTGTTGTGAACGCCGGGTGCCAGACAAGTCGTAATGTAGCTGTTGGATGGGGCTAGCGGTAGCCCGCAAATCGCCAGTACTCCGGCAATTCAAAATATCGTGGAAGGGCGGCCCCCGATAACGGGAAACAAATAATGTTGGTATTGGTCTTGACACGAGAGAGCAGGCGTTATTATTTCAGCATCTGTCTCCCAGGGGGCATGGAAAGCCGGGCGCAACATTCCTGTAAATTGATGGTTTTAGTATACGTATGTTATTAGTTTATATTACTTGATCCCCTTACTTTTAGATTGTGGACGGCTGCTGAATAATTAGAACCTACCAAAACGAATGTCGGTTTCAAGGGTAGTTGAGTTTGGCTCTTTTACGCCGCCGCCAAGCTAGCTACAATGAGCGTTTCGTCCTATCAAGTCAAACGGTACCATATCTGGAAGATGAGTCCGAGATAGGCTGTTAAACCGTAGCACTACGAGCATTGGCTAACCCGGCCATGCCGGAGTTATAACACCAGGGCTGCCGTCATCCTTCATGAAAATCCAGGATGTTCTGAGCGATATCTGCCTTCACCTGGACACCAGATGAGCTATAATACGCATTGACATGTTCTTCAACTCTGTCTGGCACAGGTCTTTCTCCGGGCTGACAGCCGGATAAGACGTGGGCTGGGGCGGGATCCGCAGGTTTACGTCGGGACGGGACGGGACACCTTGGTTGGCTAGGAGTTCCAACGCAACTCTGATTAGAGCTTCTGGATGTGGTGAGTTGTGCCGTCAGGGGCGTTGCAGGATTCTTCACGACCTGTTCCACACGTCTGGGCGCCGCAATTGCCAATGGTATGTGCCCGAGACATGAGCTATCTCACGATACAGCATACAGAAACCACGATTCAGTAGTCATATTCATGTAACATGCGTAAGCGTGCGTGGGATAATGAATTTGAATCAGGCGGGGATCTCAACGCCTGATCCCTAAGGAAGATTTGTGACGGTGATGCATCCCTGGTGCCTGGCTGACAGGGTGCGGGATCACAGCGTGCTGATCTGATCATGATAGGAAGTCAATCGTGGCGGAGCTGGAAATCCTGCTGCCGCGTTGAAGTCAGGTCACCTCGCGCATTTATGCGTTACTCTCCAGGACCTAGCGGCTTAAGCGCTGAAGGTACACACATTGGTGCTGCCGGCTCCAATTATTTTTGTTACATGCTGCGTGATCGTGTTCAGGAGAATGCACGGGCACGGGAGCGAAACCGTGCTATATTGATTCTCGTGTACATCTCCTGTGCCAACAATTCCCCTCCTCATCACCCCAGCGCGGAGCCCGTTCATAGTTAAATCGCGACAGTGATCCGTGGTACTTCTCCAATAGTGAAATTATGCTCGCAATCGCCAACAGTCTAAATCATATTTCGACGTTGGCTGGGCCACAAACCGGCGAAATATTGCCTGTTACCACGCAGCACCCCACGTTATCCGTTACATTACGTGCCAACCATCGAAATCTGCTGCGAGCTGGTTTCCGGGCGGTACAATCAACGTTGGCCCCTTTCACCGCCTTCGTTACTTTACCGTTCAATCAGATATGCTTCTGAAGTACGAATAGGAATTCCAAGAGGTGATATCCACCTGACCGCCACCATTTCGGTGCATAGATCGATCTCAACGATTCAATTTCATGCGGGATCGATTTATACCCGGCGGGGTAAGGTTGGTCATACGCGGCATGGGCAGATGGGCGTAGGATTCAGGCGACCGTTGCCAGTCAGTTGTCGGCTGGACGCATCAAAACGCGCGTTGGGAGTTATCCTGCATGTAGCCTTTCGAGTGCGTTCTCAATCAGCGTTTTGTACTGAACCGTACTTCGTCATCAATCAAGGGGAAATCGGGGAGTGCTGGCCAAGATACGTTAAAAAGCTCCTACTAACCGCTGCCCGTTGGCGGCCCGGGTCTCACGCATACTGTCTAAATACTGAAGTGCTAAGCGGTCGAAATTTACCTGTTCCACCAGACCGTACCGGCCATTCGATGCTTCATTGTGGAAGGCTAAGGCCAGGCTCATGATCTCCTGCACAAATACTACAGGCATGGTGCCCTGGTGCGACAGGCCAGGCAGATTGTGAGGGCGCCATACGCCATCCTTCTTTTGCCCATTGAATGGGCTAGGGTGCCGTCGAAGGTCATGAGGAGAATTCAGCGAGCTCACCACTACGCCGCCTGGGCACCCGTTCGCGTTTCCATCTTTATTCAAAACGCAGGCCTCCACACGAGAGAGGCACCAGCACCTATCAAAGGGCCGTCCTTCGTGGCTCACAGTATCACTCAAGACTATTGTCACGTTAGACTGGACTATCGGATAAACCATTCGTTCTCTTGGCCTATTCTTGTCGCCTTCGCGGGCTCGTATTAGGCGACGAGGGGTGGGGCACTTCTCTTCACAACATGCTTGTTGCAGCGGAGTCACCGAGGTACAACGGGCTATGCTCTACAAGCCCCCGAGCGTCTGTACTTTACATCACGCTGACGGACTAATGTCTGGTGCCAGAATGCGCACTCTGTTCCACCACGAGCAGGCGTTTGGTCGACAGTGGTGGGAGAGATACCGTTCTGTTTATG
