Bug with last version of python2.7

[lelouar]

Hi,

I've tried to test your soft but have an error during process. Only *_stats.tab are created at the end of process.

I install pymasc via pip install.

Here the command I used:
pymasc -p 10 -e * -i I -n test2 -o test2masc processed_data/ce11/NGS/ChIPseq/bam/H3k4me1_WThexCtrl_rep1.bwa_aln.sort.bam

and logs:

[2021-03-16 11:51:30,003 | INFO] PyMaSC.pymasc : PyMaSC version 0.3.2 with Python2.7.18
[2021-03-16 11:51:30,004 | INFO] PyMaSC.pymasc : Make output directory: test2masc
[2021-03-16 11:51:30,103 | INFO] PyMaSC.pymasc : Check read length: Get median from read length distribution
[2021-03-16 11:51:30,103 | INFO] PyMaSC.handler.masc : Check read length... : processed_data/ce11/NGS/ChIPseq/bam/H3k4me1_WThexCtrl_rep1.bwa_aln.sort.bam
[2021-03-16 11:52:47,362 | INFO] PyMaSC.core.readlen : Scan 6,336,378 reads, 1,038,711 reads were unmapped and 4,775,493 reads >= MAPQ 1.
[2021-03-16 11:52:47,362 | INFO] PyMaSC.core.readlen : 6,336,378 reads were paired: 3,168,189 reads were 1st and 3,168,189 reads were last segment.
[2021-03-16 11:52:47,362 | INFO] PyMaSC.core.readlen : Note that only 1st reads in the templates will be used for calculation.
[2021-03-16 11:52:47,362 | INFO] PyMaSC.core.readlen : Estimated read length = 150
[2021-03-16 11:52:47,362 | INFO] PyMaSC.pymasc : Calculate cross-correlation between 0 to 1000 base shiftwith reads MAOQ >= 1
[2021-03-16 11:52:47,362 | INFO] PyMaSC.pymasc : Process processed_data/ce11/NGS/ChIPseq/bam/H3k4me1_WThexCtrl_rep1.bwa_aln.sort.bam
[2021-03-16 11:52:47,398 | INFO] PyMaSC.bacore.mscc : Loading II reads to bit array...
[2021-03-16 11:52:47,398 | INFO] PyMaSC.bacore.mscc : Loading III reads to bit array...
[2021-03-16 11:52:47,398 | INFO] PyMaSC.bacore.mscc : Loading IV reads to bit array...
[2021-03-16 11:52:47,399 | INFO] PyMaSC.bacore.mscc : Loading V reads to bit array...
[2021-03-16 11:52:47,399 | INFO] PyMaSC.bacore.mscc : Loading MtDNA reads to bit array...
[2021-03-16 11:52:47,400 | INFO] PyMaSC.bacore.mscc : Loading X reads to bit array...
[2021-03-16 11:52:47,400 | INFO] PyMaSC.bacore.mscc : Loading I reads to bit array...
[2021-03-16 11:52:47,742 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for MtDNA...
[2021-03-16 11:52:49,955 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for II...
[2021-03-16 11:52:50,131 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for IV...
[2021-03-16 11:52:50,200 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for III...
[2021-03-16 11:52:50,252 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for X...
[2021-03-16 11:52:50,453 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for I...
[2021-03-16 11:52:50,564 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for V...
[2021-03-16 11:52:54,707 | WARNING] PyMaSC.handler.result : Whole genome Forward/Reverse read count imbalance.
[2021-03-16 11:52:54,707 | WARNING] PyMaSC.handler.result : +/- = 998928 / 1003500, Chi-squared test p-val = 0.0223354912445 <= 0.05
[2021-03-16 11:52:54,877 | INFO] PyMaSC.output.stats : Output 'test2masc/test2_stats.tab'
[2021-03-16 11:52:54,878 | INFO] PyMaSC.output.table : Output 'test2masc/test2_nreads.tab'
Traceback (most recent call last):
File "/nfs/work/gen2i/technique/tools/bin/pymasc", line 8, in
sys.exit(main())
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/init.py", line 20, in _inner
main_func()
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/pymasc.py", line 98, in main
output_results(args, output_basename, result_handler)
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/pymasc.py", line 189, in output_results
output_nreads_table(output_basename, result_handler)
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/utils/output.py", line 10, in _io_func
return func(*args, **kwargs)
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/output/table.py", line 179, in output_nreads_table
with NReadsIO(outfile, 'w') as tab:
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/output/table.py", line 36, in enter
self.open()
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/output/table.py", line 33, in open
self.fp = open(self.path, self.mode, newline='')
TypeError: 'newline' is an invalid keyword argument for this function

I will try with python 3.9.2 version but I'm waiting for the admin of HPC I use to install a devel lib to be able to correctly compile python.

Many thanks,
cheers

[ronin-gw]

Thanks for for your reporting. I will fix it in the future release.
If you want to run PyMaSC now, you can try to edit /nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/output/table.py to apply the following changes. I think this fixes your issue.

from __future__ import print_function

import logging
from functools import partial
import csv
from itertools import chain
from collections import defaultdict
from copy import copy
+ import io

import numpy as np

from PyMaSC.utils.output import catch_IOError

class TableIO(object):
    DIALECT = "excel-tab"

    def __init__(self, path, mode='r'):
        self.path = path
        self.mode = mode
        self.fp = None

        if mode not in ('r', 'w'):
            raise NotImplemented

    def open(self):
-        self.fp = open(self.path, self.mode, newline='')
+        self.fp = io.open(self.path, self.mode, newline='')

[lelouar]

I modified table.py file but another error came :

[...]
[2021-03-16 14:31:34,661 | INFO] PyMaSC.output.table : Output 'test2masc/test2_nreads.tab'
Traceback (most recent call last):
File "/nfs/work/gen2i/technique/tools/bin/pymasc", line 8, in
sys.exit(main())
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/init.py", line 20, in _inner
main_func()
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/pymasc.py", line 98, in main
output_results(args, output_basename, result_handler)
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/pymasc.py", line 189, in output_results
output_nreads_table(output_basename, result_handler)
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/utils/output.py", line 10, in _io_func
return func(*args, **kwargs)
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/output/table.py", line 185, in output_nreads_table
_make_dict_with_whole(ccr.mappable_ref2reverse_sum, "masc", "reverse_sum")
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/output/table.py", line 135, in write
tab.writerow(("shift", ) + tuple(header))
TypeError: write() argument 1 must be unicode, not str

cheers

[lelouar]

Hi,

I've tried with a fresh compiled python 3.7.10 and it works (however, I had to use "python3 -m pip install pymasc --no-binary pymasc" to recompile the cython part to be able to use it)

Cheers