ERR764952.2 channel_100_read_98/1
TCTGTTATGGTCCAGCCCTATCGGGTTAACATGGCTCTCCACGGTAGCTGCATGGATCGTAACCGTTTCCGCTTTGTAATCAGGTATATATGGGCCACGATATGACACCTTATCGACATACTTAAATCGGAGCGTAGGACTGCGTGAAGGTTATTCATTCGACTTGCCCCCTCATCAACTGGGCCAAACCGCAATGTTTCCATCCCATCCATCACGCGCCGATTATTTACTTATCGCGTGCCGACCCCATCCCATTTCTTATTAATTTCTACTCATCGACGAAGGTGCCCTCTATTTGCTCCCTCAACAACCAACTATCTTAGGTTCCGTAATCCAACTGGTTTCTTCTTCTGCGTACGTTCCCCAGCATCTAATAATTTCGACAATTGTATCACATTGTTTGTCAAGTTTACCGTATTTTAACGAACGTGCGTCTAGCGTCTTAGACGTTCAGTAACGGATTCCGTTTCATCACAACCGTAAACATGTCTCAAATCAGGCGGCTGACATAATGAAGGCTCCGAAATTAAAGGGTAACTTTCATTGAATCTCCTTATAGGCCCCACAATAGGCTAAATCCGTAAAACCATCTGCATACTACATCTCAGTCGCACCTTTCTGATACATACTGTCACTTGTTATTATTAAGATAAATCGTCCATCAGGTGTGCCAGATAATCATTCACGTATTATCTTTATTCTTACGATTTTATCGCTATGCGACACGTTAATACGGTAGAACTATCTGCACCGTGAGTAGCTCGCAGCAACTATCTGTACCTGTGGACATTCTTCAGAGGATATACTCTCCTTTCTTAATTATCAGTTCTGCTTAATGCGGATATTTTCTCATTAATCTTTACAGACAATACGCACAATTCCATATCATTACACCAGTGTGACTTCTGCGTTTCTTTCGACGAACCTACGAAGAAGTATATATATGCAATCTATCAGTTATTATTTAGCTTATACGTACAGGGAACACCACAAACGTCAGAATCCACTTAACCAGATCTGGCATCATCCGCGTATCTGGCGAAATAATCCCGACAGTGTAGATTGTTGTAACCTGCGGTCGCAACCTGATAGTTCACATCCGGCCATTTCAACCCGCATCGGGTTAACAGCCTCTCCCCCTGCGGCGTACTACGTATCTAAATCGCTTTATAATCGGATAGTTCGGGACCGGTACACGTAAAATGAAGCTTAGGCTGATACGATGCAAGGTCTCCACCTCTACCATTAGACACTTGCCCCATTCATCATATTCGCGCTCCTAGTGGTTGTCAGTCTTCGGACCGCCCCCGGAGGAGCATTGGTCGCAATCGCTAAACCCCTTTGTTGAGGCGCCATGTGTAGACTTCAACATAAATTTGGCCAGTTAACCACCGTCAAGCCGCACTGCGCAGCGCATTTCATGCTCGCAGTCTGCCGAGATTTCTTCCTCCGGGTGAGCAGCCGGAGGCGTCATAGGCGGAGAAGCGCGTGGCCGTTCTCATACAGGTCCTGCTGAGGCTTTATGCGATGAACCCCGGGCCGCTTTTCCAAGCCGTTCTCTGTCTCAACTCCAATACCATAAGCGTCGAATTCCGATAGTGACCCCGTCCCGTCTAAACCTGTGATCATTATCGCACGTCGTCAGCCTGTCTCCGTCTAGCCATACCCTAGTCAACACATTCGCAGCGCCCAAGTAGGCCGTCTATTAGCTTAGACGCACCCGTTGCCATTCGCCGTCCCGGGACGTAGAAGAAAGCACCTCCGACCGTAAGCCCCGTAAGTGTACGATTGACAGGCCCAGGCGTGGACCTGTCGTAGTATAACTCGTATGCGTGCCAGAACGGTCGTCCGTCCGTATCGCCCCACGGATGCGGTCGGTCTGTTGGCTTCAGCCTTAAGTATTCATCGTGGCAGTAAAAATCCCATCCTCCGCGTAAGTTATCTAAAAGTGAGTGTACTGTCCTAGACTGCGGCCCGATGTGGCAGCCCGGTCCGCCACAATCCGTGAAGCCAGGATGGGCAGGTCGAAGTGGGTGCGGAGGGACCGACCCAGCTGCCATTAAGTGACTAGTTCGCGTCTGTCACCGAACCGAACGGCGCACCATTACCGTTACCTCCCACCGTAGTCACGTGGGTCGCAGAGGCGTTCAGTATGTATATCAGCTGGTATACTCTCTCCCTATGCGGGGAGGAGAGTGGTGGTGTCAATTCGTTAGTGAGGCATTACTGCTGCCATGCTGCCGAAGCTGCAAGACAGTCTCTAAATCCGTAAAGTTCCAGTACAACAGGCGTCAGGGGACATTCATTCCCGCACTACCCGTCCACACATACGTCATAAAACACCGGCAGCAGAGGCTGTTCCCGTACCCATTTTGCAGGCCCCCTGCTCGTTTTGTATGCAGTGTCGTCTCGTAATCGAGGGCGTCCGCGTCTCCATTGCACCGTCGCATTCGCCATTCATAGGCTTCTCTCCTTCGACACCCATAATCGCAGCCCGGTACATTCAGACCGATAATGTCTGTCGAGCACAAGTACCTCCATCATACTTATGACCCTATGCTCTGCCTTTCACGTTCGGTGCGGGCTGATACATTCCCGTCATCGTAGTACCAAGAACTCCCCTTAGCGTAACTACACTCTGTGAGTTCCGCGGTCAAATCACTGATATGTTGCGTCCCCGTCGGGTAGTACCAGCCGGATTCCACGCATCATGGGCGCAAGCCCTGTGACATGCCGTTCTCCGCCGGTCTTCAACGGACAATACCGTCGGGACGATGTATGCTCCTTGTGTGTACCAACTACTTACGTCATGCGTGGTGCTAGCCGTTACAAGAAACGTACTCTGTGTCTTGTAAACCATTTGCCGTCCCATAATATAGGCATTCATTACATGCGGCGTTATTTCAAGCCGCGTTTCTAGCTGTGCGTGTTGTGTAGCAGATTAACCAGCCACGGTTGCCCCGGAACGGGGGCTGATGCTTCTAGACGCGAGGTCACTCTCTCGCGGTCATCTCCCCCGAGCATTCTGTTAAACGGGTCTGGTAGCCCGAGCAGTCATTACAACGCACAGATTAGAACCATCGAAAGTCATCTGCCAATGCTGCCCTTCCAAGATCACCGTTGTCGTCGCCAACCTCCCTTGTGACCCGGTGATACCCATCCTCCGTATGTCTCCCGCTGCGCGATGTCTCCGATACCGAGCTGCCCGTCATCAATTCCCGGCACTGAAATATCTCGTTTACTACCTCTACTCAGCCTACTATTCTGGACTTTCCCGTCGTTGATAATTTCGTCTCCCGCGTCCGCTTGTATTTAGTCTATCGTCGCCGACACGATTCAACCGTACTCTGTCTCTCCCCGTCCCCCGTTATCGTCTGCTAGTCAATTCCTGCCGTCAACGCTGCTAATCCTCGGGCCGTCACAGTTCTTCTTTTTCGCCCCGTTTCCTCCCGGCCGCCTTCTTATCCAGCACCGGTCGGGGTTGATACACCTATAATCCGAATTGGTTTGTGATGCTCATCACCGCCTCATACTGACCTTAAGGTTTCAGTTGCTCCACCACCCCCGTATCGTCTGACAAATCTGGAGTACCGGCTTCGCCAGTACTGCCGCCAGAGTGGATGGCCAATGGATTGGGCCGTCAACCTCGTGAAGGCCCGGGGGACATGCGTATTGCTGCGGTCACTCCACGAGAAGTCCTCGAGCTTCAATCTCGTGTAACAGAGGCGTACCGCGACGGGCAGGCGACCCATATGCGCGGGTGCATCAGCGCCGAACAATCGCCATGTCACGTATCTTCGGATGGCGGGCAGTTGGGGAGGCTGAGGCGGCGCAAAAGGGCTCAAAGGGGGAACTGTCGAAGAAAGACGAAGAGTGTAAGTAATAACGTTCGACTACATGCCTTAATCTTGGTCAGCAAGCGAGTACCCGGCGCCGTCCGTCACCATAGTGATTTCCCCAGGCATGTAGCGGGATAGACAGTACGTCAGCGTCCCCCGAATCGGCGGTTCCCCATCCCATTACACCCATCCTGAAGGAGCACCATGGCAGTACGTCGCCTCACCCCGGCACCCGATAACAAGCCCCAGTATCCACCACAGGCCTGTGCCTGTTGGTCCGAGAGGTAAGGATGCATGAACCAATATCCGGCGCAAAAGACACCCGCGAGAGGCCGCGCCGGGACCGTCTAGTGTGCTGCTGCCCTAGAGCAGCCATTATATACCTTAAGCTGTACCTAAGCCCCCGGCAGCAGCACTCAGATGCGTACTCCACGTTGGTTTGAACTGGTAAGTCCTTTGATGGGGGTCGTAACCTGTAAGCACAATATCAGAAGGCATTTCCAGCCCACCGCAACGACAGGGCTTGCAGGCGTCTTCGTTCCGGTAGCTGCTAGTGTAGGTGCGGGGAGAAGTGGAGTGAGTCGGGCGGGGTGAGAGAGAAGGAGATGCTTCCCCCTGAAGCGGCACACCTTCGCCCCCAGCAGCGATTTACCGGGATTGCCCGAATCATCCCGCCCGGGACGCCCAGCGCGCCATTGGGAGCGCCGTTATTTGACAGCTGCCGAACCTGACACCTATCAAAGCCCCCTCTGAATCATATCTAATCTCCCGCCTGGTTCCATCATATAAATCCACTTTTAATTATTTCAATGGGACGGGGCTGTGCGTTCCGTTGTCGTCGTC

Output from NanoStat:
$ NanoStat --fasta my_test.fasta
General summary:
Mean read length: 3202.5
Median read length: 2359.0
Number of reads: 4
Read length N50: 8057
Total bases: 12810

Total bases should be 8056+4682=12738. N50 should be 8056. Mean and median should be 12738/2.

haowenz commented

Note that there is '>' before the name of each read in the fasta file.

wdecoster commented

Thanks a lot for reporting this. There is an embarrassing mistake in how fasta files are handled. I never use those, so I didn't notice...

I'll have a fix up soon.

wdecoster commented

I just pushed NanoStat v1.1.1 to PyPI, in which your issue should be solved. Thanks again!

haowenz commented

Got this error when updating. Please also see #18

$ pip install nanostat --upgrade
Collecting nanostat
Downloading https://files.pythonhosted.org/packages/21/1f/ceb88dc5985145d9291c41c31a7ea185350074370f26f23c9c2ac41cf445/NanoStat-1.1.1.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "", line 1, in
File "/var_other/scratch/4110242.dedicated-sched.pace.gatech.edu/pip-install-2ur0s_vq/nanostat/setup.py", line 14, in
long_description=open(path.join(here, "README.md")).read(),
File "/nv/hswarm1/hzhang639/data/miniconda3/lib/python3.6/codecs.py", line 895, in open
file = builtins.open(filename, mode, buffering)
FileNotFoundError: [Errno 2] No such file or directory: '/var_other/scratch/4110242.dedicated-sched.pace.gatech.edu/pip-install-2ur0s_vq/nanostat/README.md'

----------------------------------------
wdecoster commented

Thanks again for reporting this. Apparently, I forgot to add the README.md to the MANIFEST.in when I started using the .md file for creating the description on PyPI. This should be solved in NanoStat v1.1.2, which I just pushed to PyPI.

Cheers,
Wouter

haowenz commented

Works now! Thanks for the quick response.